From d74f08e5a57367c425549b2e2cdbafa61047792e Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Mon, 22 May 2023 10:49:51 +0200
Subject: [PATCH 01/61] chore(github): update workflows

---
 .github/workflows/release.yml | 144 ++++++++++++++++++++++++++++++++++
 .github/workflows/shed.yml    |   2 +-
 .github/workflows/tests.yml   |   4 +-
 3 files changed, 147 insertions(+), 3 deletions(-)
 create mode 100644 .github/workflows/release.yml

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 00000000..86725ab9
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,144 @@
+name: Release
+
+on:
+  schedule:
+    - cron: '0 0 * * 2'
+
+jobs:
+
+  Diff:
+    runs-on: ubuntu-latest
+    outputs:
+      nb: ${{ steps.set-diff.outputs.nb }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+          ref: 'stable'
+      - name: "Check diff"
+        id: set-diff
+        run: |
+          nb=$(git diff --quiet stable..origin/main)
+          echo "nb=$nb" >> "${GITHUB_OUTPUT}"
+
+  TagRaw:
+    runs-on: ubuntu-latest
+    needs: [Diff]
+    if: ${{ needs.Diff.outputs.nb > 0 }}
+    outputs:
+      tag: ${{ steps.tag_label.outputs.tag }}
+      changelog: ${{ steps.tag_raw.outputs.changelog }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - name: 'Bump version and push tag - dry run'
+        id: tag_raw
+        uses: mathieudutour/github-tag-action@v6.1
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          release_branches: stable
+          tag_prefix:
+          dry_run: true
+      - name: 'Format tag'
+        id: tag_label
+        env:
+          TAG: ${{ steps.tag_raw.outputs.new_tag }}
+        run: |
+          TAG=$(echo "$TAG" | cut -f1 -d "-")
+          echo "tag=$TAG" >> "$GITHUB_OUTPUT"
+
+  Changelog:
+    runs-on: ubuntu-latest
+    needs: [TagRaw]
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - name: 'Check file present'
+        run: |
+          [[ -f CHANGELOG.md ]] || touch CHANGELOG.md
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: 3 # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+      - name: 'Generate CHANGELOG'
+        env:
+          CHANGELOG_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gem install github_changelog_generator
+          USER=$(echo "$GITHUB_REPOSITORY" | sed -e 's/\// /g' | awk '{print $1}')
+          PROJECT=$(echo "$GITHUB_REPOSITORY" | sed -e 's/\// /g' | awk '{print $2}')
+          echo "$USER $PROJECT"
+          github_changelog_generator --user "$USER" --project "$PROJECT" --no-unreleased
+      - name: 'Upload Artifact Changelog'
+        uses: actions/upload-artifact@v3
+        with:
+          name: changelog-artifact
+          path: CHANGELOG.md
+          retention-days: 1
+
+  Commit:
+    needs: [Changelog]
+    runs-on: ubuntu-latest
+    steps:
+      # Get Data
+      - name: 'Checkout'
+        uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - name: 'Download Artifact Changelog'
+        uses: actions/download-artifact@v3
+        with:
+          name: changelog-artifact
+      # Commit
+      - name: 'Commit files'
+        run: |
+          git config --local user.email "$GITHUB_EMAIL"
+          git config --local user.name "$GITHUB_USERNAME"
+          git add .
+          git commit -m "doc(changelog): update"
+        env:
+          GITHUB_USERNAME: guillaume-gricourt
+          GITHUB_EMAIL: guipagui@gmail.com
+      - name: 'Push changes'
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}
+      - name: 'Update main branch'
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: main
+
+  Tag:
+    needs: [Commit, TagRaw]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - name: 'Bump version and push tag'
+        id: tag
+        uses: mathieudutour/github-tag-action@v6.1
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          release_branches: stable
+          custom_tag: ${{ needs.TagRaw.outputs.tag }}
+          tag_prefix:
+
+  Release:
+    needs: [TagRaw, Tag]
+    runs-on: ubuntu-latest
+    steps:
+      - name: 'Create Release'
+        uses: softprops/action-gh-release@v1
+        with:
+          tag_name: ${{ needs.TagRaw.outputs.tag }}
+          body: ${{ needs.TagRaw.outputs.changelog }}
diff --git a/.github/workflows/shed.yml b/.github/workflows/shed.yml
index 36d5ba5a..6ae99990 100644
--- a/.github/workflows/shed.yml
+++ b/.github/workflows/shed.yml
@@ -2,7 +2,7 @@ name: Shed
 
 on:
   schedule:
-    - cron: '0 0 * * 1'
+    - cron: '0 0 1 * *' # Run monthly
 
 jobs:
 
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 0ceef656..888683f3 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -80,11 +80,11 @@ jobs:
             "tools/${{ matrix.repo }}"
       - name: 'Prepare artefact'
         run: |
-          zip -r -9 log.zip log
+          zip -r -9 log.zip "log/${{ matrix.repo }}"
       - name: 'Upload Artifact Version'
         uses: actions/upload-artifact@v3
         with:
-          name: log-artifact
+          name: log-artifact-${{ matrix.repo }}
           path: log.zip
       - name: 'Aggregate results'
         run: |

From 74597bdca6bed6b8236a81ad8552277619c25422 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Mon, 22 May 2023 11:07:58 +0200
Subject: [PATCH 02/61] chore(github): add CONTRIBUTING

---
 .github/CONTRIBUTING.md | 51 +++++++++++++++++++++++++++++++++++++++++
 README.md               | 14 ++++++++++-
 2 files changed, 64 insertions(+), 1 deletion(-)
 create mode 100644 .github/CONTRIBUTING.md

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
new file mode 100644
index 00000000..5c5bd886
--- /dev/null
+++ b/.github/CONTRIBUTING.md
@@ -0,0 +1,51 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
+
+## Ways you can help
+
+### Report Bugs
+
+Report bugs at <https://github.com/brsynth/synbiocad-galaxy-wrappers/issues>.
+
+If you are reporting a bug, please include:
+
+- Your operating system name and version, versions of synbiocad-galaxy-wrappers and the wrapper associated.
+- Any details about your local setup that might be helpful in troubleshooting.
+- Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with `bug` is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with `enhancement` is open to whoever wants to implement it.
+
+### Write Documentation
+
+Same as Implement Features
+
+### Submit Feedback
+
+The best way to send feedback is to file an issue at <https://github.com/brsynth/synbiocad-galaxy-wrappers/issues>.
+
+If you are proposing a feature:
+
+- Explain in detail how it would work.
+- Keep the scope as narrow as possible, to make it easier to implement.
+- This will hopefully become a community-driven project and contributions are welcome :)
+
+## Pull Request Guidelines
+
+Open a Pull Request will trigger a bunch of tests checking:
+
+1. the `.shed.yml` file
+2. the wrapper with `planemo`
+
+Add a reviewer: `@guillaume-gricourt` or `@breakthewall` or `@tduigou`
+When the Pull Request will be closed, the wrapper will be updated in the following repository:
+1. testtoolshed
+2. toolshed
+
+This policy was modified from [planemo project](https://github.com/galaxyproject/planemo/blob/master/CONTRIBUTING.rst)
diff --git a/README.md b/README.md
index 78fc0b73..60d30d70 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,15 @@
 # SynBioCAD Galaxy Wrappers
 
-To contribute, please visit the [documentation](https://github.com/brsynth/synbiocad-galaxy-docs).
+This repository hosts the Galaxy wrappers maintained by the [brsynth group](https://github.com/brsynth).  
+All are deployed under the owner `@tduigou`.  
+The wrappers are synchronized to the [testtoolshed](http://testtoolshed.g2.bx.psu.edu) and the [main toolshed](http://toolshed.g2.bx.psu.edu).  
+
+## Contribute
+
+### Members belonging to the group brsynth
+
+Please visit the [documentation](https://github.com/brsynth/synbiocad-galaxy-docs).
+
+### External members
+
+Please see [contributing](.github/CONTRIBUTING.md)

From 05a43f73a0983ab10345063d31627c42f6c9636a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Mon, 22 May 2023 16:12:02 +0200
Subject: [PATCH 03/61] fix(get_sbml_model): rm 'parent'

---
 tools/get_sbml_model/get_infos.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/get_sbml_model/get_infos.py b/tools/get_sbml_model/get_infos.py
index 2e86170e..9a23a07f 100644
--- a/tools/get_sbml_model/get_infos.py
+++ b/tools/get_sbml_model/get_infos.py
@@ -72,7 +72,7 @@ def entry_point():
             print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
         else:
             try:
-                taxid = r.json()["parent"]["id"]
+                taxid = r.json()["id"]
             except KeyError:
                 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
             with open(params.taxid, 'w') as f:

From ce6583e5d3bab0048b7ade234694f1bc2a26b5f5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Mon, 22 May 2023 16:52:38 +0200
Subject: [PATCH 04/61] chore(get_sbml_model): handle errors

---
 tools/get_sbml_model/get_infos.py | 32 +++++++++++++++++--------------
 1 file changed, 18 insertions(+), 14 deletions(-)

diff --git a/tools/get_sbml_model/get_infos.py b/tools/get_sbml_model/get_infos.py
index 9a23a07f..5523aee5 100644
--- a/tools/get_sbml_model/get_infos.py
+++ b/tools/get_sbml_model/get_infos.py
@@ -62,22 +62,26 @@ def entry_point():
             try:
                 hostname = r.json()["organism"]
             except KeyError:
-                print(f"*** Error: unable to retrieve host name for id {params.hostid}")
-                return -1
-        # TAXON ID
-        server = 'https://rest.ensembl.org'
-        ext = f'/taxonomy/id/{hostname}?'
-        r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
-        if not r.ok:
-            print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
+                print(f"Warning: unable to retrieve host name for id {params.hostid}")
+                hostname = ''
+        if not hostname:
+            taxid = ''
         else:
-            try:
-                taxid = r.json()["id"]
-            except KeyError:
+            # TAXON ID
+            server = 'https://rest.ensembl.org'
+            ext = f'/taxonomy/id/{hostname}?'
+            r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
+            if not r.ok:
                 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
-            with open(params.taxid, 'w') as f:
-                f.write('#ID\n')
-                f.write(f'{taxid}\n')
+            else:
+                try:
+                    taxid = r.json()["id"]
+                except KeyError:
+                    print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
+                    taxid = ''
+        with open(params.taxid, 'w') as f:
+            f.write('#ID\n')
+            f.write(f'{taxid}\n')
 
 
 if __name__ == "__main__":

From 34d0ed89122ef079541a7b8a4f42e968395fe457 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Mon, 22 May 2023 16:55:01 +0200
Subject: [PATCH 05/61] fix(get_sbml_model): fix 'requests' version

---
 tools/get_sbml_model/get_sbml_model.xml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/tools/get_sbml_model/get_sbml_model.xml b/tools/get_sbml_model/get_sbml_model.xml
index 60f44998..64d5c8b9 100644
--- a/tools/get_sbml_model/get_sbml_model.xml
+++ b/tools/get_sbml_model/get_sbml_model.xml
@@ -4,12 +4,17 @@
         <requirement type="package" version="7.81.0">curl</requirement>
         <requirement type="package" version="1.11">gzip</requirement>
         <requirement type="package" version="5.19.2">python-libsbml</requirement>
-        <requirement type="package" version="5.19.2">requests</requirement>
+        <requirement type="package" version="2.29">requests</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
         | gunzip > '$model';
-        python '$__tool_directory__/'get_infos.py '$model' --hostid '$input' --comp '$compartments' --biomass '$biomass' --taxid '$taxid'
+        python '$__tool_directory__/'get_infos.py
+        '$model'
+        --hostid '$input'
+        --comp '$compartments'
+        --biomass '$biomass'
+        --taxid '$taxid'
     ]]></command>
     <inputs>
         <param name="input" type="select" label="Strain">

From 4a0b08beb8cdf51ab295a1f5f8c586d6bbaf5586 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Mon, 22 May 2023 16:56:27 +0200
Subject: [PATCH 06/61] taxonid (#114)

* fix(get_sbml_model): rm 'parent'

* chore(get_sbml_model): handle errors

* fix(get_sbml_model): fix 'requests' version
---
 tools/get_sbml_model/get_infos.py       | 32 ++++++++++++++-----------
 tools/get_sbml_model/get_sbml_model.xml |  9 +++++--
 2 files changed, 25 insertions(+), 16 deletions(-)

diff --git a/tools/get_sbml_model/get_infos.py b/tools/get_sbml_model/get_infos.py
index 2e86170e..5523aee5 100644
--- a/tools/get_sbml_model/get_infos.py
+++ b/tools/get_sbml_model/get_infos.py
@@ -62,22 +62,26 @@ def entry_point():
             try:
                 hostname = r.json()["organism"]
             except KeyError:
-                print(f"*** Error: unable to retrieve host name for id {params.hostid}")
-                return -1
-        # TAXON ID
-        server = 'https://rest.ensembl.org'
-        ext = f'/taxonomy/id/{hostname}?'
-        r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
-        if not r.ok:
-            print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
+                print(f"Warning: unable to retrieve host name for id {params.hostid}")
+                hostname = ''
+        if not hostname:
+            taxid = ''
         else:
-            try:
-                taxid = r.json()["parent"]["id"]
-            except KeyError:
+            # TAXON ID
+            server = 'https://rest.ensembl.org'
+            ext = f'/taxonomy/id/{hostname}?'
+            r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
+            if not r.ok:
                 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
-            with open(params.taxid, 'w') as f:
-                f.write('#ID\n')
-                f.write(f'{taxid}\n')
+            else:
+                try:
+                    taxid = r.json()["id"]
+                except KeyError:
+                    print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
+                    taxid = ''
+        with open(params.taxid, 'w') as f:
+            f.write('#ID\n')
+            f.write(f'{taxid}\n')
 
 
 if __name__ == "__main__":
diff --git a/tools/get_sbml_model/get_sbml_model.xml b/tools/get_sbml_model/get_sbml_model.xml
index 60f44998..64d5c8b9 100644
--- a/tools/get_sbml_model/get_sbml_model.xml
+++ b/tools/get_sbml_model/get_sbml_model.xml
@@ -4,12 +4,17 @@
         <requirement type="package" version="7.81.0">curl</requirement>
         <requirement type="package" version="1.11">gzip</requirement>
         <requirement type="package" version="5.19.2">python-libsbml</requirement>
-        <requirement type="package" version="5.19.2">requests</requirement>
+        <requirement type="package" version="2.29">requests</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
         | gunzip > '$model';
-        python '$__tool_directory__/'get_infos.py '$model' --hostid '$input' --comp '$compartments' --biomass '$biomass' --taxid '$taxid'
+        python '$__tool_directory__/'get_infos.py
+        '$model'
+        --hostid '$input'
+        --comp '$compartments'
+        --biomass '$biomass'
+        --taxid '$taxid'
     ]]></command>
     <inputs>
         <param name="input" type="select" label="Strain">

From b87d547089fa9d3a919f75522afc40f981df26a9 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 23 May 2023 10:06:15 +0200
Subject: [PATCH 07/61] chore(github): workflow release

---
 .github/workflows/pr.yml               |  2 ++
 .github/workflows/release.yml          | 21 +---------------
 .github/workflows/release_schedule.yml | 35 ++++++++++++++++++++++++++
 3 files changed, 38 insertions(+), 20 deletions(-)
 create mode 100644 .github/workflows/release_schedule.yml

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index d855e8eb..07b6ca5a 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -136,3 +136,5 @@ jobs:
       - name: 'Main ToolShed'
         run: |
           planemo shed_update --force_repository_creation --shed_target toolshed --shed_key "${{ secrets.TOOLSHED }}" "tools/${{ matrix.repo }}" || planemo shed_update --force_repository_creation --shed_target toolshed --shed_key "${{ secrets.TOOLSHED }}" "tools/${{ matrix.repo }}"
+      - name: 'Create release'
+        uses: ./.github/workflows/release.yml
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 86725ab9..660dcdf8 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -1,31 +1,12 @@
 name: Release
 
 on:
-  schedule:
-    - cron: '0 0 * * 2'
+  workflow_call:
 
 jobs:
 
-  Diff:
-    runs-on: ubuntu-latest
-    outputs:
-      nb: ${{ steps.set-diff.outputs.nb }}
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          persist-credentials: false
-          fetch-depth: 0
-          ref: 'stable'
-      - name: "Check diff"
-        id: set-diff
-        run: |
-          nb=$(git diff --quiet stable..origin/main)
-          echo "nb=$nb" >> "${GITHUB_OUTPUT}"
-
   TagRaw:
     runs-on: ubuntu-latest
-    needs: [Diff]
-    if: ${{ needs.Diff.outputs.nb > 0 }}
     outputs:
       tag: ${{ steps.tag_label.outputs.tag }}
       changelog: ${{ steps.tag_raw.outputs.changelog }}
diff --git a/.github/workflows/release_schedule.yml b/.github/workflows/release_schedule.yml
new file mode 100644
index 00000000..1624e8d8
--- /dev/null
+++ b/.github/workflows/release_schedule.yml
@@ -0,0 +1,35 @@
+name: ReleaseSchedule
+
+on:
+  schedule:
+    - cron: '0 0 * * 2'
+
+jobs:
+
+  Diff:
+    runs-on: ubuntu-latest
+    outputs:
+      nb: ${{ steps.set-diff.outputs.nb }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+          ref: 'stable'
+      - name: "Check diff"
+        id: set-diff
+        run: |
+          git diff --quiet stable..origin/main
+          echo "nb=$?" >> "${GITHUB_OUTPUT}"
+
+  Call:
+    runs-on: ubuntu-latest
+    needs: [Diff]
+    if: ${{ needs.Diff.outputs.nb > 0 }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - name: 'Dispatch'
+        uses: ./.github/workflows/release.yml

From 3f1bce23f8dbaee38bb19cb4b04e4237124da892 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Tue, 23 May 2023 16:12:49 +0200
Subject: [PATCH 08/61] feat(selenzy_wrapper): give taxon ID via a file

---
 tools/selenzy_wrapper/selenzy_wrapper.xml | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/tools/selenzy_wrapper/selenzy_wrapper.xml b/tools/selenzy_wrapper/selenzy_wrapper.xml
index 88d6231e..45ce71a7 100644
--- a/tools/selenzy_wrapper/selenzy_wrapper.xml
+++ b/tools/selenzy_wrapper/selenzy_wrapper.xml
@@ -12,7 +12,11 @@
         --nb_targets '$adv.nb_targets'
         --d '$adv.direction'
         $adv.NoMSA
-        --host_taxID '$adv.host_taxID'
+        #if str($host_taxID_type_conditional.host_taxID_type) == "tsv":
+            --host_taxID `sed 1d ${host_taxID_type_conditional.host_taxID_file}`
+        #else:
+            --host_taxID '$host_taxID_type_conditional.host_taxID_int'
+        #end if
         #if str($adv.enzyme_taxIDs) != "":
             --enzyme_taxIDs '$adv.enzyme_taxIDs'
         #end if
@@ -22,8 +26,20 @@
     ]]></command>
     <inputs>
         <param name="pathway" type="data" format="sbml" label="Pathway (SBML)" />
+        <conditional name="host_taxID_type_conditional">
+            <param name="host_taxID_type" type="select" label="Host taxon ID type">
+                <option value="integer" selected="True">Value</option>
+                <option value="tsv">File</option>
+            </param>
+            <when value="integer">
+                <param name="host_taxID_int" type="integer" label="Host taxon ID value" value="83333" help="default: 83333 [E. coli K12]" />
+            </when>
+            <when value="tsv">
+                <param name="host_taxID_file" type="data" format="tsv" label="Host taxon ID file" />
+            </when>
+        </conditional>
+        <!-- <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" help="Taxon ID of the chassis (default: 83333 [E. coli K12])" /> -->
         <section name="adv" title="Advanced Options" expanded="false">
-            <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" help="Taxon ID of the chassis (default: 83333 [E. coli K12])" />
             <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
             <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" help=" Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]" />
             <param name="nb_targets" type="integer" value="500" min="1" label="Number of targets to display in results" help="Number of targets to display in results (before taxon IDs filtering) [default = 500]" />

From 45a7c182f39c67507b05e39509b865a04ecdd1f9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Tue, 23 May 2023 16:16:00 +0200
Subject: [PATCH 09/61] chore(selenzy_wrapper): rm comment (#115)

---
 tools/selenzy_wrapper/selenzy_wrapper.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tools/selenzy_wrapper/selenzy_wrapper.xml b/tools/selenzy_wrapper/selenzy_wrapper.xml
index 45ce71a7..9855ae8d 100644
--- a/tools/selenzy_wrapper/selenzy_wrapper.xml
+++ b/tools/selenzy_wrapper/selenzy_wrapper.xml
@@ -38,7 +38,6 @@
                 <param name="host_taxID_file" type="data" format="tsv" label="Host taxon ID file" />
             </when>
         </conditional>
-        <!-- <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" help="Taxon ID of the chassis (default: 83333 [E. coli K12])" /> -->
         <section name="adv" title="Advanced Options" expanded="false">
             <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
             <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" help=" Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]" />

From fbfd016123e0abfb27b9756b857463c4da84c381 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Tue, 23 May 2023 16:29:31 +0200
Subject: [PATCH 10/61] Taxonid (#116)

* chore(selenzy_wrapper): rm comment

* chore(selenzy-wrapper): rm config

* chore(selenzy-wrapper): rename
---
 tools/selenzy_wrapper/.shed.yml            | 2 +-
 tools/selenzy_wrapper/config/job_conf.xml  | 1 -
 tools/selenzy_wrapper/config/tool_conf.xml | 3 ---
 3 files changed, 1 insertion(+), 5 deletions(-)
 delete mode 100644 tools/selenzy_wrapper/config/job_conf.xml
 delete mode 100644 tools/selenzy_wrapper/config/tool_conf.xml

diff --git a/tools/selenzy_wrapper/.shed.yml b/tools/selenzy_wrapper/.shed.yml
index 23672ea4..85ce6bc7 100644
--- a/tools/selenzy_wrapper/.shed.yml
+++ b/tools/selenzy_wrapper/.shed.yml
@@ -6,7 +6,7 @@ long_description: 'Selenzy performs enzyme sequence selection from a reaction qu
   RetroRules(https://github.com/brsynth/RRParser). This feature makes this tool especially
   useful in combination with RetroPath2.0 (https://github.com/brsynth/RetroPath2-wrapper).
   Source code may be found at the following location: https://github.com/brsynth/selenzy-wrapper'
-name: selenzy
+name: selenzy-wrapper
 owner: tduigou
 homepage_url: https://github.com/brsynth/selenzy-wrapper
 remote_repository_url: https://github.com/brsynth/selenzy-wrapper
diff --git a/tools/selenzy_wrapper/config/job_conf.xml b/tools/selenzy_wrapper/config/job_conf.xml
deleted file mode 100644
index 59824328..00000000
--- a/tools/selenzy_wrapper/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="selenzy_wrapper" destination="local" />
diff --git a/tools/selenzy_wrapper/config/tool_conf.xml b/tools/selenzy_wrapper/config/tool_conf.xml
deleted file mode 100644
index d843485f..00000000
--- a/tools/selenzy_wrapper/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-util" name="SynBioCAD Utilities">
-    <tool file="synbiocad-galaxy-wrappers/selenzy_wrapper/selenzy_wrapper.xml" />
-  </section>
\ No newline at end of file

From 71e08a724df679ce0b7e7e01d5994de9ea4012a3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Tue, 23 May 2023 17:01:43 +0200
Subject: [PATCH 11/61] Taxonid (#117)

* chore(selenzy_wrapper): rm comment

* chore(selenzy-wrapper): rm config

* chore(selenzy-wrapper): rename

* chore(selenzy-wrapper): rename

* chore(selenzy_wrapper): add test
---
 tools/selenzy_wrapper/.shed.yml           |  2 +-
 tools/selenzy_wrapper/selenzy_wrapper.xml | 10 ++++++++++
 tools/selenzy_wrapper/test-data/taxID.tsv |  2 ++
 3 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 tools/selenzy_wrapper/test-data/taxID.tsv

diff --git a/tools/selenzy_wrapper/.shed.yml b/tools/selenzy_wrapper/.shed.yml
index 85ce6bc7..5633fdf8 100644
--- a/tools/selenzy_wrapper/.shed.yml
+++ b/tools/selenzy_wrapper/.shed.yml
@@ -6,7 +6,7 @@ long_description: 'Selenzy performs enzyme sequence selection from a reaction qu
   RetroRules(https://github.com/brsynth/RRParser). This feature makes this tool especially
   useful in combination with RetroPath2.0 (https://github.com/brsynth/RetroPath2-wrapper).
   Source code may be found at the following location: https://github.com/brsynth/selenzy-wrapper'
-name: selenzy-wrapper
+name: selenzy_wrapper
 owner: tduigou
 homepage_url: https://github.com/brsynth/selenzy-wrapper
 remote_repository_url: https://github.com/brsynth/selenzy-wrapper
diff --git a/tools/selenzy_wrapper/selenzy_wrapper.xml b/tools/selenzy_wrapper/selenzy_wrapper.xml
index 9855ae8d..43fa1e04 100644
--- a/tools/selenzy_wrapper/selenzy_wrapper.xml
+++ b/tools/selenzy_wrapper/selenzy_wrapper.xml
@@ -57,6 +57,16 @@
             <output name="uniprot_ids" file="uniprod_ids_out.xml" compare="diff" sort="true"/>
             <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
         </test>
+        <test>
+        <!-- test 2: check with taxon ID from a file  -->
+            <param name="pathway" value="pathway.xml" />
+            <conditional name="input_sim_type">
+                <param name="host_taxID_type" value="tsv" />
+            </conditional>
+            <param name="host_taxID_file" value="taxID.tsv" />
+            <output name="uniprot_ids" file="uniprod_ids_out.xml" compare="diff" sort="true"/>
+            <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
+        </test>
     </tests>
     <help><![CDATA[
 Selenzyme
diff --git a/tools/selenzy_wrapper/test-data/taxID.tsv b/tools/selenzy_wrapper/test-data/taxID.tsv
new file mode 100644
index 00000000..9a3c4d40
--- /dev/null
+++ b/tools/selenzy_wrapper/test-data/taxID.tsv
@@ -0,0 +1,2 @@
+#ID
+83333
\ No newline at end of file

From 2f25f890a1962e6d52d53b814aca74d89ec05563 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 30 May 2023 10:59:44 +0200
Subject: [PATCH 12/61] chore(deps): bump tj-actions/changed-files from 35 to
 36 (#120)

Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35 to 36.
- [Release notes](https://github.com/tj-actions/changed-files/releases)
- [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md)
- [Commits](https://github.com/tj-actions/changed-files/compare/v35...v36)

---
updated-dependencies:
- dependency-name: tj-actions/changed-files
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/pr.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index 07b6ca5a..17daa4d4 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -24,7 +24,7 @@ jobs:
       - name: 'Select modified files'
         id: files
         #uses: Ana06/get-changed-files@v2.2.0
-        uses: tj-actions/changed-files@v35
+        uses: tj-actions/changed-files@v36
         with:
           files: tools/**
           separator: ","

From a5b69fe4535111136076c9ee42dff64ce8088451 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 30 May 2023 11:03:44 +0200
Subject: [PATCH 13/61] fix(github): workflow syntax

---
 .github/workflows/release_schedule.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/release_schedule.yml b/.github/workflows/release_schedule.yml
index 1624e8d8..e909cd2f 100644
--- a/.github/workflows/release_schedule.yml
+++ b/.github/workflows/release_schedule.yml
@@ -20,7 +20,8 @@ jobs:
         id: set-diff
         run: |
           git diff --quiet stable..origin/main
-          echo "nb=$?" >> "${GITHUB_OUTPUT}"
+          nb=$?
+          echo "nb=$nb" >> "${GITHUB_OUTPUT}"
 
   Call:
     runs-on: ubuntu-latest

From 1e01b679611d980f87089184e7d8a538b96d68c7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Tue, 30 May 2023 22:58:47 +0200
Subject: [PATCH 14/61] chore: rm config folders (#118)

* chore: rm config folders

* fix(get_sbml_model): fix taxid md5

* fix(icfree): update test section

* fix(rp2biosensor): udpate version, add --cache-dir arg

* chore(github): skip `partsgenie` test

* fix(github): missing files

* fix(github): skip aggregate_results if test is skipped

* fix(github): increase timeout

* fix(github): skip temporarly `rpbasicdesign`

---------

Co-authored-by: Guillaume Gricourt <guipagui@gmail.com>
---
 .github/workflows/pr.yml                      |  6 +++--
 .github/workflows/test_skip.txt               |  2 ++
 .github/workflows/tests.yml                   |  4 +++-
 tools/dnabot/config/job_conf.xml              |  1 -
 tools/dnabot/config/tool_conf.xml             |  3 ---
 tools/dnaweaver/config/job_conf.xml           |  1 -
 tools/dnaweaver/config/tool_conf.xml          |  3 ---
 tools/doe_synbio/config/job_conf.xml          |  1 -
 tools/doe_synbio/config/tool_conf.xml         |  3 ---
 tools/get_sbml_model/config/job_conf.xml      |  1 -
 tools/get_sbml_model/config/tool_conf.xml     |  3 ---
 tools/get_sbml_model/get_sbml_model.xml       |  2 +-
 tools/icfree/config/job_conf.xml              |  1 -
 tools/icfree/config/tool_conf.xml             |  6 -----
 tools/icfree/instructor.xml                   | 16 +++++++-------
 tools/inchi_to_sink/config/job_conf.xml       |  1 -
 tools/inchi_to_sink/config/tool_conf.xml      |  3 ---
 tools/lcrgenie/config/job_conf.xml            |  1 -
 tools/lcrgenie/config/tool_conf.xml           |  3 ---
 tools/partsgenie/config/job_conf.xml          |  1 -
 tools/partsgenie/config/tool_conf.xml         |  3 ---
 tools/retropath2_wrapper/config/job_conf.xml  |  1 -
 tools/retropath2_wrapper/config/tool_conf.xml |  3 ---
 tools/rp2biosensor/config/job_conf.xml        |  1 -
 tools/rp2biosensor/config/tool_conf.xml       |  3 ---
 tools/rp2biosensor/rp2biosensor.xml           | 22 +++++--------------
 tools/rp2paths/config/job_conf.xml            |  1 -
 tools/rp2paths/config/tool_conf.xml           |  3 ---
 tools/rpbasicdesign/config/job_conf.xml       |  1 -
 tools/rpbasicdesign/config/tool_conf.xml      |  3 ---
 tools/rrparser/config/job_conf.xml            |  1 -
 tools/rrparser/config/tool_conf.xml           |  3 ---
 tools/sbml2sbol/config/job_conf.xml           |  1 -
 tools/sbml2sbol/config/tool_conf.xml          |  3 ---
 tools/straindesign/config/job_conf.xml        |  1 -
 tools/straindesign/config/tool_conf.xml       |  5 -----
 36 files changed, 24 insertions(+), 93 deletions(-)
 delete mode 100644 tools/dnabot/config/job_conf.xml
 delete mode 100644 tools/dnabot/config/tool_conf.xml
 delete mode 100644 tools/dnaweaver/config/job_conf.xml
 delete mode 100644 tools/dnaweaver/config/tool_conf.xml
 delete mode 100644 tools/doe_synbio/config/job_conf.xml
 delete mode 100644 tools/doe_synbio/config/tool_conf.xml
 delete mode 100644 tools/get_sbml_model/config/job_conf.xml
 delete mode 100644 tools/get_sbml_model/config/tool_conf.xml
 delete mode 100644 tools/icfree/config/job_conf.xml
 delete mode 100644 tools/icfree/config/tool_conf.xml
 delete mode 100644 tools/inchi_to_sink/config/job_conf.xml
 delete mode 100644 tools/inchi_to_sink/config/tool_conf.xml
 delete mode 100644 tools/lcrgenie/config/job_conf.xml
 delete mode 100644 tools/lcrgenie/config/tool_conf.xml
 delete mode 100644 tools/partsgenie/config/job_conf.xml
 delete mode 100644 tools/partsgenie/config/tool_conf.xml
 delete mode 100644 tools/retropath2_wrapper/config/job_conf.xml
 delete mode 100644 tools/retropath2_wrapper/config/tool_conf.xml
 delete mode 100644 tools/rp2biosensor/config/job_conf.xml
 delete mode 100644 tools/rp2biosensor/config/tool_conf.xml
 delete mode 100644 tools/rp2paths/config/job_conf.xml
 delete mode 100644 tools/rp2paths/config/tool_conf.xml
 delete mode 100644 tools/rpbasicdesign/config/job_conf.xml
 delete mode 100644 tools/rpbasicdesign/config/tool_conf.xml
 delete mode 100644 tools/rrparser/config/job_conf.xml
 delete mode 100644 tools/rrparser/config/tool_conf.xml
 delete mode 100644 tools/sbml2sbol/config/job_conf.xml
 delete mode 100644 tools/sbml2sbol/config/tool_conf.xml
 delete mode 100644 tools/straindesign/config/job_conf.xml
 delete mode 100644 tools/straindesign/config/tool_conf.xml

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index 17daa4d4..b02f18c0 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -85,7 +85,7 @@ jobs:
           ./scripts/shed_lint.py -i "tools/${{ matrix.repo }}"
       - name: 'Test tool'
         if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
-        timeout-minutes: 60
+        timeout-minutes: 120
         continue-on-error: true
         run: |
           planemo test \
@@ -95,9 +95,10 @@ jobs:
             --galaxy_source https://github.com/galaxyproject/galaxy \
             --galaxy_branch release_22.05 \
             --galaxy_python_version 3.7 \
-            "tools/${{ matrix.repo }}" || { touch tool_test_output.html tool_test_output.json; }
+            "tools/${{ matrix.repo }}"
       - name: 'Prepare artefact'
         run: |
+          touch tool_test_output.html tool_test_output.json
           zip -9 ${{ matrix.repo }}.zip tool_test_output.html tool_test_output.json
       - name: 'Upload Artifact Version'
         uses: actions/upload-artifact@v3
@@ -105,6 +106,7 @@ jobs:
           name: ${{ matrix.repo }}-artifact
           path: ${{ matrix.repo }}.zip
       - name: 'Aggregate results'
+        if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
         run: |
           ./scripts/aggregate_test.py -i .
 
diff --git a/.github/workflows/test_skip.txt b/.github/workflows/test_skip.txt
index 56fe0bec..4512586d 100644
--- a/.github/workflows/test_skip.txt
+++ b/.github/workflows/test_skip.txt
@@ -1 +1,3 @@
 retropath2_wrapper
+rpbasicdesign
+partsgenie
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 888683f3..95024bdd 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -65,7 +65,7 @@ jobs:
           ./scripts/shed_lint.py -i "tools/${{ matrix.repo }}"
       - name: 'Test tool'
         if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
-        timeout-minutes: 60
+        timeout-minutes: 120
         continue-on-error: true
         run: |
           mkdir -p "log/${{ matrix.repo }}"
@@ -80,6 +80,7 @@ jobs:
             "tools/${{ matrix.repo }}"
       - name: 'Prepare artefact'
         run: |
+          mkdir -p "log/${{ matrix.repo }}"
           zip -r -9 log.zip "log/${{ matrix.repo }}"
       - name: 'Upload Artifact Version'
         uses: actions/upload-artifact@v3
@@ -87,5 +88,6 @@ jobs:
           name: log-artifact-${{ matrix.repo }}
           path: log.zip
       - name: 'Aggregate results'
+        if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
         run: |
           ./scripts/aggregate_test.py -i .
diff --git a/tools/dnabot/config/job_conf.xml b/tools/dnabot/config/job_conf.xml
deleted file mode 100644
index 074bb5ff..00000000
--- a/tools/dnabot/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="dnabot" destination="local" />
diff --git a/tools/dnabot/config/tool_conf.xml b/tools/dnabot/config/tool_conf.xml
deleted file mode 100644
index 2bd575fa..00000000
--- a/tools/dnabot/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-util" name="SynBioCAD Utilities">
-    <tool file="synbiocad-galaxy-wrappers/dnabot/dnabot.xml" />
-  </section>
diff --git a/tools/dnaweaver/config/job_conf.xml b/tools/dnaweaver/config/job_conf.xml
deleted file mode 100644
index 26e6611b..00000000
--- a/tools/dnaweaver/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="dnaweaver" destination="local" />
diff --git a/tools/dnaweaver/config/tool_conf.xml b/tools/dnaweaver/config/tool_conf.xml
deleted file mode 100644
index 276006ba..00000000
--- a/tools/dnaweaver/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-gd" name="SynBioCAD Genetic Design">
-    <tool file="synbiocad-galaxy-wrappers/dnaweaver/dnaweaver.xml" />
-  </section>
diff --git a/tools/doe_synbio/config/job_conf.xml b/tools/doe_synbio/config/job_conf.xml
deleted file mode 100644
index 29e4469d..00000000
--- a/tools/doe_synbio/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="optdoe" destination="local" />
diff --git a/tools/doe_synbio/config/tool_conf.xml b/tools/doe_synbio/config/tool_conf.xml
deleted file mode 100644
index 0d0a82a0..00000000
--- a/tools/doe_synbio/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-gd" name="SynBioCAD Genetic Design">
-    <tool file="synbiocad-galaxy-wrappers/optdoe/optdoe.xml" />
-  </section>
diff --git a/tools/get_sbml_model/config/job_conf.xml b/tools/get_sbml_model/config/job_conf.xml
deleted file mode 100644
index a256854f..00000000
--- a/tools/get_sbml_model/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="get_sbml_model" destination="local" />
diff --git a/tools/get_sbml_model/config/tool_conf.xml b/tools/get_sbml_model/config/tool_conf.xml
deleted file mode 100644
index 93afd9e7..00000000
--- a/tools/get_sbml_model/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-util" name="SynBioCAD Utilities">
-    <tool file="synbiocad-galaxy-wrappers/get_sbml_model/get_sbml_model.xml" />
-  </section>
diff --git a/tools/get_sbml_model/get_sbml_model.xml b/tools/get_sbml_model/get_sbml_model.xml
index 64d5c8b9..c19e620a 100644
--- a/tools/get_sbml_model/get_sbml_model.xml
+++ b/tools/get_sbml_model/get_sbml_model.xml
@@ -78,7 +78,7 @@
         <!-- test 1: check if identical outputs are produced with iML1515 model input  -->
             <param name="input" value="iML1515" />
             <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/>
-            <output name="taxid" md5="ec29688652dd49becf7be2a6c2469287"/>
+            <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e"/>
             <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/>
             <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/>
         </test>
diff --git a/tools/icfree/config/job_conf.xml b/tools/icfree/config/job_conf.xml
deleted file mode 100644
index 7c88a103..00000000
--- a/tools/icfree/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="suite_icfree" destination="local" />
diff --git a/tools/icfree/config/tool_conf.xml b/tools/icfree/config/tool_conf.xml
deleted file mode 100644
index 38c31a44..00000000
--- a/tools/icfree/config/tool_conf.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-  <section id="sbc-pa" name="SynBioCAD Pathway Analysis">
-    <tool file="synbiocad-galaxy-wrappers/icfree/converter.xml" />
-    <tool file="synbiocad-galaxy-wrappers/icfree/instructor.xml" />
-    <tool file="synbiocad-galaxy-wrappers/icfree/plates_generator.xml" />
-    <tool file="synbiocad-galaxy-wrappers/icfree/sampler.xml" />
-  </section>
diff --git a/tools/icfree/instructor.xml b/tools/icfree/instructor.xml
index 90f6342e..0ff386a3 100644
--- a/tools/icfree/instructor.xml
+++ b/tools/icfree/instructor.xml
@@ -37,10 +37,10 @@
             --robot '$robot'
             --output-folder '.' &&
         mv instructions.csv '$output_instruction' &&
-        #if not os.path.isfile('volume_warning.tsv')
-            touch volume_warning.tsv &&
+        #if not os.path.isfile('volumes_warnings.tsv')
+            touch volumes_warnings.tsv &&
         #end if
-        mv volume_warning.tsv '$output_warning'
+        mv volumes_warnings.tsv '$output_warning'
     ]]></command>
     <inputs>
         <param name="plates_generator" type="data_collection" collection_type="list" format="json,tabular" label="Source/Destination corresponding to plate/wells" help="Output from iCFree plates generator"/>
@@ -53,7 +53,7 @@
         </param>
     </inputs>
     <outputs>
-        <data name="output_warning" format="tsv" label="${tool.name} - Warning" />
+        <data name="output_warning" format="tabular" label="${tool.name} - Warning" />
         <data name="output_instruction" format="csv" label="${tool.name} - Instruction" />
     </outputs>
     <tests>
@@ -61,10 +61,10 @@
             <!-- test 1: check if identical outputs are produced with default parameters  -->
             <param name="plates_generator">
                 <collection type="list">
-                    <element name="plates_generator_source_plate_1" value="plates_generator_source_plate_1.test-1.json" />
-                    <element name="plates_generator_source_plate_1.test-1.tsv" value="plates_generator_source_plate_1.test-1.tsv" />
-                    <element name="plates_generator_destination_plate_1.test-1.json" value="plates_generator_destination_plate_1.test-1.json" />
-                    <element name="plates_generator_destination_plate_1.test-1.tsv" value="plates_generator_destination_plate_1.test-1.tsv" />
+                    <element name="source_plate_1.json" value="plates_generator_source_plate_1.test-1.json" />
+                    <element name="source_plate_1.tsv" value="plates_generator_source_plate_1.test-1.tsv" />
+                    <element name="destination_plate_1.json" value="plates_generator_destination_plate_1.test-1.json" />
+                    <element name="destination_plate_1.tsv" value="plates_generator_destination_plate_1.test-1.tsv" />
                 </collection>
             </param>
             <output name="output_warning" ftype="tabular">
diff --git a/tools/inchi_to_sink/config/job_conf.xml b/tools/inchi_to_sink/config/job_conf.xml
deleted file mode 100644
index 90fd0239..00000000
--- a/tools/inchi_to_sink/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="inchi_to_sink" destination="local" />
diff --git a/tools/inchi_to_sink/config/tool_conf.xml b/tools/inchi_to_sink/config/tool_conf.xml
deleted file mode 100644
index 29d37ee4..00000000
--- a/tools/inchi_to_sink/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-util" name="SynBioCAD Utilities">
-    <tool file="synbiocad-galaxy-wrappers/inchi_to_sink/inchi_to_sink.xml" />
-  </section>
diff --git a/tools/lcrgenie/config/job_conf.xml b/tools/lcrgenie/config/job_conf.xml
deleted file mode 100644
index 0a375e2e..00000000
--- a/tools/lcrgenie/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="lcrgenie" destination="local" />
diff --git a/tools/lcrgenie/config/tool_conf.xml b/tools/lcrgenie/config/tool_conf.xml
deleted file mode 100644
index ac766f83..00000000
--- a/tools/lcrgenie/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-gd" name="SynBioCAD Genetic Design">
-    <tool file="synbiocad-galaxy-wrappers/lcrgenie/lcrgenie.xml" />
-  </section>
diff --git a/tools/partsgenie/config/job_conf.xml b/tools/partsgenie/config/job_conf.xml
deleted file mode 100644
index d76ec419..00000000
--- a/tools/partsgenie/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="partsgenie" destination="local" />
diff --git a/tools/partsgenie/config/tool_conf.xml b/tools/partsgenie/config/tool_conf.xml
deleted file mode 100644
index 66363c79..00000000
--- a/tools/partsgenie/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-gd" name="SynBioCAD Genetic Design">
-    <tool file="synbiocad-galaxy-wrappers/partsgenie/partsgenie.xml" />
-  </section>
diff --git a/tools/retropath2_wrapper/config/job_conf.xml b/tools/retropath2_wrapper/config/job_conf.xml
deleted file mode 100644
index 116db138..00000000
--- a/tools/retropath2_wrapper/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="retropath2" destination="local" />
diff --git a/tools/retropath2_wrapper/config/tool_conf.xml b/tools/retropath2_wrapper/config/tool_conf.xml
deleted file mode 100644
index 8ec97bc6..00000000
--- a/tools/retropath2_wrapper/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-rs" name="SynBioCAD RetroSynthesis">
-    <tool file="synbiocad-galaxy-wrappers/retropath2_wrapper/retropath2_wrapper.xml" />
-  </section>
diff --git a/tools/rp2biosensor/config/job_conf.xml b/tools/rp2biosensor/config/job_conf.xml
deleted file mode 100644
index c135e571..00000000
--- a/tools/rp2biosensor/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="rp2biosensor" destination="local" />
diff --git a/tools/rp2biosensor/config/tool_conf.xml b/tools/rp2biosensor/config/tool_conf.xml
deleted file mode 100644
index 0ad53392..00000000
--- a/tools/rp2biosensor/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-util" name="SynBioCAD Utilities">
-    <tool file="synbiocad-galaxy-wrappers/rp2biosensor/rp2biosensor.xml" />
-  </section>
diff --git a/tools/rp2biosensor/rp2biosensor.xml b/tools/rp2biosensor/rp2biosensor.xml
index 606cf5ef..e17f73b0 100644
--- a/tools/rp2biosensor/rp2biosensor.xml
+++ b/tools/rp2biosensor/rp2biosensor.xml
@@ -1,8 +1,8 @@
-<tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+<tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
     <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description>
     <macros>
         <token name="@VERSION_SUFFIX@">0</token>
-        <token name="@TOOL_VERSION@">3.1.0</token>
+        <token name="@TOOL_VERSION@">3.2.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
@@ -15,6 +15,7 @@
         #if str($adv.json_graph) == "true"
             --ojson '$json_file'
         #end if
+        --cache-dir "\${TMPDIR:-.}"
     ]]></command>
     <inputs>
         <param name="rp2_results" type="data" format="csv" label="RetroPath2 output" help="Retrosynthesis network generated by RetroPath2.0 in CSV format."/>
@@ -43,7 +44,7 @@
     </tests>
     <help><![CDATA[
 rp2biosensor
-================
+============
 
 **rp2biosensor** is an open-source Python software that extracts from the retrosynthetic network generated by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ the subnetwork of interest, linking the biosensor to the compound to be detected, and produce an interactive web page showing the transducing reactions.
 
@@ -65,22 +66,11 @@ Output
 Optional:
 
 * **JSON file**\ : Output the graph as JSON file.
-
-Project Links
-------------------
-
-* `GitHub <https://github.com/brsynth/rp2biosensor>`_
-
-License
--------
-
-* `MIT <https://github.com/brsynth/rp2biosensor/blob/master/LICENSE.md>`_
-
     ]]></help>
     <creator>
-        <person givenName="Thomas" familyName="Duigou" email="thomas.duigou@inrae.fr" identifier="https://orcid.org/0000-0002-2649-2950" />
+        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
     </creator>
     <citations>
         <citation type="doi">10.1021/acssynbio.2c00138</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/rp2paths/config/job_conf.xml b/tools/rp2paths/config/job_conf.xml
deleted file mode 100644
index 30042210..00000000
--- a/tools/rp2paths/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="rp2paths" destination="local" />
diff --git a/tools/rp2paths/config/tool_conf.xml b/tools/rp2paths/config/tool_conf.xml
deleted file mode 100644
index 4242cb9e..00000000
--- a/tools/rp2paths/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-rs" name="SynBioCAD RetroSynthesis">
-    <tool file="synbiocad-galaxy-wrappers/rp2paths/rp2paths.xml" />
-  </section>
diff --git a/tools/rpbasicdesign/config/job_conf.xml b/tools/rpbasicdesign/config/job_conf.xml
deleted file mode 100644
index 326cc69e..00000000
--- a/tools/rpbasicdesign/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="rpbasicdesign" destination="local" />
diff --git a/tools/rpbasicdesign/config/tool_conf.xml b/tools/rpbasicdesign/config/tool_conf.xml
deleted file mode 100644
index 8ebe11f8..00000000
--- a/tools/rpbasicdesign/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-util" name="SynBioCAD Utilities">
-    <tool file="synbiocad-galaxy-wrappers/rpbasicdesign/rpbasicdesign.xml" />
-  </section>
diff --git a/tools/rrparser/config/job_conf.xml b/tools/rrparser/config/job_conf.xml
deleted file mode 100644
index c0d779ec..00000000
--- a/tools/rrparser/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="rrparser" destination="local" />
diff --git a/tools/rrparser/config/tool_conf.xml b/tools/rrparser/config/tool_conf.xml
deleted file mode 100644
index 5c0c9561..00000000
--- a/tools/rrparser/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-rs" name="SynBioCAD RetroSynthesis">
-    <tool file="synbiocad-galaxy-wrappers/rrparser/rrparser.xml" />
-  </section>
diff --git a/tools/sbml2sbol/config/job_conf.xml b/tools/sbml2sbol/config/job_conf.xml
deleted file mode 100644
index a40bf1a0..00000000
--- a/tools/sbml2sbol/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="sbml2sbol" destination="local" />
diff --git a/tools/sbml2sbol/config/tool_conf.xml b/tools/sbml2sbol/config/tool_conf.xml
deleted file mode 100644
index 5bc56da5..00000000
--- a/tools/sbml2sbol/config/tool_conf.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-  <section id="sbc-util" name="SynBioCAD Utilities">
-    <tool file="synbiocad-galaxy-wrappers/sbml2sbol/sbml2sbol.xml" />
-  </section>
diff --git a/tools/straindesign/config/job_conf.xml b/tools/straindesign/config/job_conf.xml
deleted file mode 100644
index fa7b339f..00000000
--- a/tools/straindesign/config/job_conf.xml
+++ /dev/null
@@ -1 +0,0 @@
-    <tool id="suite_straindesign" destination="local" />
diff --git a/tools/straindesign/config/tool_conf.xml b/tools/straindesign/config/tool_conf.xml
deleted file mode 100644
index 5decfe1b..00000000
--- a/tools/straindesign/config/tool_conf.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-  <section id="sbc-pa" name="SynBioCAD Pathway Analysis">
-    <tool file="synbiocad-galaxy-wrappers/straindesign/analyzing-model.xml" />
-    <tool file="synbiocad-galaxy-wrappers/straindesign/reduce-model.xml" />
-    <tool file="synbiocad-galaxy-wrappers/straindesign/simulate-deletion.xml" />
-  </section>

From 00bca561a4d1aa67ea9dd9139c79d526a0878357 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Mon, 5 Jun 2023 10:44:36 +0200
Subject: [PATCH 15/61] Workflows `basic_assembly_workflow` (#119)

* feat(workflows): add one workflow
---
 .github/workflows/pr.yml                      |   2 +-
 .github/workflows/prworkflows.yml             | 128 +++++
 .../{test_skip.txt => test_tools_skip.txt}    |   0
 .github/workflows/test_workflows_skip.txt     |   0
 .../workflows/{tests.yml => testtools.yml}    |   6 +-
 .github/workflows/testworkflows.yml           |  82 ++++
 .gitignore                                    |   1 +
 scripts/upload_workflow.py                    |  54 +++
 workflows/basic_assembly_workflow/.shed.yml   |  12 +
 .../basic_assembly_workflow-job.yml           |  11 +
 .../basic_assembly_workflow-tests.yml         |  17 +
 .../basic_assembly_workflow.ga                | 436 ++++++++++++++++++
 .../test-data/dna_bot_scripts.tar             | Bin 0 -> 174080 bytes
 13 files changed, 745 insertions(+), 4 deletions(-)
 create mode 100644 .github/workflows/prworkflows.yml
 rename .github/workflows/{test_skip.txt => test_tools_skip.txt} (100%)
 create mode 100644 .github/workflows/test_workflows_skip.txt
 rename .github/workflows/{tests.yml => testtools.yml} (97%)
 create mode 100644 .github/workflows/testworkflows.yml
 create mode 100755 scripts/upload_workflow.py
 create mode 100644 workflows/basic_assembly_workflow/.shed.yml
 create mode 100644 workflows/basic_assembly_workflow/basic_assembly_workflow-job.yml
 create mode 100644 workflows/basic_assembly_workflow/basic_assembly_workflow-tests.yml
 create mode 100644 workflows/basic_assembly_workflow/basic_assembly_workflow.ga
 create mode 100644 workflows/basic_assembly_workflow/test-data/dna_bot_scripts.tar

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index b02f18c0..e83fac63 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -50,7 +50,7 @@ jobs:
       - name: 'List repos'
         id: set-matrix
         run: |
-          matrix=$(jq -R -s -c '[split("\n")[] | select(.|length>0)]' .github/workflows/test_skip.txt)
+          matrix=$(jq -R -s -c '[split("\n")[] | select(.|length>0)]' .github/workflows/test_tools_skip.txt)
           echo "Number of repos: ${matrix}"
           echo "matrix=$matrix" >> "${GITHUB_OUTPUT}"
 
diff --git a/.github/workflows/prworkflows.yml b/.github/workflows/prworkflows.yml
new file mode 100644
index 00000000..36b44bc1
--- /dev/null
+++ b/.github/workflows/prworkflows.yml
@@ -0,0 +1,128 @@
+name: PullRequest
+
+on:
+  pull_request:
+    types:
+      - edited
+      - opened
+      - reopened
+      - synchronize
+  pull_request_target:
+    types:
+      - closed
+
+jobs:
+
+  list:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+      nb: ${{ steps.set-matrix.outputs.nb }}
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v3
+      - name: 'Select modified files'
+        id: files
+        #uses: Ana06/get-changed-files@v2.2.0
+        uses: tj-actions/changed-files@v36
+        with:
+          files: tools/**
+          separator: ","
+      - name: 'List repos'
+        id: set-matrix
+        run: |
+          echo "list file modified"
+          echo ${{ steps.files.outputs.all_changed_and_modified_files }}
+          matrix=$(echo ${{ steps.files.outputs.all_changed_and_modified_files }} | jq -R -s -c 'split(",") | map(select(contains("workflows"))) | map(split("/")[1]) | sort | unique')
+          echo "list of repo: ${matrix}"
+          echo "matrix=$matrix" >> "${GITHUB_OUTPUT}"
+          nb=$(echo ${matrix} | jq -s -c '.[] | length')
+          echo "Number of repos: ${nb}"
+          echo "nb=$nb" >> "${GITHUB_OUTPUT}"
+
+  skip:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v3
+      - name: 'List repos'
+        id: set-matrix
+        run: |
+          matrix=$(jq -R -s -c '[split("\n")[] | select(.|length>0)]' .github/workflows/test_workflows_skip.txt)
+          echo "Number of repos: ${matrix}"
+          echo "matrix=$matrix" >> "${GITHUB_OUTPUT}"
+
+  test:
+    needs: [list, skip]
+    if: ${{ github.event.pull_request.merged == false && needs.list.outputs.nb > 0 }}
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 1
+      matrix:
+        repo: ${{ fromJson(needs.list.outputs.matrix) }}
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v3
+      - name: "Setup python"
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: 'pip' # caching pip dependencies
+          cache-dependency-path: |
+            env/requirements.txt
+      - name: 'Install packages'
+        run: |
+          pip install -r env/requirements.txt
+      - name: 'Worfklow Lint'
+        run: |
+          planemo workflow_lint \
+            --fail_level error \
+            "workflows/${{ matrix.repo }}"
+      - name: 'Shed lint'
+        run: |
+          planemo shed_lint --urls --xsd --ensure_metadata "workflows/${{ matrix.repo }}"
+          ./scripts/shed_lint.py -i "workflows/${{ matrix.repo }}"
+      - name: 'Test tool'
+        if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
+        timeout-minutes: 60
+        run: |
+          echo "list workflows"
+          ls workflows
+          echo "list repo"
+          ls  "workflows/${{ matrix.repo }}"
+          planemo test \
+            --engine external_galaxy \
+            --galaxy_url https://galaxy-synbiocad.org \
+            --galaxy_user_key "${{ secrets.GG_SYNBIOCAD_TOKEN }}" \
+            "workflows/${{ matrix.repo }}/${{ matrix.repo }}.ga"
+
+  shed:
+    needs: list
+    if: ${{ github.event.pull_request.merged == true && needs.list.outputs.nb > 0 }}
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    strategy:
+      max-parallel: 1
+      matrix:
+        repo: ${{ fromJson(needs.list.outputs.matrix) }}
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v3
+      - name: "Setup python"
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: 'pip' # caching pip dependencies
+          cache-dependency-path: |
+            env/requirements.txt
+      - name: 'Install packages'
+        run: |
+          pip install -r env/requirements.txt
+      - name: 'Deploy'
+        run: |
+          ./scripts/upload_workflow.py \
+            --workflow "workflows/${{ matrix.repo }}/${{ matrix.repo }}.ga" \
+            --galaxy_url https://galaxy-synbiocad.org \
+            --galaxy_user_key "${{ secrets.GG_SYNBIOCAD_TOKEN }}"
diff --git a/.github/workflows/test_skip.txt b/.github/workflows/test_tools_skip.txt
similarity index 100%
rename from .github/workflows/test_skip.txt
rename to .github/workflows/test_tools_skip.txt
diff --git a/.github/workflows/test_workflows_skip.txt b/.github/workflows/test_workflows_skip.txt
new file mode 100644
index 00000000..e69de29b
diff --git a/.github/workflows/tests.yml b/.github/workflows/testtools.yml
similarity index 97%
rename from .github/workflows/tests.yml
rename to .github/workflows/testtools.yml
index 95024bdd..afd4ea07 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/testtools.yml
@@ -1,4 +1,4 @@
-name: Tests
+name: TestTools
 
 on:
   schedule:
@@ -27,7 +27,7 @@ jobs:
       - name: 'List repos'
         id: set-matrix
         run: |
-          matrix=$(jq -R -s -c '[split("\n")[] | select(.|length>0)]' .github/workflows/test_skip.txt)
+          matrix=$(jq -R -s -c '[split("\n")[] | select(.|length>0)]' .github/workflows/test_tools_skip.txt)
           echo "Number of repos: ${matrix}"
           echo "matrix=$matrix" >> "${GITHUB_OUTPUT}"
 
@@ -42,7 +42,7 @@ jobs:
       - name: 'Checkout'
         uses: actions/checkout@v3
         with:
-          ref: main
+          fetch-depth: 0
       - name: "Setup python"
         uses: actions/setup-python@v4
         with:
diff --git a/.github/workflows/testworkflows.yml b/.github/workflows/testworkflows.yml
new file mode 100644
index 00000000..e7ff61a6
--- /dev/null
+++ b/.github/workflows/testworkflows.yml
@@ -0,0 +1,82 @@
+name: TestWorkflows
+
+on:
+  schedule:
+    - cron: '0 0 * * 1'
+  pull_request:
+    types:
+      - edited
+      - opened
+      - reopened
+      - synchronize
+  pull_request_target:
+    types:
+      - closed
+
+jobs:
+
+  list:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v3
+      - name: 'List repos'
+        id: set-matrix
+        run: echo "matrix=$(find workflows -mindepth 1 -maxdepth 1 -type d | jq -R -s -c 'split("\n")[:-1] | map(split("/")[-1])')" >> "${GITHUB_OUTPUT}"
+
+  skip:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v3
+      - name: 'List repos'
+        id: set-matrix
+        run: |
+          matrix=$(jq -R -s -c '[split("\n")[] | select(.|length>0)]' .github/workflows/test_workflows_skip.txt)
+          echo "Number of repos: ${matrix}"
+          echo "matrix=$matrix" >> "${GITHUB_OUTPUT}"
+
+  test:
+    needs: [list, skip]
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 1
+      matrix:
+        repo: ${{ fromJson(needs.list.outputs.matrix) }}
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: "Setup python"
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: 'pip' # caching pip dependencies
+          cache-dependency-path: |
+            env/requirements.txt
+      - name: 'Install packages'
+        run: |
+          pip install -r env/requirements.txt
+      - name: 'Worfklow Lint'
+        run: |
+          planemo workflow_lint \
+            --fail_level error \
+            "workflows/${{ matrix.repo }}"
+      - name: 'Shed lint'
+        run: |
+          planemo shed_lint --urls --xsd --ensure_metadata "workflows/${{ matrix.repo }}"
+          ./scripts/shed_lint.py -i "workflows/${{ matrix.repo }}"
+      - name: 'Test tool'
+        if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
+        timeout-minutes: 60
+        run: |
+          planemo test \
+            --engine external_galaxy \
+            --galaxy_url https://galaxy-synbiocad.org \
+            --galaxy_user_key "${{ secrets.GG_SYNBIOCAD_TOKEN }}" \
+            "workflows/${{ matrix.repo }}/${{ matrix.repo }}.ga"
diff --git a/.gitignore b/.gitignore
index 3a5cc03c..9bfb4d39 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@ node_modules
 *.code-workspace
 tool_test_output.html
 tool_test_output.json
+.hg_archival.txt
diff --git a/scripts/upload_workflow.py b/scripts/upload_workflow.py
new file mode 100755
index 00000000..e959bebf
--- /dev/null
+++ b/scripts/upload_workflow.py
@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+from typing import Any, Dict
+
+from bioblend.galaxy import GalaxyInstance
+from bioblend.galaxy.workflows import WorkflowClient
+
+
+class GalaxyUploadWorkflow(object):
+    def __init__(self, url: str, key: str):
+        self.gi = GalaxyInstance(url=url, key=key)
+        self.wc = WorkflowClient(galaxy_instance=self.gi)
+
+    def upload(self, workflow: str) -> None:
+        data = GalaxyUploadWorkflow.read_workflow(path=workflow)
+
+        self.wc.update_workflow(
+            workflow_id=data["uuid"],
+            workflow=data["steps"],
+            name=data["name"],
+            annotation=data["annotation"],
+            menu_entry=True,
+            tags=data["tags"],
+            published=True,
+        )
+
+    @classmethod
+    def read_workflow(cls, path: str) -> Dict[str, Any]:
+        with open(path) as fd:
+            return json.load(fd)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser_input = parser.add_argument_group("Input")
+    parser_input.add_argument(
+        "--galaxy_url",
+        required=True,
+        help="Url of Galaxy Instance",
+    )
+    parser_input.add_argument(
+        "--galaxy_user_key",
+        required=True,
+        help="Token for Galaxy Instance",
+    )
+    parser_input.add_argument("--workflow", required=True, help="Worfklow file (.ga)")
+
+    args = parser.parse_args()
+
+    guw = GalaxyUploadWorkflow(url=args.galaxy_url, key=args.galaxy_user_key)
+    guw.upload(workflow=args.workflow)
diff --git a/workflows/basic_assembly_workflow/.shed.yml b/workflows/basic_assembly_workflow/.shed.yml
new file mode 100644
index 00000000..aba24099
--- /dev/null
+++ b/workflows/basic_assembly_workflow/.shed.yml
@@ -0,0 +1,12 @@
+Typical workflow:  
+name: basic_assembly_workflow
+owner: tduigou
+remote_repository_url: https://github.com/brsynth/galaxytools/tree/master/workflows/basic_assembly_workflow
+homepage_url: https://github.com/brsynth/galaxytools
+type: unrestricted
+categories:
+  - Systems Biology
+  - Synthetic Biology
+description: BASIC Assembly Workflow
+long_description: |
+  'This workflow proposes an alternative route to design plasmids encoding predicted pathways by using the BASIC assembly method. Importantly, it generates scripts enabling the automatic build of these plasmids using an Opentrons liquid handler robot. Source code may be found at the following location: https://github.com/brsynth/selenzy-wrapper , https://github.com/brsynth/rpbasicdesign , https://github.com/brsynth/DNA-BOT/tree/DNA-BOT-APIv2'
diff --git a/workflows/basic_assembly_workflow/basic_assembly_workflow-job.yml b/workflows/basic_assembly_workflow/basic_assembly_workflow-job.yml
new file mode 100644
index 00000000..30a535ad
--- /dev/null
+++ b/workflows/basic_assembly_workflow/basic_assembly_workflow-job.yml
@@ -0,0 +1,11 @@
+Linkers and user parts:
+  class: File
+  location: https://zenodo.org/record/6123887/files/parts_for_lycopene.csv
+Pathway (SBML):
+  class: File
+  location: https://zenodo.org/record/6123887/files/rp_002_0011.xml
+DNA-Bot settings:
+  class: File
+  location: https://zenodo.org/record/6123887/files/dnabot_paris_settings.yaml
+Host taxon ID: 83333
+Enzyme taxon IDs: 553
diff --git a/workflows/basic_assembly_workflow/basic_assembly_workflow-tests.yml b/workflows/basic_assembly_workflow/basic_assembly_workflow-tests.yml
new file mode 100644
index 00000000..9840a875
--- /dev/null
+++ b/workflows/basic_assembly_workflow/basic_assembly_workflow-tests.yml
@@ -0,0 +1,17 @@
+- doc: Test for BASIC Assembly workflow
+  job:
+    Linkers and user parts:
+      class: File
+      location: https://zenodo.org/record/6123887/files/parts_for_lycopene.csv
+    Pathway (SBML):
+      class: File
+      location: https://zenodo.org/record/6123887/files/rp_002_0011.xml
+    DNA-Bot settings:
+      class: File
+      location: https://zenodo.org/record/6123887/files/dnabot_paris_settings.yaml
+    Host taxon ID: 83333
+    Enzyme taxon IDs: 553
+  outputs:
+    dnabot_scripts:
+      path: test-data/dna_bot_scripts.tar
+      compare: sim_size
diff --git a/workflows/basic_assembly_workflow/basic_assembly_workflow.ga b/workflows/basic_assembly_workflow/basic_assembly_workflow.ga
new file mode 100644
index 00000000..e24dbf29
--- /dev/null
+++ b/workflows/basic_assembly_workflow/basic_assembly_workflow.ga
@@ -0,0 +1,436 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Design plasmids encoding predicted pathways by using the BASIC assembly method.",
+    "format-version": "0.1",
+    "name": "Genetic Design (BASIC Assembly)",
+    "steps": {
+        "0": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "Pathway (SBML)"
+                }
+            ],
+            "label": "Pathway (SBML)",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 314.8000030517578,
+                "height": 61.80000305175781,
+                "left": 239,
+                "right": 439,
+                "top": 253,
+                "width": 200,
+                "x": 239,
+                "y": 253
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "c24c8466-a2fa-40e6-b218-9e857ede1368",
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "Host taxon ID"
+                }
+            ],
+            "label": "Host taxon ID",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 404.8000030517578,
+                "height": 61.80000305175781,
+                "left": 241,
+                "right": 441,
+                "top": 343,
+                "width": 200,
+                "x": 241,
+                "y": 343
+            },
+            "tool_id": null,
+            "tool_state": "{\"default\": 83333, \"parameter_type\": \"integer\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "421174ff-5277-4144-9624-d55db17be30d",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "fa443ca9-5251-4bde-92db-c7cf8894001b"
+                }
+            ]
+        },
+        "2": {
+            "annotation": "Comma separated values",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Comma separated values",
+                    "name": "Enzyme taxon IDs"
+                }
+            ],
+            "label": "Enzyme taxon IDs",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 517.1999969482422,
+                "height": 82.19999694824219,
+                "left": 241,
+                "right": 441,
+                "top": 435,
+                "width": 200,
+                "x": 241,
+                "y": 435
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "008f4464-c232-483a-a07e-7e9dc60c9ebf",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "46a410ab-1e02-4452-8551-690bb3d7b708"
+                }
+            ]
+        },
+        "3": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 3,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "Linkers and user parts"
+                }
+            ],
+            "label": "Linkers and user parts",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 628.1999969482422,
+                "height": 82.19999694824219,
+                "left": 243,
+                "right": 443,
+                "top": 546,
+                "width": 200,
+                "x": 243,
+                "y": 546
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "818a252c-d3f9-4627-83bd-60cbac258497",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "6c8f6c11-c878-4dc5-9064-cc44a4b96358"
+                }
+            ]
+        },
+        "4": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 4,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "DNA-Bot settings"
+                }
+            ],
+            "label": "DNA-Bot settings",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 852.1999969482422,
+                "height": 82.19999694824219,
+                "left": 246,
+                "right": 446,
+                "top": 770,
+                "width": 200,
+                "x": 246,
+                "y": 770
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": true}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "824b42b7-4ca0-4104-83f1-2145d1472b64",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "cf85648b-2ba9-4600-b0d7-b00e4db69ba0"
+                }
+            ]
+        },
+        "5": {
+            "annotation": "Performs enzyme selection from a reaction query.",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0",
+            "errors": null,
+            "id": 5,
+            "input_connections": {
+                "adv|enzyme_taxIDs": {
+                    "id": 2,
+                    "output_name": "output"
+                },
+                "adv|host_taxID": {
+                    "id": 1,
+                    "output_name": "output"
+                },
+                "pathway": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Selenzyme",
+                    "name": "pathway"
+                }
+            ],
+            "label": "Selenzyme",
+            "name": "Selenzyme",
+            "outputs": [
+                {
+                    "name": "uniprot_ids",
+                    "type": "xml"
+                },
+                {
+                    "name": "uniprot_ids_csv",
+                    "type": "csv"
+                }
+            ],
+            "position": {
+                "bottom": 508.1999969482422,
+                "height": 225.1999969482422,
+                "left": 553,
+                "right": 753,
+                "top": 283,
+                "width": 200,
+                "x": 553,
+                "y": 283
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0",
+            "tool_shed_repository": {
+                "changeset_revision": "34a9d136a5bf",
+                "name": "selenzy",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"host_taxID\": {\"__class__\": \"ConnectedValue\"}, \"enzyme_taxIDs\": {\"__class__\": \"ConnectedValue\"}, \"nb_ids\": \"-1\", \"nb_targets\": \"500\", \"direction\": \"0.0\", \"NoMSA\": \"true\"}, \"pathway\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": null,
+            "type": "tool",
+            "uuid": "69b876a0-0dac-4592-94ed-19820860998c",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "uniprot_ids_csv",
+                    "uuid": "bf22d3b6-7500-49ed-9f0d-fad0d5a93e80"
+                },
+                {
+                    "label": "Uniprot IDs",
+                    "output_name": "uniprot_ids",
+                    "uuid": "eab193c0-12aa-40d1-944a-062813653cb9"
+                }
+            ]
+        },
+        "6": {
+            "annotation": "Extracts enzyme IDs from rpSBML files.",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
+            "errors": null,
+            "id": 6,
+            "input_connections": {
+                "adv|parts_files": {
+                    "id": 3,
+                    "output_name": "output"
+                },
+                "rpsbml_file": {
+                    "id": 5,
+                    "output_name": "uniprot_ids"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool BasicDesign",
+                    "name": "adv"
+                },
+                {
+                    "description": "runtime parameter for tool BasicDesign",
+                    "name": "rpsbml_file"
+                }
+            ],
+            "label": "BasicDesign",
+            "name": "BasicDesign",
+            "outputs": [
+                {
+                    "name": "sbol_dir",
+                    "type": "input"
+                },
+                {
+                    "name": "Constructs",
+                    "type": "csv"
+                },
+                {
+                    "name": "User parts plate",
+                    "type": "csv"
+                },
+                {
+                    "name": "Biolegio plate",
+                    "type": "csv"
+                }
+            ],
+            "position": {
+                "bottom": 646.8000030517578,
+                "height": 214.8000030517578,
+                "left": 816,
+                "right": 1016,
+                "top": 432,
+                "width": 200,
+                "x": 816,
+                "y": 432
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
+            "tool_shed_repository": {
+                "changeset_revision": "de9f53630349",
+                "name": "rpbasicdesign",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"parts_files\": {\"__class__\": \"RuntimeValue\"}, \"lms_id\": \"LMS\", \"lmp_id\": \"LMP\", \"cds_permutation\": \"true\"}, \"backbone_id\": \"BASIC_SEVA_37_CmR-p15A.1\", \"rpsbml_file\": {\"__class__\": \"RuntimeValue\"}, \"sample_size\": \"88\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": null,
+            "type": "tool",
+            "uuid": "77649640-9d17-417f-9195-18e10b50d9d6",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "Constructs",
+                    "uuid": "e653f383-afb6-4cc1-a862-d4946512b50b"
+                },
+                {
+                    "label": null,
+                    "output_name": "User parts plate",
+                    "uuid": "780352cb-695e-4ca0-b391-7f624e8dd8cb"
+                },
+                {
+                    "label": null,
+                    "output_name": "sbol_dir",
+                    "uuid": "4d464905-d571-4f21-b8a6-d7f1b2c31eab"
+                },
+                {
+                    "label": null,
+                    "output_name": "Biolegio plate",
+                    "uuid": "16de9e3c-a177-4228-b2b8-de2d51fa11b4"
+                }
+            ]
+        },
+        "7": {
+            "annotation": "DNA assembly using BASIC on OpenTrons.",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0",
+            "errors": null,
+            "id": 7,
+            "input_connections": {
+                "adv|default_settings_file": {
+                    "id": 4,
+                    "output_name": "output"
+                },
+                "construct_file": {
+                    "id": 6,
+                    "output_name": "Constructs"
+                },
+                "plate_files": [
+                    {
+                        "id": 6,
+                        "output_name": "User parts plate"
+                    },
+                    {
+                        "id": 6,
+                        "output_name": "Biolegio plate"
+                    }
+                ]
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool DNA-Bot",
+                    "name": "adv"
+                },
+                {
+                    "description": "runtime parameter for tool DNA-Bot",
+                    "name": "construct_file"
+                },
+                {
+                    "description": "runtime parameter for tool DNA-Bot",
+                    "name": "plate_files"
+                }
+            ],
+            "label": "DNA-Bot",
+            "name": "DNA-Bot",
+            "outputs": [
+                {
+                    "name": "dnabot_scripts",
+                    "type": "tar"
+                }
+            ],
+            "position": {
+                "bottom": 728.8000030517578,
+                "height": 194.8000030517578,
+                "left": 1073,
+                "right": 1273,
+                "top": 534,
+                "width": 200,
+                "x": 1073,
+                "y": 534
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0",
+            "tool_shed_repository": {
+                "changeset_revision": "de6812daba39",
+                "name": "dnabot",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"default_settings_file\": {\"__class__\": \"RuntimeValue\"}, \"etoh_well\": \"A11\", \"soc_column\": \"1\"}, \"construct_file\": {\"__class__\": \"RuntimeValue\"}, \"plate_files\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": null,
+            "type": "tool",
+            "uuid": "4a917d61-47a7-4f71-922d-740231461a83",
+            "workflow_outputs": [
+                {
+                    "label": "dnabot_scripts",
+                    "output_name": "dnabot_scripts",
+                    "uuid": "346c5730-0a87-4848-b6bf-4e455b5f2505"
+                }
+            ]
+        }
+    },
+    "tags": [
+        "brs", "assembly"
+    ],
+    "uuid": "22764e28-d3c7-40d2-888c-7a3722d29d26",
+    "version": 0
+}
diff --git a/workflows/basic_assembly_workflow/test-data/dna_bot_scripts.tar b/workflows/basic_assembly_workflow/test-data/dna_bot_scripts.tar
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literal 0
HcmV?d00001


From f7df6238cbaa188a138cb48217658b6c7b22a181 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Mon, 5 Jun 2023 11:30:18 +0200
Subject: [PATCH 16/61] fix(tools): update `sbol_converter` commands (#122)

---
 tools/sbol_converter/sbol_converter.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tools/sbol_converter/sbol_converter.xml b/tools/sbol_converter/sbol_converter.xml
index ee7920fa..92169629 100644
--- a/tools/sbol_converter/sbol_converter.xml
+++ b/tools/sbol_converter/sbol_converter.xml
@@ -10,22 +10,22 @@
     <command detect_errors="exit_code"><![CDATA[
         #if str($convert_type.type) == "SBOL2 to SBOL3"
             ln -sv '$sbol2_input' 'input.$sbol2_input.ext' &&
-            sbol2to3 -o '$output' 'input.$sbol2_input.ext'
+            sbol2-to-sbol3 -o '$output' 'input.$sbol2_input.ext'
         #elif str($convert_type.type) == "SBOL3 to SBOL2"
             ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
-            sbol3to2 -o '$output' 'input.$sbol3_input.ext'
+            sbol3-to-sbol2 -o '$output' 'input.$sbol3_input.ext'
         #elif str($convert_type.type) == "SBOL3 to GENBANK"
             ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
-            sbol2genbank -o '$output' 'input.$sbol3_input.ext'
+            sbol-to-genbank -o '$output' 'input.$sbol3_input.ext'
         #elif str($convert_type.type) == "GENBANK to SBOL3"
             ln -sv '$genbank_input' 'input.$genbank_input.ext' &&
-            genbank2sbol -o '$output' 'input.$genbank_input.ext' --namespace '$convert_type.namespace'
+            genbank-to-sbol -o '$output' 'input.$genbank_input.ext' --namespace '$convert_type.namespace'
         #elif str($convert_type.type) == "SBOL3 to FASTA"
             ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
-            sbol2fasta -o '$output' 'input.$sbol3_input.ext'
+            sbol-to-fasta -o '$output' 'input.$sbol3_input.ext'
         #elif str($convert_type.type) == "FASTA to SBOL3"
             ln -sv '$fasta_input' 'input.$fasta_input.ext' &&
-            fasta2sbol -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace'
+            fasta-to-sbol -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace'
         #elif str($convert_type.type) == "SBOL2 to FASTA"
             ln -sv '$sbol2_input' 'input.$sbol2_input.ext' &&
             sbol-converter SBOL2 FASTA -o '$output' 'input.$sbol2_input.ext'

From 22da397d467114cb455f7b08e9cf7481ac439542 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 6 Jun 2023 09:49:47 +0200
Subject: [PATCH 17/61] chore(github): fix syntax

---
 .github/workflows/release_schedule.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/release_schedule.yml b/.github/workflows/release_schedule.yml
index e909cd2f..2750de15 100644
--- a/.github/workflows/release_schedule.yml
+++ b/.github/workflows/release_schedule.yml
@@ -18,10 +18,12 @@ jobs:
           ref: 'stable'
       - name: "Check diff"
         id: set-diff
+        continue-on-error: true
         run: |
           git diff --quiet stable..origin/main
           nb=$?
-          echo "nb=$nb" >> "${GITHUB_OUTPUT}"
+          echo "Find diff: ${nb}"
+          echo "nb=${nb}" >> "${GITHUB_OUTPUT}"
 
   Call:
     runs-on: ubuntu-latest

From 5a21330bb75fe5b6433862f09802ddb3334051c1 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Thu, 8 Jun 2023 17:17:01 +0200
Subject: [PATCH 18/61] Add `pathway_analysis` workflow (#128)

* fix(workflows): rm unused files

* feat(workflows): add `pathway_analysis`
---
 .github/workflows/prworkflows.yml             |  12 +-
 .github/workflows/testworkflows.yml           |  15 +-
 workflows/basic_assembly_workflow/.shed.yml   |  12 -
 .../basic_assembly_workflow-job.yml           |  11 -
 .../pathway_analysis_workflow-tests.yml       |  42 ++
 .../pathway_analysis_workflow.ga              | 381 ++++++++++++++++++
 .../test-data/ranked_pathways.csv             |  10 +
 7 files changed, 436 insertions(+), 47 deletions(-)
 delete mode 100644 workflows/basic_assembly_workflow/.shed.yml
 delete mode 100644 workflows/basic_assembly_workflow/basic_assembly_workflow-job.yml
 create mode 100644 workflows/pathway_analysis_workflow/pathway_analysis_workflow-tests.yml
 create mode 100644 workflows/pathway_analysis_workflow/pathway_analysis_workflow.ga
 create mode 100644 workflows/pathway_analysis_workflow/test-data/ranked_pathways.csv

diff --git a/.github/workflows/prworkflows.yml b/.github/workflows/prworkflows.yml
index 36b44bc1..e3ab3686 100644
--- a/.github/workflows/prworkflows.yml
+++ b/.github/workflows/prworkflows.yml
@@ -1,4 +1,4 @@
-name: PullRequest
+name: PullRequestWorkflow
 
 on:
   pull_request:
@@ -26,7 +26,7 @@ jobs:
         #uses: Ana06/get-changed-files@v2.2.0
         uses: tj-actions/changed-files@v36
         with:
-          files: tools/**
+          files: workflows/**
           separator: ","
       - name: 'List repos'
         id: set-matrix
@@ -80,18 +80,10 @@ jobs:
           planemo workflow_lint \
             --fail_level error \
             "workflows/${{ matrix.repo }}"
-      - name: 'Shed lint'
-        run: |
-          planemo shed_lint --urls --xsd --ensure_metadata "workflows/${{ matrix.repo }}"
-          ./scripts/shed_lint.py -i "workflows/${{ matrix.repo }}"
       - name: 'Test tool'
         if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
         timeout-minutes: 60
         run: |
-          echo "list workflows"
-          ls workflows
-          echo "list repo"
-          ls  "workflows/${{ matrix.repo }}"
           planemo test \
             --engine external_galaxy \
             --galaxy_url https://galaxy-synbiocad.org \
diff --git a/.github/workflows/testworkflows.yml b/.github/workflows/testworkflows.yml
index e7ff61a6..acb1fd2e 100644
--- a/.github/workflows/testworkflows.yml
+++ b/.github/workflows/testworkflows.yml
@@ -3,15 +3,6 @@ name: TestWorkflows
 on:
   schedule:
     - cron: '0 0 * * 1'
-  pull_request:
-    types:
-      - edited
-      - opened
-      - reopened
-      - synchronize
-  pull_request_target:
-    types:
-      - closed
 
 jobs:
 
@@ -67,11 +58,7 @@ jobs:
           planemo workflow_lint \
             --fail_level error \
             "workflows/${{ matrix.repo }}"
-      - name: 'Shed lint'
-        run: |
-          planemo shed_lint --urls --xsd --ensure_metadata "workflows/${{ matrix.repo }}"
-          ./scripts/shed_lint.py -i "workflows/${{ matrix.repo }}"
-      - name: 'Test tool'
+      - name: 'Test worflow'
         if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
         timeout-minutes: 60
         run: |
diff --git a/workflows/basic_assembly_workflow/.shed.yml b/workflows/basic_assembly_workflow/.shed.yml
deleted file mode 100644
index aba24099..00000000
--- a/workflows/basic_assembly_workflow/.shed.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-Typical workflow:  
-name: basic_assembly_workflow
-owner: tduigou
-remote_repository_url: https://github.com/brsynth/galaxytools/tree/master/workflows/basic_assembly_workflow
-homepage_url: https://github.com/brsynth/galaxytools
-type: unrestricted
-categories:
-  - Systems Biology
-  - Synthetic Biology
-description: BASIC Assembly Workflow
-long_description: |
-  'This workflow proposes an alternative route to design plasmids encoding predicted pathways by using the BASIC assembly method. Importantly, it generates scripts enabling the automatic build of these plasmids using an Opentrons liquid handler robot. Source code may be found at the following location: https://github.com/brsynth/selenzy-wrapper , https://github.com/brsynth/rpbasicdesign , https://github.com/brsynth/DNA-BOT/tree/DNA-BOT-APIv2'
diff --git a/workflows/basic_assembly_workflow/basic_assembly_workflow-job.yml b/workflows/basic_assembly_workflow/basic_assembly_workflow-job.yml
deleted file mode 100644
index 30a535ad..00000000
--- a/workflows/basic_assembly_workflow/basic_assembly_workflow-job.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-Linkers and user parts:
-  class: File
-  location: https://zenodo.org/record/6123887/files/parts_for_lycopene.csv
-Pathway (SBML):
-  class: File
-  location: https://zenodo.org/record/6123887/files/rp_002_0011.xml
-DNA-Bot settings:
-  class: File
-  location: https://zenodo.org/record/6123887/files/dnabot_paris_settings.yaml
-Host taxon ID: 83333
-Enzyme taxon IDs: 553
diff --git a/workflows/pathway_analysis_workflow/pathway_analysis_workflow-tests.yml b/workflows/pathway_analysis_workflow/pathway_analysis_workflow-tests.yml
new file mode 100644
index 00000000..c723fb75
--- /dev/null
+++ b/workflows/pathway_analysis_workflow/pathway_analysis_workflow-tests.yml
@@ -0,0 +1,42 @@
+- doc: Evaluating and ranking a set of pathways based on multiple metrics
+  job:
+    Heterologous pathways:
+      class: Collection
+      collection_type: list
+      elements:
+        - identifier: rp_001_0001.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_001_0001.xml
+        - identifier: rp_001_0006.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_001_0006.xml
+        - identifier: rp_001_0011.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_001_0011.xml
+        - identifier: rp_002_0001.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_002_0001.xml
+        - identifier: rp_002_0006.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_002_0006.xml
+        - identifier: rp_002_0011.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_002_0011.xml
+        - identifier: rp_003_0001.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_003_0001.xml
+        - identifier: rp_003_0116.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_003_0116.xml
+        - identifier: rp_003_0231.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_003_0231.xml
+    Chassis where to produce target from:
+      class: File
+      location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/SBML_Model_iML1515.xml
+    Biomass reaction ID: R_BIOMASS_Ec_iML1515_core_75p37M
+    Cell compartment ID: c
+  outputs:
+    Ranked Pathways:
+      path: test-data/ranked_pathways.csv
+      compare: sim_size
diff --git a/workflows/pathway_analysis_workflow/pathway_analysis_workflow.ga b/workflows/pathway_analysis_workflow/pathway_analysis_workflow.ga
new file mode 100644
index 00000000..ad8497aa
--- /dev/null
+++ b/workflows/pathway_analysis_workflow/pathway_analysis_workflow.ga
@@ -0,0 +1,381 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Evaluating and ranking a set of pathways based on multiple metrics",
+    "creator": [
+        {
+            "class": "Organization",
+            "name": "BioRetroSynth",
+            "url": "https://github.com/brsynth"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "name": "Pathway Analysis",
+    "steps": {
+        "0": {
+            "annotation": "An identifier like \"biomass\"",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "An identifier like \"biomass\"",
+                    "name": "Biomass reaction ID"
+                }
+            ],
+            "label": "Biomass reaction ID",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 340.6434088812934,
+                "height": 75.60000610351562,
+                "left": -340.35936143663196,
+                "right": -160.35936143663196,
+                "top": 265.04340277777777,
+                "width": 180,
+                "x": -340.35936143663196,
+                "y": 265.04340277777777
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "d2ebc0df-8d14-471a-a940-f9163d309d70",
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "Dataset of rpsbml pathways",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Dataset of rpsbml pathways",
+                    "name": "Heterologous pathways"
+                }
+            ],
+            "label": "Heterologous pathways",
+            "name": "Input dataset collection",
+            "outputs": [],
+            "position": {
+                "bottom": 462.64339531792535,
+                "height": 75.60000610351562,
+                "left": -340.35936143663196,
+                "right": -160.35936143663196,
+                "top": 387.04338921440973,
+                "width": 180,
+                "x": -340.35936143663196,
+                "y": 387.04338921440973
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+            "tool_version": null,
+            "type": "data_collection_input",
+            "uuid": "396a82be-e939-4c16-95d7-cfafb0e472bd",
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "SBML model",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "SBML model",
+                    "name": "Chassis where to produce target from"
+                }
+            ],
+            "label": "Chassis where to produce target from",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 584.6434156629774,
+                "height": 75.60000610351562,
+                "left": -340.35936143663196,
+                "right": -160.35936143663196,
+                "top": 509.0434095594618,
+                "width": 180,
+                "x": -340.35936143663196,
+                "y": 509.0434095594618
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "ca69a88b-c781-4d72-ab5c-92df2afc720a",
+            "workflow_outputs": []
+        },
+        "3": {
+            "annotation": "An identifier like \"c\"",
+            "content_id": null,
+            "errors": null,
+            "id": 3,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "An identifier like \"c\"",
+                    "name": "Cell compartment ID"
+                }
+            ],
+            "label": "Cell compartment ID",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 707.7527533637152,
+                "height": 75.5999755859375,
+                "left": -340.35936143663196,
+                "right": -160.35936143663196,
+                "top": 632.1527777777777,
+                "width": 180,
+                "x": -340.35936143663196,
+                "y": 632.1527777777777
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "d92f3120-93f4-4341-aab7-7432a889fd40",
+            "workflow_outputs": []
+        },
+        "4": {
+            "annotation": "Perform FBA",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1",
+            "errors": null,
+            "id": 4,
+            "input_connections": {
+                "biomass_rxn_id": {
+                    "id": 0,
+                    "output_name": "output"
+                },
+                "compartment_id": {
+                    "id": 3,
+                    "output_name": "output"
+                },
+                "model": {
+                    "id": 2,
+                    "output_name": "output"
+                },
+                "pathway": {
+                    "id": 1,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Flux balance analysis",
+                    "name": "model"
+                },
+                {
+                    "description": "runtime parameter for tool Flux balance analysis",
+                    "name": "pathway"
+                }
+            ],
+            "label": "Flux Balance Analysis",
+            "name": "Flux balance analysis",
+            "outputs": [
+                {
+                    "name": "pathway_with_fba",
+                    "type": "sbml"
+                }
+            ],
+            "position": {
+                "bottom": 527.1434156629774,
+                "height": 188.10000610351562,
+                "left": -52.29688856336806,
+                "right": 127.703126695421,
+                "top": 339.0434095594618,
+                "width": 180.00001525878906,
+                "x": -52.29688856336806,
+                "y": 339.0434095594618
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1",
+            "tool_shed_repository": {
+                "changeset_revision": "19be43e96154",
+                "name": "rpfba",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"merge\": \"false\", \"ignore_orphan_species\": \"true\"}, \"biomass_rxn_id\": {\"__class__\": \"ConnectedValue\"}, \"compartment_id\": {\"__class__\": \"ConnectedValue\"}, \"input_sim_type\": {\"sim_type\": \"fraction\", \"__current_case__\": 0, \"fraction_of\": \"0.75\"}, \"model\": {\"__class__\": \"RuntimeValue\"}, \"objective_rxn_id\": \"rxn_target\", \"pathway\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.12.1",
+            "type": "tool",
+            "uuid": "84470349-6e9c-4810-b2c8-3d5fdae0cca4",
+            "workflow_outputs": [
+                {
+                    "label": "pathway_fba",
+                    "output_name": "pathway_with_fba",
+                    "uuid": "5691075c-3a81-427b-b12d-5df59b988edc"
+                }
+            ]
+        },
+        "5": {
+            "annotation": "Calculate the formation energy of chemical species and the Gibbs free energy of their reactions and pathways in an SBML",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1",
+            "errors": null,
+            "id": 5,
+            "input_connections": {
+                "input": {
+                    "id": 4,
+                    "output_name": "pathway_with_fba"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Thermo",
+                    "name": "input"
+                }
+            ],
+            "label": "Thermo",
+            "name": "Thermo",
+            "outputs": [
+                {
+                    "name": "pathway_with_thermo",
+                    "type": "xml"
+                }
+            ],
+            "position": {
+                "bottom": 481.54339599609375,
+                "height": 85.5,
+                "left": 225.703125,
+                "right": 405.703125,
+                "top": 396.04339599609375,
+                "width": 180,
+                "x": 225.703125,
+                "y": 396.04339599609375
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1",
+            "tool_shed_repository": {
+                "changeset_revision": "21a900eee812",
+                "name": "rpthermo",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"ph\": \"7.5\", \"ionic_strength\": \"0.25\", \"pMg\": \"3.0\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.12.1",
+            "type": "tool",
+            "uuid": "7b32553d-b992-4a54-a863-815f9b946581",
+            "workflow_outputs": [
+                {
+                    "label": "pathay_thermo",
+                    "output_name": "pathway_with_thermo",
+                    "uuid": "bbb6a168-236b-4e28-a1c4-18dbb8538eb0"
+                }
+            ]
+        },
+        "6": {
+            "annotation": "Computes a global score for a heterologous pathway.",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1",
+            "errors": null,
+            "id": 6,
+            "input_connections": {
+                "pathway": {
+                    "id": 5,
+                    "output_name": "pathway_with_thermo"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Score Pathway",
+                    "name": "pathway"
+                }
+            ],
+            "label": "Score Pathway",
+            "name": "Score Pathway",
+            "outputs": [
+                {
+                    "name": "scored_pathway",
+                    "type": "xml"
+                }
+            ],
+            "position": {
+                "bottom": 491.54339599609375,
+                "height": 85.5,
+                "left": 503.70313856336804,
+                "right": 683.703138563368,
+                "top": 406.04339599609375,
+                "width": 180,
+                "x": 503.70313856336804,
+                "y": 406.04339599609375
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1",
+            "tool_shed_repository": {
+                "changeset_revision": "da8ae7fa5ed3",
+                "name": "rpscore",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"no_of_rxns_thres\": \"10\"}, \"pathway\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.12.1",
+            "type": "tool",
+            "uuid": "6b680491-6b40-4f44-943e-9026a9264b54",
+            "workflow_outputs": [
+                {
+                    "label": "pathway_score",
+                    "output_name": "scored_pathway",
+                    "uuid": "87b486d0-6923-47d8-9d4f-0afcacbaca95"
+                }
+            ]
+        },
+        "7": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1",
+            "errors": null,
+            "id": 7,
+            "input_connections": {
+                "pathway_collection": {
+                    "id": 6,
+                    "output_name": "scored_pathway"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Rank Pathways",
+            "outputs": [
+                {
+                    "name": "sorted_pathways",
+                    "type": "csv"
+                }
+            ],
+            "position": {
+                "bottom": 510.54340277777777,
+                "height": 85.5,
+                "left": 781.7031521267361,
+                "right": 961.7031521267361,
+                "top": 425.04340277777777,
+                "width": 180,
+                "x": 781.7031521267361,
+                "y": 425.04340277777777
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1",
+            "tool_shed_repository": {
+                "changeset_revision": "bab690866445",
+                "name": "rpranker",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"pathway_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.12.1",
+            "type": "tool",
+            "uuid": "39986296-e23e-4af7-ac3d-e84de3cb1b4c",
+            "workflow_outputs": [
+                {
+                    "label": "Ranked Pathways",
+                    "output_name": "sorted_pathways",
+                    "uuid": "561c935b-6ccb-4aa6-9b23-31f374acec9e"
+                }
+            ]
+        }
+    },
+    "tags": [
+        "brs",
+        "retrosynthesis"
+    ],
+    "uuid": "f1011985-7282-45df-8326-b91a873fcd00",
+    "version": 10
+}
\ No newline at end of file
diff --git a/workflows/pathway_analysis_workflow/test-data/ranked_pathways.csv b/workflows/pathway_analysis_workflow/test-data/ranked_pathways.csv
new file mode 100644
index 00000000..151bac2d
--- /dev/null
+++ b/workflows/pathway_analysis_workflow/test-data/ranked_pathways.csv
@@ -0,0 +1,10 @@
+#Name,Score
+002_0011,0.9894743263721466
+001_0011,0.989453911781311
+002_0006,0.9892315685749054
+001_0006,0.9890591621398924
+003_0231,0.9878535568714142
+003_0116,0.9863117098808288
+003_0001,0.975385755300522
+002_0001,0.9752638757228852
+001_0001,0.975147980451584

From 023843343989a124130115957ccdb2b279a72996 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Fri, 9 Jun 2023 16:25:21 +0200
Subject: [PATCH 19/61] feat(workflows): add `retrosynthesis` (#129)

---
 .github/workflows/test_workflows_skip.txt     |   1 +
 .../retrosynthesis_workflow-tests.yml         |  44 ++
 .../retrosynthesis_workflow.ga                | 378 ++++++++++++++++++
 3 files changed, 423 insertions(+)
 create mode 100644 workflows/retrosynthesis_workflow/retrosynthesis_workflow-tests.yml
 create mode 100644 workflows/retrosynthesis_workflow/retrosynthesis_workflow.ga

diff --git a/.github/workflows/test_workflows_skip.txt b/.github/workflows/test_workflows_skip.txt
index e69de29b..59da3239 100644
--- a/.github/workflows/test_workflows_skip.txt
+++ b/.github/workflows/test_workflows_skip.txt
@@ -0,0 +1 @@
+retrosynthesis_workflow
diff --git a/workflows/retrosynthesis_workflow/retrosynthesis_workflow-tests.yml b/workflows/retrosynthesis_workflow/retrosynthesis_workflow-tests.yml
new file mode 100644
index 00000000..c6bbab9d
--- /dev/null
+++ b/workflows/retrosynthesis_workflow/retrosynthesis_workflow-tests.yml
@@ -0,0 +1,44 @@
+- doc: Retrosynthesis
+  job:
+    Target to produce: 'InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3/b12-11+,25-15+,26-16+,31-17+,32-18+,35-21+,36-22+,37-27+,38-28+,39-29+,40-30+'
+  outputs:
+    rpCompletion:
+      class: Collection
+      collection_type: list
+      elements:
+        - identifier: rp_001_0001.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_001_0001.xml
+          compare: sim_size
+        - identifier: rp_001_0006.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_001_0006.xml
+          compare: sim_size
+        - identifier: rp_001_0011.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_001_0011.xml
+          compare: sim_size
+        - identifier: rp_002_0001.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_002_0001.xml
+          compare: sim_size
+        - identifier: rp_002_0006.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_002_0006.xml
+          compare: sim_size
+        - identifier: rp_002_0011.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_002_0011.xml
+          compare: sim_size
+        - identifier: rp_003_0001.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_003_0001.xml
+          compare: sim_size
+        - identifier: rp_003_0116.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_003_0116.xml
+          compare: sim_size
+        - identifier: rp_003_0231.xml
+          class: File
+          location: https://zenodo.org/api/files/5db78fa1-b8cb-4046-b57c-8a9d00806f42/rp_003_0231.xml
+          compare: sim_size
diff --git a/workflows/retrosynthesis_workflow/retrosynthesis_workflow.ga b/workflows/retrosynthesis_workflow/retrosynthesis_workflow.ga
new file mode 100644
index 00000000..9fd6009f
--- /dev/null
+++ b/workflows/retrosynthesis_workflow/retrosynthesis_workflow.ga
@@ -0,0 +1,378 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools",
+    "creator": [
+        {
+            "class": "Organization",
+            "name": "BioRetroSynth",
+            "url": "https://github.com/brsynth"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "name": "RetroSynthesis",
+    "steps": {
+        "0": {
+            "annotation": "The International Chemical Identifier (InChI) of the compound of interest to produce",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "The International Chemical Identifier (InChI) of the compound of interest to produce",
+                    "name": "Target to produce"
+                }
+            ],
+            "label": "Target to produce",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 718.09375,
+                "height": 84,
+                "left": 359.375,
+                "right": 559.375,
+                "top": 634.09375,
+                "width": 200,
+                "x": 359.375,
+                "y": 634.09375
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "832d6ff4-18ac-4728-a776-277ba25b6b74",
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "Pick a SBML model",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/get_sbml_model/get_sbml_model/0.0.1",
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Pick SBML Model",
+                    "name": "SBML model"
+                }
+            ],
+            "label": "SBML model",
+            "name": "Pick SBML Model",
+            "outputs": [
+                {
+                    "name": "sbml_model",
+                    "type": "xml"
+                }
+            ],
+            "position": {
+                "bottom": 808.59375,
+                "height": 84,
+                "left": 356,
+                "right": 556,
+                "top": 724.59375,
+                "width": 200,
+                "x": 356,
+                "y": 724.59375
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/get_sbml_model/get_sbml_model/0.0.1",
+            "tool_shed_repository": {
+                "changeset_revision": "4797d0b36ff3",
+                "name": "get_sbml_model",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.0.1",
+            "type": "tool",
+            "uuid": "bb68ae97-ef17-41c3-8e99-d62a6a4508ee",
+            "workflow_outputs": [
+                {
+                    "label": "Pick SBML Model - iML1515",
+                    "output_name": "sbml_model",
+                    "uuid": "a1ea773f-4da4-4154-a9c5-403c3eb24789"
+                }
+            ]
+        },
+        "2": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6",
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [],
+            "label": null,
+            "name": "RRules Parser",
+            "outputs": [
+                {
+                    "name": "out_rules",
+                    "type": "csv"
+                }
+            ],
+            "position": {
+                "bottom": 936.375,
+                "height": 105,
+                "left": 601,
+                "right": 801,
+                "top": 831.375,
+                "width": 200,
+                "x": 601,
+                "y": 831.375
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6",
+            "tool_shed_repository": {
+                "changeset_revision": "ea590c609fec",
+                "name": "rrparser",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"compress\": \"false\", \"diameters\": [\"2\", \"4\", \"6\", \"8\", \"10\", \"12\", \"14\", \"16\"], \"rules\": {\"type\": \"retro\", \"__current_case__\": 2}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.4.6",
+            "type": "tool",
+            "uuid": "5bcc6c73-b4cf-45fc-96f6-9e3cbf31832e",
+            "workflow_outputs": [
+                {
+                    "label": "RRules Parser(retro, d=['2', '4', '6', '8', '10', '12', '14', '16'])",
+                    "output_name": "out_rules",
+                    "uuid": "cbbe5eb3-a09b-43f0-a680-6fbdfae47f27"
+                }
+            ]
+        },
+        "3": {
+            "annotation": "The sinks expected to be bound in a chassis",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "input": {
+                    "id": 1,
+                    "output_name": "sbml_model"
+                }
+            },
+            "inputs": [],
+            "label": "Sink from SBML",
+            "name": "Sink from SBML",
+            "outputs": [
+                {
+                    "name": "sink",
+                    "type": "csv"
+                }
+            ],
+            "position": {
+                "bottom": 804.578125,
+                "height": 95,
+                "left": 604,
+                "right": 804,
+                "top": 709.578125,
+                "width": 200,
+                "x": 604,
+                "y": 709.578125
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1",
+            "tool_shed_repository": {
+                "changeset_revision": "47bb93e7832b",
+                "name": "rpextractsink",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"remove_dead_end\": \"true\"}, \"compartment_id\": \"c\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.12.1",
+            "type": "tool",
+            "uuid": "4dd55661-fbf3-484a-8df4-f884973e06cf",
+            "workflow_outputs": [
+                {
+                    "label": "sink",
+                    "output_name": "sink",
+                    "uuid": "538da761-7ef7-4f12-bbfa-b09f02450835"
+                }
+            ]
+        },
+        "4": {
+            "annotation": "Run Retropath2.0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0",
+            "errors": null,
+            "id": 4,
+            "input_connections": {
+                "rulesfile": {
+                    "id": 2,
+                    "output_name": "out_rules"
+                },
+                "sinkfile": {
+                    "id": 3,
+                    "output_name": "sink"
+                },
+                "source_inchi_type|source_inchi": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": "Retropath2.0",
+            "name": "RetroPath2.0",
+            "outputs": [
+                {
+                    "name": "Reaction_Network",
+                    "type": "csv"
+                }
+            ],
+            "position": {
+                "bottom": 751.578125,
+                "height": 157,
+                "left": 847,
+                "right": 1047,
+                "top": 594.578125,
+                "width": 200,
+                "x": 847,
+                "y": 594.578125
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0",
+            "tool_shed_repository": {
+                "changeset_revision": "9c8ac9980bd6",
+                "name": "retropath2",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"version\": \"r20220104\", \"topx\": \"100\", \"dmin\": \"0\", \"dmax\": \"1000\", \"mwmax_source\": \"1000\", \"timeout\": \"60\"}, \"max_steps\": \"3\", \"rulesfile\": {\"__class__\": \"ConnectedValue\"}, \"sinkfile\": {\"__class__\": \"ConnectedValue\"}, \"source_inchi_type\": {\"inchi_type\": \"string\", \"__current_case__\": 0, \"source_inchi\": {\"__class__\": \"ConnectedValue\"}}, \"source_name\": \"target\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.3.0",
+            "type": "tool",
+            "uuid": "61f75528-3c9f-412b-b5ed-ecde3d5f3533",
+            "workflow_outputs": [
+                {
+                    "label": "Retropath2.0",
+                    "output_name": "Reaction_Network",
+                    "uuid": "8e3eb073-046b-41a1-a3ad-15d6fa3dae85"
+                }
+            ]
+        },
+        "5": {
+            "annotation": "Enumerate pathways",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.5.0",
+            "errors": null,
+            "id": 5,
+            "input_connections": {
+                "rp2_pathways": {
+                    "id": 4,
+                    "output_name": "Reaction_Network"
+                }
+            },
+            "inputs": [],
+            "label": "RP2paths",
+            "name": "RP2paths",
+            "outputs": [
+                {
+                    "name": "master_pathways",
+                    "type": "csv"
+                },
+                {
+                    "name": "compounds",
+                    "type": "tsv"
+                }
+            ],
+            "position": {
+                "bottom": 679,
+                "height": 168,
+                "left": 1101.296875,
+                "right": 1301.296875,
+                "top": 511,
+                "width": 200,
+                "x": 1101.296875,
+                "y": 511
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.5.0",
+            "tool_shed_repository": {
+                "changeset_revision": "e3db7fb2c85e",
+                "name": "rp2paths",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"timeout\": \"1800\"}, \"rp2_pathways\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.5.0",
+            "type": "tool",
+            "uuid": "dbb47e06-b8c4-4ba3-9385-8a84ca952c7f",
+            "workflow_outputs": [
+                {
+                    "label": "RP2paths (pathways)",
+                    "output_name": "master_pathways",
+                    "uuid": "5c89b9e1-cdde-4672-b14a-a62dc07b726b"
+                },
+                {
+                    "label": "RP2paths (compounds)",
+                    "output_name": "compounds",
+                    "uuid": "5662c480-168b-4841-96d7-14fe138720a4"
+                }
+            ]
+        },
+        "6": {
+            "annotation": "SBML file compiling output from rp2paths, sink, retropath2.0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.2",
+            "errors": null,
+            "id": 6,
+            "input_connections": {
+                "rp2_pathways": {
+                    "id": 4,
+                    "output_name": "Reaction_Network"
+                },
+                "rp2paths_compounds": {
+                    "id": 5,
+                    "output_name": "compounds"
+                },
+                "rp2paths_pathways": {
+                    "id": 5,
+                    "output_name": "master_pathways"
+                },
+                "sink": {
+                    "id": 3,
+                    "output_name": "sink"
+                }
+            },
+            "inputs": [],
+            "label": "Complete Reactions",
+            "name": "Complete Reactions",
+            "outputs": [
+                {
+                    "name": "pathways",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "bottom": 846.5,
+                "height": 230,
+                "left": 1375.5,
+                "right": 1575.5,
+                "top": 616.5,
+                "width": 200,
+                "x": 1375.5,
+                "y": 616.5
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.2",
+            "tool_shed_repository": {
+                "changeset_revision": "d5c53a916005",
+                "name": "rpcompletion",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"max_subpaths_filter\": \"10\", \"upper_flux_bound\": \"999999\", \"lower_flux_bound\": \"0\"}, \"rp2_pathways\": {\"__class__\": \"ConnectedValue\"}, \"rp2paths_compounds\": {\"__class__\": \"ConnectedValue\"}, \"rp2paths_pathways\": {\"__class__\": \"ConnectedValue\"}, \"sink\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.12.2",
+            "type": "tool",
+            "uuid": "4f7eded9-10da-4459-9345-f8058fc94905",
+            "workflow_outputs": [
+                {
+                    "label": "rpCompletion",
+                    "output_name": "pathways",
+                    "uuid": "ce8df96b-0296-4736-b183-33500eb2533c"
+                }
+            ]
+        }
+    },
+    "tags": [
+        "brs",
+        "retrosynthesis"
+    ],
+    "uuid": "06357c34-cf77-4251-9fab-09fafd6ce21a",
+    "version": 14
+}

From a28bed08736e066fe805d55e2917054cc14e2106 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Mon, 12 Jun 2023 13:04:33 +0200
Subject: [PATCH 20/61] rp2biosensor: syntax (#130)

* fix(rp2biosensor): add attribute to test tag
---
 tools/rp2biosensor/rp2biosensor.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/rp2biosensor/rp2biosensor.xml b/tools/rp2biosensor/rp2biosensor.xml
index e17f73b0..8b05c689 100644
--- a/tools/rp2biosensor/rp2biosensor.xml
+++ b/tools/rp2biosensor/rp2biosensor.xml
@@ -25,13 +25,13 @@
         </section>
     </inputs>
     <outputs>
-        <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/>
-        <data name="json_file" format="json" label="${tool.name} -${rp2_results.name}">
+        <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name} (html)"/>
+        <data name="json_file" format="json" label="${tool.name} - ${rp2_results.name} (json)">
             <filter> adv['json_graph'] </filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 1: check if identical outputs are produced -->
             <param name="rp2_results" value="rp2-results-lactate.csv" />
             <param name="sink_file" value="sink-h2o2.csv" />

From 5a51e961c57d475d474b6872d63eb0f2c9fa9684 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Mon, 12 Jun 2023 14:00:31 +0200
Subject: [PATCH 21/61] feat(workflows): add `biosensor` (#131)

---
 .../biosensor_workflow-tests.yml              |    7 +
 .../biosensor_workflow/biosensor_workflow.ga  |  440 +++++++
 .../test-data/biosensor.html                  | 1105 +++++++++++++++++
 3 files changed, 1552 insertions(+)
 create mode 100644 workflows/biosensor_workflow/biosensor_workflow-tests.yml
 create mode 100644 workflows/biosensor_workflow/biosensor_workflow.ga
 create mode 100644 workflows/biosensor_workflow/test-data/biosensor.html

diff --git a/workflows/biosensor_workflow/biosensor_workflow-tests.yml b/workflows/biosensor_workflow/biosensor_workflow-tests.yml
new file mode 100644
index 00000000..179d0bfc
--- /dev/null
+++ b/workflows/biosensor_workflow/biosensor_workflow-tests.yml
@@ -0,0 +1,7 @@
+- doc: Biosensor
+  job:
+    Compound InChI: 'InChI=1S/C3H6O3/c1-2(4)3(5)6/h2,4H,1H3,(H,5,6)/p-1/t2-/m0/s1'
+  outputs:
+    biosensor:
+      path: test-data/biosensor.html
+      compare: sim_size
diff --git a/workflows/biosensor_workflow/biosensor_workflow.ga b/workflows/biosensor_workflow/biosensor_workflow.ga
new file mode 100644
index 00000000..87358713
--- /dev/null
+++ b/workflows/biosensor_workflow/biosensor_workflow.ga
@@ -0,0 +1,440 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Predicts metabolic reactions connecting any query metabolite to a given biosensor.",
+    "creator": [
+        {
+            "class": "Organization",
+            "name": "BioRetroSynth",
+            "url": "https://github.com/brsynth"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "name": "BioSensor",
+    "steps": {
+        "0": {
+            "annotation": "Name of the biosensor",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Name of the biosensor",
+                    "name": "BioSensor name"
+                }
+            ],
+            "label": "BioSensor name",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 349,
+                "height": 63,
+                "left": -48.5,
+                "right": 151.5,
+                "top": 286,
+                "width": 200,
+                "x": -48.5,
+                "y": 286
+            },
+            "tool_id": null,
+            "tool_state": "{\"default\": \"H2O2\", \"parameter_type\": \"text\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "6c743f9a-f4d5-44ad-9b18-41c631b89c26",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "baf1d70e-3f00-4ed3-ba3e-4a5e8c087bf8"
+                }
+            ]
+        },
+        "1": {
+            "annotation": "InChI of the biosensor. Default: InChI of H2O2.",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "InChI of the biosensor. Default: InChI of H2O2.",
+                    "name": "BioSensor InChI"
+                }
+            ],
+            "label": "BioSensor InChI",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 439,
+                "height": 63,
+                "left": -47.5,
+                "right": 152.5,
+                "top": 376,
+                "width": 200,
+                "x": -47.5,
+                "y": 376
+            },
+            "tool_id": null,
+            "tool_state": "{\"default\": \"InChI=1S/H2O2/c1-2/h1-2H\", \"parameter_type\": \"text\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "5dc9e2bb-09e4-4cd1-8931-4b40fef15f5d",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "64ed0ece-c8b9-4ad3-ae4f-caa41cd839c2"
+                }
+            ]
+        },
+        "2": {
+            "annotation": "Name of the compound to detect",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Name of the compound to detect",
+                    "name": "Compound name"
+                }
+            ],
+            "label": "Compound name",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 577,
+                "height": 84,
+                "left": -45.5,
+                "right": 154.5,
+                "top": 493,
+                "width": 200,
+                "x": -45.5,
+                "y": 493
+            },
+            "tool_id": null,
+            "tool_state": "{\"default\": \"Target\", \"parameter_type\": \"text\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "398b9893-c88b-4690-bb83-c3e8c064d595",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "310a24d5-1d0a-4851-a9b4-c24ddd6feb78"
+                }
+            ]
+        },
+        "3": {
+            "annotation": "InChI of the compound to detect",
+            "content_id": null,
+            "errors": null,
+            "id": 3,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "InChI of the compound to detect",
+                    "name": "Compound InChI"
+                }
+            ],
+            "label": "Compound InChI",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 666,
+                "height": 63,
+                "left": -42.5,
+                "right": 157.5,
+                "top": 603,
+                "width": 200,
+                "x": -42.5,
+                "y": 603
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "c4987b08-dd9c-465d-858f-b3caeb4ee748",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "00a3c0ad-8253-427c-86e7-3c250c3fe431"
+                }
+            ]
+        },
+        "4": {
+            "annotation": "InChI of the biosensor",
+            "content_id": null,
+            "errors": null,
+            "id": 4,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "InChI of the biosensor",
+                    "name": "Number of steps"
+                }
+            ],
+            "label": "Number of steps",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 762,
+                "height": 63,
+                "left": -40.5,
+                "right": 159.5,
+                "top": 699,
+                "width": 200,
+                "x": -40.5,
+                "y": 699
+            },
+            "tool_id": null,
+            "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "649e1211-0c09-4195-a3ec-e38f45355925",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "af169980-4524-43d4-a32f-b945f87860d7"
+                }
+            ]
+        },
+        "5": {
+            "annotation": "Extract reaction rules from RetroRules.",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6",
+            "errors": null,
+            "id": 5,
+            "input_connections": {},
+            "inputs": [],
+            "label": "rrparser",
+            "name": "RRules Parser",
+            "outputs": [
+                {
+                    "name": "out_rules",
+                    "type": "csv"
+                }
+            ],
+            "position": {
+                "bottom": 920,
+                "height": 105,
+                "left": 265.5,
+                "right": 465.5,
+                "top": 815,
+                "width": 200,
+                "x": 265.5,
+                "y": 815
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6",
+            "tool_shed_repository": {
+                "changeset_revision": "ea590c609fec",
+                "name": "rrparser",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"compress\": \"false\", \"diameters\": [\"2\", \"4\", \"6\", \"8\", \"10\", \"12\"], \"rules\": {\"type\": \"all\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.4.6",
+            "type": "tool",
+            "uuid": "2b726baf-728a-465c-ba23-9acac5b67bae",
+            "workflow_outputs": [
+                {
+                    "label": "RRules Parser(retro, d=['2', '4', '6', '8', '10', '12', '14', '16'])",
+                    "output_name": "out_rules",
+                    "uuid": "2c9da489-ff1d-4523-9227-4bb6e81a4b17"
+                }
+            ]
+        },
+        "6": {
+            "annotation": "Convert sink information into a RetroPath2.0-ready sink file",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/inchi_to_sink/inchi_to_sink/1.0.0",
+            "errors": null,
+            "id": 6,
+            "input_connections": {
+                "source_inchi": {
+                    "id": 1,
+                    "output_name": "output"
+                },
+                "source_name": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": "inchi to sink",
+            "name": "Inchi to sink",
+            "outputs": [
+                {
+                    "name": "sink",
+                    "type": "csv"
+                }
+            ],
+            "position": {
+                "bottom": 523,
+                "height": 147,
+                "left": 256.5,
+                "right": 456.5,
+                "top": 376,
+                "width": 200,
+                "x": 256.5,
+                "y": 376
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/inchi_to_sink/inchi_to_sink/1.0.0",
+            "tool_shed_repository": {
+                "changeset_revision": "3627d3e49889",
+                "name": "inchi_to_sink",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"source_inchi\": {\"__class__\": \"ConnectedValue\"}, \"source_name\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.0.0",
+            "type": "tool",
+            "uuid": "d5d107ee-b25a-41d8-ab23-d1dda2106288",
+            "workflow_outputs": [
+                {
+                    "label": "Inchi to sink - Biosensor",
+                    "output_name": "sink",
+                    "uuid": "b72ea03a-4c0d-41b9-b74b-6655ce70cbef"
+                }
+            ]
+        },
+        "7": {
+            "annotation": "",
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+                    "uuid": "f4279ed9-48e8-44a1-a76f-b2db9fd0836f"
+                }
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+    "tags": [
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+        "biosensor"
+    ],
+    "uuid": "b8d05692-eccc-4288-b1e4-33399b403876",
+    "version": 2
+}
diff --git a/workflows/biosensor_workflow/test-data/biosensor.html b/workflows/biosensor_workflow/test-data/biosensor.html
new file mode 100644
index 00000000..cf79a99e
--- /dev/null
+++ b/workflows/biosensor_workflow/test-data/biosensor.html
@@ -0,0 +1,1105 @@
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+/*!
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+  Copyright (c) 2013-2014 Ralf S. Engelschall (http://engelschall.com)
+  Licensed under The MIT License (http://opensource.org/licenses/MIT)
+  */
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+/*! Bezier curve function generator. Copyright Gaetan Renaudeau. MIT License: http://en.wikipedia.org/wiki/MIT_License */
+/*! Runge-Kutta spring physics function generator. Adapted from Framer.js, copyright Koen Bok. MIT License: http://en.wikipedia.org/wiki/MIT_License */
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t=Qa(e),r=t.depth,i=t.index,a=x[r].length,o=Math.max(u.w/((n.grid?U:a)+1),L),s=Math.max(u.h/(x.length+1),L),l=Math.min(u.w/2/x.length,u.h/2/x.length);if(l=Math.max(l,L),n.circle){var c=l*r+l-(x.length>0&&x[0].length<=3?l/2:0),d=2*Math.PI/x[r].length*i;return 0===r&&1===x[0].length&&(c=1),{x:G+c*Math.cos(d),y:Z+c*Math.sin(d)}}return{x:G+(i+1-(a+1)/2)*o,y:(r+1)*s}})),this};var to={fit:!0,padding:30,boundingBox:void 0,avoidOverlap:!0,nodeDimensionsIncludeLabels:!1,spacingFactor:void 0,radius:void 0,startAngle:1.5*Math.PI,sweep:void 0,clockwise:!0,sort:void 0,animate:!1,animationDuration:500,animationEasing:void 0,animateFilter:function(e,t){return!0},ready:void 0,stop:void 0,transform:function(e,t){return t}};function no(e){this.options=I({},to,e)}no.prototype.run=function(){var e=this.options,t=e,n=e.cy,r=t.eles,i=void 0!==t.counterclockwise?!t.counterclockwise:t.clockwise,a=r.nodes().not(":parent");t.sort&&(a=a.sort(t.sort));for(var o,s=ht(t.boundingBox?t.boundingBox:{x1:0,y1:0,w:n.width(),h:n.height()}),l=s.x1+s.w/2,u=s.y1+s.h/2,c=(void 0===t.sweep?2*Math.PI-2*Math.PI/a.length:t.sweep)/Math.max(1,a.length-1),d=0,h=0;h<a.length;h++){var p=a[h].layoutDimensions(t),f=p.w,g=p.h;d=Math.max(d,f,g)}if(o=y(t.radius)?t.radius:a.length<=1?0:Math.min(s.h,s.w)/2-d,a.length>1&&t.avoidOverlap){d*=1.75;var v=Math.cos(c)-Math.cos(0),m=Math.sin(c)-Math.sin(0),b=Math.sqrt(d*d/(v*v+m*m));o=Math.max(b,o)}return r.nodes().layoutPositions(this,t,(function(e,n){var r=t.startAngle+n*c*(i?1:-1),a=o*Math.cos(r),s=o*Math.sin(r);return{x:l+a,y:u+s}})),this};var ro,io={fit:!0,padding:30,startAngle:1.5*Math.PI,sweep:void 0,clockwise:!0,equidistant:!1,minNodeSpacing:10,boundingBox:void 0,avoidOverlap:!0,nodeDimensionsIncludeLabels:!1,height:void 0,width:void 0,spacingFactor:void 0,concentric:function(e){return e.degree()},levelWidth:function(e){return e.maxDegree()/4},animate:!1,animationDuration:500,animationEasing:void 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d=(y=i[l]).layoutDimensions(n);(I={}).isLocked=y.locked(),I.id=y.data("id"),I.parentId=y.data("parent"),I.cmptId=s[y.id()],I.children=[],I.positionX=y.position("x"),I.positionY=y.position("y"),I.offsetX=0,I.offsetY=0,I.height=d.w,I.width=d.h,I.maxX=I.positionX+I.width/2,I.minX=I.positionX-I.width/2,I.maxY=I.positionY+I.height/2,I.minY=I.positionY-I.height/2,I.padLeft=parseFloat(y.style("padding")),I.padRight=parseFloat(y.style("padding")),I.padTop=parseFloat(y.style("padding")),I.padBottom=parseFloat(y.style("padding")),I.nodeRepulsion=f(n.nodeRepulsion)?n.nodeRepulsion(y):n.nodeRepulsion,a.layoutNodes.push(I),a.idToIndex[I.id]=l}var h=[],p=0,g=-1,v=[];for(l=0;l<a.nodeSize;l++){var y,m=(y=a.layoutNodes[l]).parentId;null!=m?a.layoutNodes[a.idToIndex[m]].children.push(y.id):(h[++g]=y.id,v.push(y.id))}for(a.graphSet.push(v);p<=g;){var 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S,P;C=(S=f.length/2-1)+2;x=ut(f[P=S-2],f[S],f[C],.4999),w=ut(f[P+1],f[S+1],f[C+1],.4999),E=ut(f[P],f[S],f[C],.5),k=ut(f[P+1],f[S+1],f[C+1],.5)}t=E-x,n=k-w}(s.midtgtArrowAngle=rt(t,n),s.midDispX=t,s.midDispY=n,t*=-1,n*=-1,d)&&((f=s.allpts).length/2%2==0||(t=-(f[b=(m=f.length/2-1)+2]-f[m]),n=-(f[b+1]-f[m+1])));if(s.midsrcArrowAngle=rt(t,n),d)t=a-s.segpts[s.segpts.length-2],n=o-s.segpts[s.segpts.length-1];else if(c||h||p||u){var D=(f=s.allpts).length;t=a-ut(f[D-6],f[D-4],f[D-2],.9),n=o-ut(f[D-5],f[D-3],f[D-1],.9)}else t=a-g,n=o-v;s.tgtArrowAngle=rt(t,n)}};jo.getArrowWidth=jo.getArrowHeight=function(e,t){var n=this.arrowWidthCache=this.arrowWidthCache||{},r=n[e+", "+t];return r||(r=Math.max(Math.pow(13.37*e,.9),29)*t,n[e+", "+t]=r,r)};var Yo={};function Xo(e){var t=[];if(null!=e){for(var n=0;n<e.length;n+=2){var r=e[n],i=e[n+1];t.push({x:r,y:i})}return t}}Yo.findHaystackPoints=function(e){for(var t=0;t<e.length;t++){var n=e[t],r=n._private,i=r.rscratch;if(!i.haystack){var a=2*Math.random()*Math.PI;i.source={x:Math.cos(a),y:Math.sin(a)},a=2*Math.random()*Math.PI,i.target={x:Math.cos(a),y:Math.sin(a)}}var o=r.source,s=r.target,l=o.position(),u=s.position(),c=o.width(),d=s.width(),h=o.height(),p=s.height(),f=n.pstyle("haystack-radius").value/2;i.haystackPts=i.allpts=[i.source.x*c*f+l.x,i.source.y*h*f+l.y,i.target.x*d*f+u.x,i.target.y*p*f+u.y],i.midX=(i.allpts[0]+i.allpts[2])/2,i.midY=(i.allpts[1]+i.allpts[3])/2,i.edgeType="haystack",i.haystack=!0,this.storeEdgeProjections(n),this.calculateArrowAngles(n),this.recalculateEdgeLabelProjections(n),this.calculateLabelAngles(n)}},Yo.findSegmentsPoints=function(e,t){var n=e._private.rscratch,r=t.posPts,i=t.intersectionPts,a=t.vectorNormInverse,o=e.pstyle("edge-distances").value,s=e.pstyle("segment-weights"),l=e.pstyle("segment-distances"),u=Math.min(s.pfValue.length,l.pfValue.length);n.edgeType="segments",n.segpts=[];for(var c=0;c<u;c++){var d=s.pfValue[c],h=l.pfValue[c],p=1-d,f=d,g="node-position"===o?r:i,v={x:g.x1*p+g.x2*f,y:g.y1*p+g.y2*f};n.segpts.push(v.x+a.x*h,v.y+a.y*h)}},Yo.findLoopPoints=function(e,t,n,r){var i=e._private.rscratch,a=t.dirCounts,o=t.srcPos,s=e.pstyle("control-point-distances"),l=s?s.pfValue[0]:void 0,u=e.pstyle("loop-direction").pfValue,c=e.pstyle("loop-sweep").pfValue,d=e.pstyle("control-point-step-size").pfValue;i.edgeType="self";var h=n,p=d;r&&(h=0,p=l);var f=u-Math.PI/2,g=f-c/2,v=f+c/2,y=String(u+"_"+c);h=void 0===a[y]?a[y]=0:++a[y],i.ctrlpts=[o.x+1.4*Math.cos(g)*p*(h/3+1),o.y+1.4*Math.sin(g)*p*(h/3+1),o.x+1.4*Math.cos(v)*p*(h/3+1),o.y+1.4*Math.sin(v)*p*(h/3+1)]},Yo.findCompoundLoopPoints=function(e,t,n,r){var i=e._private.rscratch;i.edgeType="compound";var a=t.srcPos,o=t.tgtPos,s=t.srcW,l=t.srcH,u=t.tgtW,c=t.tgtH,d=e.pstyle("control-point-step-size").pfValue,h=e.pstyle("control-point-distances"),p=h?h.pfValue[0]:void 0,f=n,g=d;r&&(f=0,g=p);var v={x:a.x-s/2,y:a.y-l/2},y={x:o.x-u/2,y:o.y-c/2},m={x:Math.min(v.x,y.x),y:Math.min(v.y,y.y)},b=Math.max(.5,Math.log(.01*s)),x=Math.max(.5,Math.log(.01*u));i.ctrlpts=[m.x,m.y-(1+Math.pow(50,1.12)/100)*g*(f/3+1)*b,m.x-(1+Math.pow(50,1.12)/100)*g*(f/3+1)*x,m.y]},Yo.findStraightEdgePoints=function(e){e._private.rscratch.edgeType="straight"},Yo.findBezierPoints=function(e,t,n,r,i){var a=e._private.rscratch,o=t.vectorNormInverse,s=t.posPts,l=t.intersectionPts,u=e.pstyle("edge-distances").value,c=e.pstyle("control-point-step-size").pfValue,d=e.pstyle("control-point-distances"),h=e.pstyle("control-point-weights"),p=d&&h?Math.min(d.value.length,h.value.length):1,f=d?d.pfValue[0]:void 0,g=h.value[0],v=r;a.edgeType=v?"multibezier":"bezier",a.ctrlpts=[];for(var y=0;y<p;y++){var m=(.5-t.eles.length/2+n)*c*(i?-1:1),b=void 0,x=at(m);v&&(f=d?d.pfValue[y]:c,g=h.value[y]);var w=void 0!==(b=r?f:void 0!==f?x*f:void 0)?b:m,E=1-g,k=g,C="node-position"===u?s:l,S={x:C.x1*E+C.x2*k,y:C.y1*E+C.y2*k};a.ctrlpts.push(S.x+o.x*w,S.y+o.y*w)}},Yo.findTaxiPoints=function(e,t){var n=e._private.rscratch;n.edgeType="segments";var r=t.posPts,i=t.srcW,a=t.srcH,o=t.tgtW,s=t.tgtH,l="node-position"!==e.pstyle("edge-distances").value,u=e.pstyle("taxi-direction").value,c=u,d=e.pstyle("taxi-turn"),h="%"===d.units,p=d.pfValue,f=p<0,g=e.pstyle("taxi-turn-min-distance").pfValue,v=l?(i+o)/2:0,y=l?(a+s)/2:0,m=r.x2-r.x1,b=r.y2-r.y1,x=function(e,t){return e>0?Math.max(e-t,0):Math.min(e+t,0)},w=x(m,v),E=x(b,y),k=!1;"auto"===c?u=Math.abs(w)>Math.abs(E)?"horizontal":"vertical":"upward"===c||"downward"===c?(u="vertical",k=!0):"leftward"!==c&&"rightward"!==c||(u="horizontal",k=!0);var C,S="vertical"===u,P=S?E:w,D=S?b:m,T=at(D),M=!1;(k&&(h||f)||!("downward"===c&&D<0||"upward"===c&&D>0||"leftward"===c&&D>0||"rightward"===c&&D<0)||(P=(T*=-1)*Math.abs(P),M=!0),h)?C=(p<0?1+p:p)*P:C=(p<0?P:0)+p*T;var B=function(e){return Math.abs(e)<g||Math.abs(e)>=Math.abs(P)},_=B(C),N=B(Math.abs(P)-Math.abs(C));if((_||N)&&!M)if(S){var I=Math.abs(D)<=a/2,z=Math.abs(m)<=o/2;if(I){var L=(r.x1+r.x2)/2,A=r.y1,O=r.y2;n.segpts=[L,A,L,O]}else if(z){var R=(r.y1+r.y2)/2,V=r.x1,F=r.x2;n.segpts=[V,R,F,R]}else n.segpts=[r.x1,r.y2]}else{var q=Math.abs(D)<=i/2,j=Math.abs(b)<=s/2;if(q){var Y=(r.y1+r.y2)/2,X=r.x1,W=r.x2;n.segpts=[X,Y,W,Y]}else if(j){var H=(r.x1+r.x2)/2,K=r.y1,G=r.y2;n.segpts=[H,K,H,G]}else n.segpts=[r.x2,r.y1]}else if(S){var Z=r.y1+C+(l?a/2*T:0),U=r.x1,$=r.x2;n.segpts=[U,Z,$,Z]}else{var Q=r.x1+C+(l?i/2*T:0),J=r.y1,ee=r.y2;n.segpts=[Q,J,Q,ee]}},Yo.tryToCorrectInvalidPoints=function(e,t){var n=e._private.rscratch;if("bezier"===n.edgeType){var r=t.srcPos,i=t.tgtPos,a=t.srcW,o=t.srcH,s=t.tgtW,l=t.tgtH,u=t.srcShape,c=t.tgtShape,d=!y(n.startX)||!y(n.startY),h=!y(n.arrowStartX)||!y(n.arrowStartY),p=!y(n.endX)||!y(n.endY),f=!y(n.arrowEndX)||!y(n.arrowEndY),g=3*(this.getArrowWidth(e.pstyle("width").pfValue,e.pstyle("arrow-scale").value)*this.arrowShapeWidth),v=ot({x:n.ctrlpts[0],y:n.ctrlpts[1]},{x:n.startX,y:n.startY}),m=v<g,b=ot({x:n.ctrlpts[0],y:n.ctrlpts[1]},{x:n.endX,y:n.endY}),x=b<g,w=!1;if(d||h||m){w=!0;var E={x:n.ctrlpts[0]-r.x,y:n.ctrlpts[1]-r.y},k=Math.sqrt(E.x*E.x+E.y*E.y),C={x:E.x/k,y:E.y/k},S=Math.max(a,o),P={x:n.ctrlpts[0]+2*C.x*S,y:n.ctrlpts[1]+2*C.y*S},D=u.intersectLine(r.x,r.y,a,o,P.x,P.y,0);m?(n.ctrlpts[0]=n.ctrlpts[0]+C.x*(g-v),n.ctrlpts[1]=n.ctrlpts[1]+C.y*(g-v)):(n.ctrlpts[0]=D[0]+C.x*g,n.ctrlpts[1]=D[1]+C.y*g)}if(p||f||x){w=!0;var T={x:n.ctrlpts[0]-i.x,y:n.ctrlpts[1]-i.y},M=Math.sqrt(T.x*T.x+T.y*T.y),B={x:T.x/M,y:T.y/M},_=Math.max(a,o),N={x:n.ctrlpts[0]+2*B.x*_,y:n.ctrlpts[1]+2*B.y*_},I=c.intersectLine(i.x,i.y,s,l,N.x,N.y,0);x?(n.ctrlpts[0]=n.ctrlpts[0]+B.x*(g-b),n.ctrlpts[1]=n.ctrlpts[1]+B.y*(g-b)):(n.ctrlpts[0]=I[0]+B.x*g,n.ctrlpts[1]=I[1]+B.y*g)}w&&this.findEndpoints(e)}},Yo.storeAllpts=function(e){var t=e._private.rscratch;if("multibezier"===t.edgeType||"bezier"===t.edgeType||"self"===t.edgeType||"compound"===t.edgeType){t.allpts=[],t.allpts.push(t.startX,t.startY);for(var n=0;n+1<t.ctrlpts.length;n+=2)t.allpts.push(t.ctrlpts[n],t.ctrlpts[n+1]),n+3<t.ctrlpts.length&&t.allpts.push((t.ctrlpts[n]+t.ctrlpts[n+2])/2,(t.ctrlpts[n+1]+t.ctrlpts[n+3])/2);var r;t.allpts.push(t.endX,t.endY),t.ctrlpts.length/2%2==0?(r=t.allpts.length/2-1,t.midX=t.allpts[r],t.midY=t.allpts[r+1]):(r=t.allpts.length/2-3,.5,t.midX=ut(t.allpts[r],t.allpts[r+2],t.allpts[r+4],.5),t.midY=ut(t.allpts[r+1],t.allpts[r+3],t.allpts[r+5],.5))}else if("straight"===t.edgeType)t.allpts=[t.startX,t.startY,t.endX,t.endY],t.midX=(t.startX+t.endX+t.arrowStartX+t.arrowEndX)/4,t.midY=(t.startY+t.endY+t.arrowStartY+t.arrowEndY)/4;else if("segments"===t.edgeType)if(t.allpts=[],t.allpts.push(t.startX,t.startY),t.allpts.push.apply(t.allpts,t.segpts),t.allpts.push(t.endX,t.endY),t.segpts.length%4==0){var i=t.segpts.length/2,a=i-2;t.midX=(t.segpts[a]+t.segpts[i])/2,t.midY=(t.segpts[a+1]+t.segpts[i+1])/2}else{var o=t.segpts.length/2-1;t.midX=t.segpts[o],t.midY=t.segpts[o+1]}},Yo.checkForInvalidEdgeWarning=function(e){var t=e[0]._private.rscratch;t.nodesOverlap||y(t.startX)&&y(t.startY)&&y(t.endX)&&y(t.endY)?t.loggedErr=!1:t.loggedErr||(t.loggedErr=!0,Ce("Edge `"+e.id()+"` has invalid endpoints and so it is impossible to draw.  Adjust your edge style (e.g. control points) accordingly or use an alternative edge type.  This is expected behaviour when the source node and the target node overlap."))},Yo.findEdgeControlPoints=function(e){var t=this;if(e&&0!==e.length){for(var n=this,r=n.cy.hasCompoundNodes(),i={map:new ze,get:function(e){var t=this.map.get(e[0]);return null!=t?t.get(e[1]):null},set:function(e,t){var n=this.map.get(e[0]);null==n&&(n=new ze,this.map.set(e[0],n)),n.set(e[1],t)}},a=[],o=[],s=0;s<e.length;s++){var l=e[s],u=l._private,c=l.pstyle("curve-style").value;if(!l.removed()&&l.takesUpSpace())if("haystack"!==c){var d="unbundled-bezier"===c||"segments"===c||"straight"===c||"taxi"===c,h="unbundled-bezier"===c||"bezier"===c,p=u.source,f=u.target,g=[p.poolIndex(),f.poolIndex()].sort(),v=i.get(g);null==v&&(v={eles:[]},i.set(g,v),a.push(g)),v.eles.push(l),d&&(v.hasUnbundled=!0),h&&(v.hasBezier=!0)}else o.push(l)}for(var m=function(e){var o=a[e],s=i.get(o),l=void 0;if(!s.hasUnbundled){var u=s.eles[0].parallelEdges().filter((function(e){return e.isBundledBezier()}));_e(s.eles),u.forEach((function(e){return s.eles.push(e)})),s.eles.sort((function(e,t){return e.poolIndex()-t.poolIndex()}))}var c=s.eles[0],d=c.source(),h=c.target();if(d.poolIndex()>h.poolIndex()){var p=d;d=h,h=p}var f=s.srcPos=d.position(),g=s.tgtPos=h.position(),v=s.srcW=d.outerWidth(),m=s.srcH=d.outerHeight(),b=s.tgtW=h.outerWidth(),x=s.tgtH=h.outerHeight(),w=s.srcShape=n.nodeShapes[t.getNodeShape(d)],E=s.tgtShape=n.nodeShapes[t.getNodeShape(h)];s.dirCounts={north:0,west:0,south:0,east:0,northwest:0,southwest:0,northeast:0,southeast:0};for(var k=0;k<s.eles.length;k++){var C=s.eles[k],S=C[0]._private.rscratch,P=C.pstyle("curve-style").value,D="unbundled-bezier"===P||"segments"===P||"taxi"===P,T=!d.same(C.source());if(!s.calculatedIntersection&&d!==h&&(s.hasBezier||s.hasUnbundled)){s.calculatedIntersection=!0;var M=w.intersectLine(f.x,f.y,v,m,g.x,g.y,0),B=s.srcIntn=M,_=E.intersectLine(g.x,g.y,b,x,f.x,f.y,0),N=s.tgtIntn=_,I=s.intersectionPts={x1:M[0],x2:_[0],y1:M[1],y2:_[1]},z=s.posPts={x1:f.x,x2:g.x,y1:f.y,y2:g.y},L=_[1]-M[1],A=_[0]-M[0],O=Math.sqrt(A*A+L*L),R=s.vector={x:A,y:L},V=s.vectorNorm={x:R.x/O,y:R.y/O},F={x:-V.y,y:V.x};s.nodesOverlap=!y(O)||E.checkPoint(M[0],M[1],0,b,x,g.x,g.y)||w.checkPoint(_[0],_[1],0,v,m,f.x,f.y),s.vectorNormInverse=F,l={nodesOverlap:s.nodesOverlap,dirCounts:s.dirCounts,calculatedIntersection:!0,hasBezier:s.hasBezier,hasUnbundled:s.hasUnbundled,eles:s.eles,srcPos:g,tgtPos:f,srcW:b,srcH:x,tgtW:v,tgtH:m,srcIntn:N,tgtIntn:B,srcShape:E,tgtShape:w,posPts:{x1:z.x2,y1:z.y2,x2:z.x1,y2:z.y1},intersectionPts:{x1:I.x2,y1:I.y2,x2:I.x1,y2:I.y1},vector:{x:-R.x,y:-R.y},vectorNorm:{x:-V.x,y:-V.y},vectorNormInverse:{x:-F.x,y:-F.y}}}var q=T?l:s;S.nodesOverlap=q.nodesOverlap,S.srcIntn=q.srcIntn,S.tgtIntn=q.tgtIntn,r&&(d.isParent()||d.isChild()||h.isParent()||h.isChild())&&(d.parents().anySame(h)||h.parents().anySame(d)||d.same(h)&&d.isParent())?t.findCompoundLoopPoints(C,q,k,D):d===h?t.findLoopPoints(C,q,k,D):"segments"===P?t.findSegmentsPoints(C,q):"taxi"===P?t.findTaxiPoints(C,q):"straight"===P||!D&&s.eles.length%2==1&&k===Math.floor(s.eles.length/2)?t.findStraightEdgePoints(C):t.findBezierPoints(C,q,k,D,T),t.findEndpoints(C),t.tryToCorrectInvalidPoints(C,q),t.checkForInvalidEdgeWarning(C),t.storeAllpts(C),t.storeEdgeProjections(C),t.calculateArrowAngles(C),t.recalculateEdgeLabelProjections(C),t.calculateLabelAngles(C)}},b=0;b<a.length;b++)m(b);this.findHaystackPoints(o)}},Yo.getSegmentPoints=function(e){var t=e[0]._private.rscratch;if("segments"===t.edgeType)return this.recalculateRenderedStyle(e),Xo(t.segpts)},Yo.getControlPoints=function(e){var t=e[0]._private.rscratch,n=t.edgeType;if("bezier"===n||"multibezier"===n||"self"===n||"compound"===n)return this.recalculateRenderedStyle(e),Xo(t.ctrlpts)},Yo.getEdgeMidpoint=function(e){var t=e[0]._private.rscratch;return this.recalculateRenderedStyle(e),{x:t.midX,y:t.midY}};var Wo={manualEndptToPx:function(e,t){var n=e.position(),r=e.outerWidth(),i=e.outerHeight();if(2===t.value.length){var a=[t.pfValue[0],t.pfValue[1]];return"%"===t.units[0]&&(a[0]=a[0]*r),"%"===t.units[1]&&(a[1]=a[1]*i),a[0]+=n.x,a[1]+=n.y,a}var o=t.pfValue[0];o=-Math.PI/2+o;var s=2*Math.max(r,i),l=[n.x+Math.cos(o)*s,n.y+Math.sin(o)*s];return this.nodeShapes[this.getNodeShape(e)].intersectLine(n.x,n.y,r,i,l[0],l[1],0)},findEndpoints:function(e){var 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if("outside-to-node"===M||"outside-to-node-or-label"===M?i=n:"outside-to-line"!==M&&"outside-to-line-or-label"!==M||(i=[u.x,u.y]),t=o.nodeShapes[this.getNodeShape(l)].intersectLine(c.x,c.y,l.outerWidth(),l.outerHeight(),i[0],i[1],0),"outside-to-node-or-label"===M||"outside-to-line-or-label"===M){var N=l._private.rscratch,I=N.labelWidth,z=N.labelHeight,L=N.labelX,A=N.labelY,O=I/2,R=z/2,V=l.pstyle("text-valign").value;"top"===V?A-=R:"bottom"===V&&(A+=R);var F=l.pstyle("text-halign").value;"left"===F?L-=O:"right"===F&&(L+=O);var q=It(i[0],i[1],[L-O,A-R,L+O,A-R,L+O,A+R,L-O,A+R],c.x,c.y);if(q.length>0){var j=u,Y=st(j,nt(t)),X=st(j,nt(q)),W=Y;if(X<Y&&(t=q,W=X),q.length>2)st(j,{x:q[2],y:q[3]})<W&&(t=[q[2],q[3]])}}var H=zt(t,n,o.arrowShapes[d].spacing(e)+p),K=zt(t,n,o.arrowShapes[d].gap(e)+p);if(v.endX=K[0],v.endY=K[1],v.arrowEndX=H[0],v.arrowEndY=H[1],"inside-to-node"===D)t=[u.x,u.y];else if(P.units)t=this.manualEndptToPx(s,P);else if("outside-to-line"===D)t=v.srcIntn;else 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r&&n.supportsPassiveEvents&&(o[2]={capture:null!=a&&a,passive:!1,once:!1}),n.bindings.push({target:e,args:o}),(e.addEventListener||e.on).apply(e,o),this};return{on:o,addEventListener:o,addListener:o,bind:o}},rs.nodeIsDraggable=function(e){return e&&e.isNode()&&!e.locked()&&e.grabbable()},rs.nodeIsGrabbable=function(e){return this.nodeIsDraggable(e)&&e.interactive()},rs.load=function(){var e=this,t=function(e){return e.selected()},n=function(t,n,r,i){null==t&&(t=e.cy);for(var a=0;a<n.length;a++){var o=n[a];t.emit({originalEvent:r,type:o,position:i})}},r=function(e){return e.shiftKey||e.metaKey||e.ctrlKey},i=function(t,n){var r=!0;if(e.cy.hasCompoundNodes()&&t&&t.pannable())for(var i=0;n&&i<n.length;i++){if((t=n[i]).isNode()&&t.isParent()&&!t.pannable()){r=!1;break}}else r=!0;return r},a=function(e){e[0]._private.rscratch.inDragLayer=!0},o=function(e){e[0]._private.rscratch.isGrabTarget=!0},s=function(e,t){var n=t.addToList;n.has(e)||(n.merge(e),function(e){e[0]._private.grabbed=!0}(e))},l=function(t,n){n=n||{};var r=t.cy().hasCompoundNodes();n.inDragLayer&&(t.forEach(a),t.neighborhood().stdFilter((function(e){return!r||e.isEdge()})).forEach(a)),n.addToList&&t.forEach((function(e){s(e,n)})),function(e,t){if(e.cy().hasCompoundNodes()&&(null!=t.inDragLayer||null!=t.addToList)){var n=e.descendants();t.inDragLayer&&(n.forEach(a),n.connectedEdges().forEach(a)),t.addToList&&t.addToList.unmerge(n)}}(t,n),d(t,{inDragLayer:n.inDragLayer}),e.updateCachedGrabbedEles()},u=l,c=function(t){t&&(e.getCachedZSortedEles().forEach((function(e){!function(e){e[0]._private.grabbed=!1}(e),function(e){e[0]._private.rscratch.inDragLayer=!1}(e),function(e){e[0]._private.rscratch.isGrabTarget=!1}(e)})),e.updateCachedGrabbedEles())},d=function(e,t){if((null!=t.inDragLayer||null!=t.addToList)&&e.cy().hasCompoundNodes()){var n=e.ancestors().orphans();if(!n.same(e)){var r=n.descendants().spawnSelf().merge(n).unmerge(e).unmerge(e.descendants()),i=r.connectedEdges();t.inDragLayer&&(i.forEach(a),r.forEach(a)),t.addToList&&r.forEach((function(e){s(e,t)}))}}},h=function(){null!=document.activeElement&&null!=document.activeElement.blur&&document.activeElement.blur()},p="undefined"!=typeof MutationObserver,f="undefined"!=typeof ResizeObserver;p?(e.removeObserver=new MutationObserver((function(t){for(var n=0;n<t.length;n++){var r=t[n].removedNodes;if(r)for(var i=0;i<r.length;i++){if(r[i]===e.container){e.destroy();break}}}})),e.container.parentNode&&e.removeObserver.observe(e.container.parentNode,{childList:!0})):e.registerBinding(e.container,"DOMNodeRemoved",(function(t){e.destroy()}));var g=J((function(){e.cy.resize()}),100);p&&(e.styleObserver=new MutationObserver(g),e.styleObserver.observe(e.container,{attributes:!0})),e.registerBinding(window,"resize",g),f&&(e.resizeObserver=new ResizeObserver(g),e.resizeObserver.observe(e.container));var v=function(){e.invalidateContainerClientCoordsCache()};!function(e,t){for(;null!=e;)t(e),e=e.parentNode}(e.container,(function(t){e.registerBinding(t,"transitionend",v),e.registerBinding(t,"animationend",v),e.registerBinding(t,"scroll",v)})),e.registerBinding(e.container,"contextmenu",(function(e){e.preventDefault()}));var m=function(t){for(var n=e.findContainerClientCoords(),r=n[0],i=n[1],a=n[2],o=n[3],s=t.touches?t.touches:[t],l=!1,u=0;u<s.length;u++){var c=s[u];if(r<=c.clientX&&c.clientX<=r+a&&i<=c.clientY&&c.clientY<=i+o){l=!0;break}}if(!l)return!1;for(var d=e.container,h=t.target.parentNode,p=!1;h;){if(h===d){p=!0;break}h=h.parentNode}return!!p};e.registerBinding(e.container,"mousedown",(function(t){if(m(t)){t.preventDefault(),h(),e.hoverData.capture=!0,e.hoverData.which=t.which;var r=e.cy,i=[t.clientX,t.clientY],a=e.projectIntoViewport(i[0],i[1]),s=e.selection,c=e.findNearestElements(a[0],a[1],!0,!1),d=c[0],p=e.dragData.possibleDragElements;e.hoverData.mdownPos=a,e.hoverData.mdownGPos=i;if(3==t.which){e.hoverData.cxtStarted=!0;var f={originalEvent:t,type:"cxttapstart",position:{x:a[0],y:a[1]}};d?(d.activate(),d.emit(f),e.hoverData.down=d):r.emit(f),e.hoverData.downTime=(new Date).getTime(),e.hoverData.cxtDragged=!1}else if(1==t.which){if(d&&d.activate(),null!=d&&e.nodeIsGrabbable(d)){var g=function(e){return{originalEvent:t,type:e,position:{x:a[0],y:a[1]}}};if(o(d),d.selected()){p=e.dragData.possibleDragElements=r.collection();var v=r.$((function(t){return t.isNode()&&t.selected()&&e.nodeIsGrabbable(t)}));l(v,{addToList:p}),d.emit(g("grabon")),v.forEach((function(e){e.emit(g("grab"))}))}else p=e.dragData.possibleDragElements=r.collection(),u(d,{addToList:p}),d.emit(g("grabon")).emit(g("grab"));e.redrawHint("eles",!0),e.redrawHint("drag",!0)}e.hoverData.down=d,e.hoverData.downs=c,e.hoverData.downTime=(new Date).getTime(),n(d,["mousedown","tapstart","vmousedown"],t,{x:a[0],y:a[1]}),null==d?(s[4]=1,e.data.bgActivePosistion={x:a[0],y:a[1]},e.redrawHint("select",!0),e.redraw()):d.pannable()&&(s[4]=1),e.hoverData.tapholdCancelled=!1,clearTimeout(e.hoverData.tapholdTimeout),e.hoverData.tapholdTimeout=setTimeout((function(){if(!e.hoverData.tapholdCancelled){var n=e.hoverData.down;n?n.emit({originalEvent:t,type:"taphold",position:{x:a[0],y:a[1]}}):r.emit({originalEvent:t,type:"taphold",position:{x:a[0],y:a[1]}})}}),e.tapholdDuration)}s[0]=s[2]=a[0],s[1]=s[3]=a[1]}}),!1),e.registerBinding(window,"mousemove",(function(t){if(e.hoverData.capture||m(t)){var a=!1,o=e.cy,s=o.zoom(),u=[t.clientX,t.clientY],d=e.projectIntoViewport(u[0],u[1]),h=e.hoverData.mdownPos,p=e.hoverData.mdownGPos,f=e.selection,g=null;e.hoverData.draggingEles||e.hoverData.dragging||e.hoverData.selecting||(g=e.findNearestElement(d[0],d[1],!0,!1));var v,b=e.hoverData.last,x=e.hoverData.down,w=[d[0]-f[2],d[1]-f[3]],E=e.dragData.possibleDragElements;if(p){var k=u[0]-p[0],C=k*k,S=u[1]-p[1],P=C+S*S;e.hoverData.isOverThresholdDrag=v=P>=e.desktopTapThreshold2}var D=r(t);v&&(e.hoverData.tapholdCancelled=!0);a=!0,n(g,["mousemove","vmousemove","tapdrag"],t,{x:d[0],y:d[1]});var T=function(){e.data.bgActivePosistion=void 0,e.hoverData.selecting||o.emit({originalEvent:t,type:"boxstart",position:{x:d[0],y:d[1]}}),f[4]=1,e.hoverData.selecting=!0,e.redrawHint("select",!0),e.redraw()};if(3===e.hoverData.which){if(v){var M={originalEvent:t,type:"cxtdrag",position:{x:d[0],y:d[1]}};x?x.emit(M):o.emit(M),e.hoverData.cxtDragged=!0,e.hoverData.cxtOver&&g===e.hoverData.cxtOver||(e.hoverData.cxtOver&&e.hoverData.cxtOver.emit({originalEvent:t,type:"cxtdragout",position:{x:d[0],y:d[1]}}),e.hoverData.cxtOver=g,g&&g.emit({originalEvent:t,type:"cxtdragover",position:{x:d[0],y:d[1]}}))}}else if(e.hoverData.dragging){if(a=!0,o.panningEnabled()&&o.userPanningEnabled()){var B;if(e.hoverData.justStartedPan){var _=e.hoverData.mdownPos;B={x:(d[0]-_[0])*s,y:(d[1]-_[1])*s},e.hoverData.justStartedPan=!1}else B={x:w[0]*s,y:w[1]*s};o.panBy(B),o.emit("dragpan"),e.hoverData.dragged=!0}d=e.projectIntoViewport(t.clientX,t.clientY)}else if(1!=f[4]||null!=x&&!x.pannable()){if(x&&x.pannable()&&x.active()&&x.unactivate(),x&&x.grabbed()||g==b||(b&&n(b,["mouseout","tapdragout"],t,{x:d[0],y:d[1]}),g&&n(g,["mouseover","tapdragover"],t,{x:d[0],y:d[1]}),e.hoverData.last=g),x)if(v){if(o.boxSelectionEnabled()&&D)x&&x.grabbed()&&(c(E),x.emit("freeon"),E.emit("free"),e.dragData.didDrag&&(x.emit("dragfreeon"),E.emit("dragfree"))),T();else if(x&&x.grabbed()&&e.nodeIsDraggable(x)){var N=!e.dragData.didDrag;N&&e.redrawHint("eles",!0),e.dragData.didDrag=!0;var I=o.collection();e.hoverData.draggingEles||l(E,{inDragLayer:!0});var z={x:0,y:0};if(y(w[0])&&y(w[1])&&(z.x+=w[0],z.y+=w[1],N)){var L=e.hoverData.dragDelta;L&&y(L[0])&&y(L[1])&&(z.x+=L[0],z.y+=L[1])}for(var A=0;A<E.length;A++){var O=E[A];e.nodeIsDraggable(O)&&O.grabbed()&&I.push(O)}e.hoverData.draggingEles=!0,I.silentShift(z).emit("position drag"),e.redrawHint("drag",!0),e.redraw()}}else!function(){var t=e.hoverData.dragDelta=e.hoverData.dragDelta||[];0===t.length?(t.push(w[0]),t.push(w[1])):(t[0]+=w[0],t[1]+=w[1])}();a=!0}else if(v){if(e.hoverData.dragging||!o.boxSelectionEnabled()||!D&&o.panningEnabled()&&o.userPanningEnabled()){if(!e.hoverData.selecting&&o.panningEnabled()&&o.userPanningEnabled()){i(x,e.hoverData.downs)&&(e.hoverData.dragging=!0,e.hoverData.justStartedPan=!0,f[4]=0,e.data.bgActivePosistion=nt(h),e.redrawHint("select",!0),e.redraw())}}else T();x&&x.pannable()&&x.active()&&x.unactivate()}return f[2]=d[0],f[3]=d[1],a?(t.stopPropagation&&t.stopPropagation(),t.preventDefault&&t.preventDefault(),!1):void 0}}),!1),e.registerBinding(window,"mouseup",(function(i){if(e.hoverData.capture){e.hoverData.capture=!1;var a=e.cy,o=e.projectIntoViewport(i.clientX,i.clientY),s=e.selection,l=e.findNearestElement(o[0],o[1],!0,!1),u=e.dragData.possibleDragElements,d=e.hoverData.down,h=r(i);if(e.data.bgActivePosistion&&(e.redrawHint("select",!0),e.redraw()),e.hoverData.tapholdCancelled=!0,e.data.bgActivePosistion=void 0,d&&d.unactivate(),3===e.hoverData.which){var p={originalEvent:i,type:"cxttapend",position:{x:o[0],y:o[1]}};if(d?d.emit(p):a.emit(p),!e.hoverData.cxtDragged){var f={originalEvent:i,type:"cxttap",position:{x:o[0],y:o[1]}};d?d.emit(f):a.emit(f)}e.hoverData.cxtDragged=!1,e.hoverData.which=null}else if(1===e.hoverData.which){if(n(l,["mouseup","tapend","vmouseup"],i,{x:o[0],y:o[1]}),e.dragData.didDrag||e.hoverData.dragged||e.hoverData.selecting||e.hoverData.isOverThresholdDrag||n(d,["click","tap","vclick"],i,{x:o[0],y:o[1]}),null!=d||e.dragData.didDrag||e.hoverData.selecting||e.hoverData.dragged||r(i)||(a.$(t).unselect(["tapunselect"]),u.length>0&&e.redrawHint("eles",!0),e.dragData.possibleDragElements=u=a.collection()),l!=d||e.dragData.didDrag||e.hoverData.selecting||null!=l&&l._private.selectable&&(e.hoverData.dragging||("additive"===a.selectionType()||h?l.selected()?l.unselect(["tapunselect"]):l.select(["tapselect"]):h||(a.$(t).unmerge(l).unselect(["tapunselect"]),l.select(["tapselect"]))),e.redrawHint("eles",!0)),e.hoverData.selecting){var g=a.collection(e.getAllInBox(s[0],s[1],s[2],s[3]));e.redrawHint("select",!0),g.length>0&&e.redrawHint("eles",!0),a.emit({type:"boxend",originalEvent:i,position:{x:o[0],y:o[1]}});var v=function(e){return e.selectable()&&!e.selected()};"additive"===a.selectionType()||h||a.$(t).unmerge(g).unselect(),g.emit("box").stdFilter(v).select().emit("boxselect"),e.redraw()}if(e.hoverData.dragging&&(e.hoverData.dragging=!1,e.redrawHint("select",!0),e.redrawHint("eles",!0),e.redraw()),!s[4]){e.redrawHint("drag",!0),e.redrawHint("eles",!0);var y=d&&d.grabbed();c(u),y&&(d.emit("freeon"),u.emit("free"),e.dragData.didDrag&&(d.emit("dragfreeon"),u.emit("dragfree")))}}s[4]=0,e.hoverData.down=null,e.hoverData.cxtStarted=!1,e.hoverData.draggingEles=!1,e.hoverData.selecting=!1,e.hoverData.isOverThresholdDrag=!1,e.dragData.didDrag=!1,e.hoverData.dragged=!1,e.hoverData.dragDelta=[],e.hoverData.mdownPos=null,e.hoverData.mdownGPos=null}}),!1);var b,x,w,E,k,C,S,P,D,T,M,B,_,N=function(t){if(!e.scrollingPage){var n=e.cy,r=n.zoom(),i=n.pan(),a=e.projectIntoViewport(t.clientX,t.clientY),o=[a[0]*r+i.x,a[1]*r+i.y];if(e.hoverData.draggingEles||e.hoverData.dragging||e.hoverData.cxtStarted||0!==e.selection[4])t.preventDefault();else if(n.panningEnabled()&&n.userPanningEnabled()&&n.zoomingEnabled()&&n.userZoomingEnabled()){var s;t.preventDefault(),e.data.wheelZooming=!0,clearTimeout(e.data.wheelTimeout),e.data.wheelTimeout=setTimeout((function(){e.data.wheelZooming=!1,e.redrawHint("eles",!0),e.redraw()}),150),s=null!=t.deltaY?t.deltaY/-250:null!=t.wheelDeltaY?t.wheelDeltaY/1e3:t.wheelDelta/1e3,s*=e.wheelSensitivity,1===t.deltaMode&&(s*=33);var l=n.zoom()*Math.pow(10,s);"gesturechange"===t.type&&(l=e.gestureStartZoom*t.scale),n.zoom({level:l,renderedPosition:{x:o[0],y:o[1]}}),n.emit("gesturechange"===t.type?"pinchzoom":"scrollzoom")}}};e.registerBinding(e.container,"wheel",N,!0),e.registerBinding(window,"scroll",(function(t){e.scrollingPage=!0,clearTimeout(e.scrollingPageTimeout),e.scrollingPageTimeout=setTimeout((function(){e.scrollingPage=!1}),250)}),!0),e.registerBinding(e.container,"gesturestart",(function(t){e.gestureStartZoom=e.cy.zoom(),e.hasTouchStarted||t.preventDefault()}),!0),e.registerBinding(e.container,"gesturechange",(function(t){e.hasTouchStarted||N(t)}),!0),e.registerBinding(e.container,"mouseout",(function(t){var n=e.projectIntoViewport(t.clientX,t.clientY);e.cy.emit({originalEvent:t,type:"mouseout",position:{x:n[0],y:n[1]}})}),!1),e.registerBinding(e.container,"mouseover",(function(t){var n=e.projectIntoViewport(t.clientX,t.clientY);e.cy.emit({originalEvent:t,type:"mouseover",position:{x:n[0],y:n[1]}})}),!1);var I,z,L,A,O=function(e,t,n,r){return Math.sqrt((n-e)*(n-e)+(r-t)*(r-t))},R=function(e,t,n,r){return(n-e)*(n-e)+(r-t)*(r-t)};if(e.registerBinding(e.container,"touchstart",I=function(t){if(e.hasTouchStarted=!0,m(t)){h(),e.touchData.capture=!0,e.data.bgActivePosistion=void 0;var r=e.cy,i=e.touchData.now,a=e.touchData.earlier;if(t.touches[0]){var s=e.projectIntoViewport(t.touches[0].clientX,t.touches[0].clientY);i[0]=s[0],i[1]=s[1]}if(t.touches[1]){s=e.projectIntoViewport(t.touches[1].clientX,t.touches[1].clientY);i[2]=s[0],i[3]=s[1]}if(t.touches[2]){s=e.projectIntoViewport(t.touches[2].clientX,t.touches[2].clientY);i[4]=s[0],i[5]=s[1]}if(t.touches[1]){e.touchData.singleTouchMoved=!0,c(e.dragData.touchDragEles);var d=e.findContainerClientCoords();D=d[0],T=d[1],M=d[2],B=d[3],b=t.touches[0].clientX-D,x=t.touches[0].clientY-T,w=t.touches[1].clientX-D,E=t.touches[1].clientY-T,_=0<=b&&b<=M&&0<=w&&w<=M&&0<=x&&x<=B&&0<=E&&E<=B;var p=r.pan(),f=r.zoom();k=O(b,x,w,E),C=R(b,x,w,E),P=[((S=[(b+w)/2,(x+E)/2])[0]-p.x)/f,(S[1]-p.y)/f];if(C<4e4&&!t.touches[2]){var g=e.findNearestElement(i[0],i[1],!0,!0),v=e.findNearestElement(i[2],i[3],!0,!0);return g&&g.isNode()?(g.activate().emit({originalEvent:t,type:"cxttapstart",position:{x:i[0],y:i[1]}}),e.touchData.start=g):v&&v.isNode()?(v.activate().emit({originalEvent:t,type:"cxttapstart",position:{x:i[0],y:i[1]}}),e.touchData.start=v):r.emit({originalEvent:t,type:"cxttapstart",position:{x:i[0],y:i[1]}}),e.touchData.start&&(e.touchData.start._private.grabbed=!1),e.touchData.cxt=!0,e.touchData.cxtDragged=!1,e.data.bgActivePosistion=void 0,void e.redraw()}}if(t.touches[2])r.boxSelectionEnabled()&&t.preventDefault();else if(t.touches[1]);else if(t.touches[0]){var y=e.findNearestElements(i[0],i[1],!0,!0),N=y[0];if(null!=N&&(N.activate(),e.touchData.start=N,e.touchData.starts=y,e.nodeIsGrabbable(N))){var I=e.dragData.touchDragEles=r.collection(),z=null;e.redrawHint("eles",!0),e.redrawHint("drag",!0),N.selected()?(z=r.$((function(t){return t.selected()&&e.nodeIsGrabbable(t)})),l(z,{addToList:I})):u(N,{addToList:I}),o(N);var L=function(e){return{originalEvent:t,type:e,position:{x:i[0],y:i[1]}}};N.emit(L("grabon")),z?z.forEach((function(e){e.emit(L("grab"))})):N.emit(L("grab"))}n(N,["touchstart","tapstart","vmousedown"],t,{x:i[0],y:i[1]}),null==N&&(e.data.bgActivePosistion={x:s[0],y:s[1]},e.redrawHint("select",!0),e.redraw()),e.touchData.singleTouchMoved=!1,e.touchData.singleTouchStartTime=+new Date,clearTimeout(e.touchData.tapholdTimeout),e.touchData.tapholdTimeout=setTimeout((function(){!1!==e.touchData.singleTouchMoved||e.pinching||e.touchData.selecting||n(e.touchData.start,["taphold"],t,{x:i[0],y:i[1]})}),e.tapholdDuration)}if(t.touches.length>=1){for(var A=e.touchData.startPosition=[],V=0;V<i.length;V++)A[V]=a[V]=i[V];var F=t.touches[0];e.touchData.startGPosition=[F.clientX,F.clientY]}}},!1),e.registerBinding(window,"touchmove",z=function(t){var r=e.touchData.capture;if(r||m(t)){var a=e.selection,o=e.cy,s=e.touchData.now,u=e.touchData.earlier,d=o.zoom();if(t.touches[0]){var h=e.projectIntoViewport(t.touches[0].clientX,t.touches[0].clientY);s[0]=h[0],s[1]=h[1]}if(t.touches[1]){h=e.projectIntoViewport(t.touches[1].clientX,t.touches[1].clientY);s[2]=h[0],s[3]=h[1]}if(t.touches[2]){h=e.projectIntoViewport(t.touches[2].clientX,t.touches[2].clientY);s[4]=h[0],s[5]=h[1]}var p,f=e.touchData.startGPosition;if(r&&t.touches[0]&&f){for(var g=[],v=0;v<s.length;v++)g[v]=s[v]-u[v];var S=t.touches[0].clientX-f[0],M=S*S,B=t.touches[0].clientY-f[1];p=M+B*B>=e.touchTapThreshold2}if(r&&e.touchData.cxt){t.preventDefault();var N=t.touches[0].clientX-D,I=t.touches[0].clientY-T,z=t.touches[1].clientX-D,L=t.touches[1].clientY-T,A=R(N,I,z,L);if(A/C>=2.25||A>=22500){e.touchData.cxt=!1,e.data.bgActivePosistion=void 0,e.redrawHint("select",!0);var V={originalEvent:t,type:"cxttapend",position:{x:s[0],y:s[1]}};e.touchData.start?(e.touchData.start.unactivate().emit(V),e.touchData.start=null):o.emit(V)}}if(r&&e.touchData.cxt){V={originalEvent:t,type:"cxtdrag",position:{x:s[0],y:s[1]}};e.data.bgActivePosistion=void 0,e.redrawHint("select",!0),e.touchData.start?e.touchData.start.emit(V):o.emit(V),e.touchData.start&&(e.touchData.start._private.grabbed=!1),e.touchData.cxtDragged=!0;var F=e.findNearestElement(s[0],s[1],!0,!0);e.touchData.cxtOver&&F===e.touchData.cxtOver||(e.touchData.cxtOver&&e.touchData.cxtOver.emit({originalEvent:t,type:"cxtdragout",position:{x:s[0],y:s[1]}}),e.touchData.cxtOver=F,F&&F.emit({originalEvent:t,type:"cxtdragover",position:{x:s[0],y:s[1]}}))}else if(r&&t.touches[2]&&o.boxSelectionEnabled())t.preventDefault(),e.data.bgActivePosistion=void 0,this.lastThreeTouch=+new Date,e.touchData.selecting||o.emit({originalEvent:t,type:"boxstart",position:{x:s[0],y:s[1]}}),e.touchData.selecting=!0,e.touchData.didSelect=!0,a[4]=1,a&&0!==a.length&&void 0!==a[0]?(a[2]=(s[0]+s[2]+s[4])/3,a[3]=(s[1]+s[3]+s[5])/3):(a[0]=(s[0]+s[2]+s[4])/3,a[1]=(s[1]+s[3]+s[5])/3,a[2]=(s[0]+s[2]+s[4])/3+1,a[3]=(s[1]+s[3]+s[5])/3+1),e.redrawHint("select",!0),e.redraw();else if(r&&t.touches[1]&&!e.touchData.didSelect&&o.zoomingEnabled()&&o.panningEnabled()&&o.userZoomingEnabled()&&o.userPanningEnabled()){if(t.preventDefault(),e.data.bgActivePosistion=void 0,e.redrawHint("select",!0),ee=e.dragData.touchDragEles){e.redrawHint("drag",!0);for(var q=0;q<ee.length;q++){var j=ee[q]._private;j.grabbed=!1,j.rscratch.inDragLayer=!1}}var Y=e.touchData.start,X=(N=t.touches[0].clientX-D,I=t.touches[0].clientY-T,z=t.touches[1].clientX-D,L=t.touches[1].clientY-T,O(N,I,z,L)),W=X/k;if(_){var H=(N-b+(z-w))/2,K=(I-x+(L-E))/2,G=o.zoom(),Z=G*W,U=o.pan(),$=P[0]*G+U.x,Q=P[1]*G+U.y,J={x:-Z/G*($-U.x-H)+$,y:-Z/G*(Q-U.y-K)+Q};if(Y&&Y.active()){var ee=e.dragData.touchDragEles;c(ee),e.redrawHint("drag",!0),e.redrawHint("eles",!0),Y.unactivate().emit("freeon"),ee.emit("free"),e.dragData.didDrag&&(Y.emit("dragfreeon"),ee.emit("dragfree"))}o.viewport({zoom:Z,pan:J,cancelOnFailedZoom:!0}),o.emit("pinchzoom"),k=X,b=N,x=I,w=z,E=L,e.pinching=!0}if(t.touches[0]){h=e.projectIntoViewport(t.touches[0].clientX,t.touches[0].clientY);s[0]=h[0],s[1]=h[1]}if(t.touches[1]){h=e.projectIntoViewport(t.touches[1].clientX,t.touches[1].clientY);s[2]=h[0],s[3]=h[1]}if(t.touches[2]){h=e.projectIntoViewport(t.touches[2].clientX,t.touches[2].clientY);s[4]=h[0],s[5]=h[1]}}else if(t.touches[0]&&!e.touchData.didSelect){var te=e.touchData.start,ne=e.touchData.last;if(e.hoverData.draggingEles||e.swipePanning||(F=e.findNearestElement(s[0],s[1],!0,!0)),r&&null!=te&&t.preventDefault(),r&&null!=te&&e.nodeIsDraggable(te))if(p){ee=e.dragData.touchDragEles;var re=!e.dragData.didDrag;re&&l(ee,{inDragLayer:!0}),e.dragData.didDrag=!0;var ie={x:0,y:0};if(y(g[0])&&y(g[1]))if(ie.x+=g[0],ie.y+=g[1],re)e.redrawHint("eles",!0),(ae=e.touchData.dragDelta)&&y(ae[0])&&y(ae[1])&&(ie.x+=ae[0],ie.y+=ae[1]);e.hoverData.draggingEles=!0,ee.silentShift(ie).emit("position drag"),e.redrawHint("drag",!0),e.touchData.startPosition[0]==u[0]&&e.touchData.startPosition[1]==u[1]&&e.redrawHint("eles",!0),e.redraw()}else{var ae;0===(ae=e.touchData.dragDelta=e.touchData.dragDelta||[]).length?(ae.push(g[0]),ae.push(g[1])):(ae[0]+=g[0],ae[1]+=g[1])}if(n(te||F,["touchmove","tapdrag","vmousemove"],t,{x:s[0],y:s[1]}),te&&te.grabbed()||F==ne||(ne&&ne.emit({originalEvent:t,type:"tapdragout",position:{x:s[0],y:s[1]}}),F&&F.emit({originalEvent:t,type:"tapdragover",position:{x:s[0],y:s[1]}})),e.touchData.last=F,r)for(q=0;q<s.length;q++)s[q]&&e.touchData.startPosition[q]&&p&&(e.touchData.singleTouchMoved=!0);if(r&&(null==te||te.pannable())&&o.panningEnabled()&&o.userPanningEnabled()){i(te,e.touchData.starts)&&(t.preventDefault(),e.data.bgActivePosistion||(e.data.bgActivePosistion=nt(e.touchData.startPosition)),e.swipePanning?(o.panBy({x:g[0]*d,y:g[1]*d}),o.emit("dragpan")):p&&(e.swipePanning=!0,o.panBy({x:S*d,y:B*d}),o.emit("dragpan"),te&&(te.unactivate(),e.redrawHint("select",!0),e.touchData.start=null)));h=e.projectIntoViewport(t.touches[0].clientX,t.touches[0].clientY);s[0]=h[0],s[1]=h[1]}}for(v=0;v<s.length;v++)u[v]=s[v];r&&t.touches.length>0&&!e.hoverData.draggingEles&&!e.swipePanning&&null!=e.data.bgActivePosistion&&(e.data.bgActivePosistion=void 0,e.redrawHint("select",!0),e.redraw())}},!1),e.registerBinding(window,"touchcancel",L=function(t){var n=e.touchData.start;e.touchData.capture=!1,n&&n.unactivate()}),e.registerBinding(window,"touchend",A=function(r){var i=e.touchData.start;if(e.touchData.capture){0===r.touches.length&&(e.touchData.capture=!1),r.preventDefault();var a=e.selection;e.swipePanning=!1,e.hoverData.draggingEles=!1;var o,s=e.cy,l=s.zoom(),u=e.touchData.now,d=e.touchData.earlier;if(r.touches[0]){var h=e.projectIntoViewport(r.touches[0].clientX,r.touches[0].clientY);u[0]=h[0],u[1]=h[1]}if(r.touches[1]){h=e.projectIntoViewport(r.touches[1].clientX,r.touches[1].clientY);u[2]=h[0],u[3]=h[1]}if(r.touches[2]){h=e.projectIntoViewport(r.touches[2].clientX,r.touches[2].clientY);u[4]=h[0],u[5]=h[1]}if(i&&i.unactivate(),e.touchData.cxt){if(o={originalEvent:r,type:"cxttapend",position:{x:u[0],y:u[1]}},i?i.emit(o):s.emit(o),!e.touchData.cxtDragged){var p={originalEvent:r,type:"cxttap",position:{x:u[0],y:u[1]}};i?i.emit(p):s.emit(p)}return e.touchData.start&&(e.touchData.start._private.grabbed=!1),e.touchData.cxt=!1,e.touchData.start=null,void e.redraw()}if(!r.touches[2]&&s.boxSelectionEnabled()&&e.touchData.selecting){e.touchData.selecting=!1;var f=s.collection(e.getAllInBox(a[0],a[1],a[2],a[3]));a[0]=void 0,a[1]=void 0,a[2]=void 0,a[3]=void 0,a[4]=0,e.redrawHint("select",!0),s.emit({type:"boxend",originalEvent:r,position:{x:u[0],y:u[1]}});f.emit("box").stdFilter((function(e){return e.selectable()&&!e.selected()})).select().emit("boxselect"),f.nonempty()&&e.redrawHint("eles",!0),e.redraw()}if(null!=i&&i.unactivate(),r.touches[2])e.data.bgActivePosistion=void 0,e.redrawHint("select",!0);else if(r.touches[1]);else if(r.touches[0]);else if(!r.touches[0]){e.data.bgActivePosistion=void 0,e.redrawHint("select",!0);var g=e.dragData.touchDragEles;if(null!=i){var v=i._private.grabbed;c(g),e.redrawHint("drag",!0),e.redrawHint("eles",!0),v&&(i.emit("freeon"),g.emit("free"),e.dragData.didDrag&&(i.emit("dragfreeon"),g.emit("dragfree"))),n(i,["touchend","tapend","vmouseup","tapdragout"],r,{x:u[0],y:u[1]}),i.unactivate(),e.touchData.start=null}else{var y=e.findNearestElement(u[0],u[1],!0,!0);n(y,["touchend","tapend","vmouseup","tapdragout"],r,{x:u[0],y:u[1]})}var m=e.touchData.startPosition[0]-u[0],b=m*m,x=e.touchData.startPosition[1]-u[1],w=(b+x*x)*l*l;e.touchData.singleTouchMoved||(i||s.$(":selected").unselect(["tapunselect"]),n(i,["tap","vclick"],r,{x:u[0],y:u[1]})),null!=i&&!e.dragData.didDrag&&i._private.selectable&&w<e.touchTapThreshold2&&!e.pinching&&("single"===s.selectionType()?(s.$(t).unmerge(i).unselect(["tapunselect"]),i.select(["tapselect"])):i.selected()?i.unselect(["tapunselect"]):i.select(["tapselect"]),e.redrawHint("eles",!0)),e.touchData.singleTouchMoved=!0}for(var E=0;E<u.length;E++)d[E]=u[E];e.dragData.didDrag=!1,0===r.touches.length&&(e.touchData.dragDelta=[],e.touchData.startPosition=null,e.touchData.startGPosition=null,e.touchData.didSelect=!1),r.touches.length<2&&(1===r.touches.length&&(e.touchData.startGPosition=[r.touches[0].clientX,r.touches[0].clientY]),e.pinching=!1,e.redrawHint("eles",!0),e.redraw())}},!1),"undefined"==typeof TouchEvent){var V=[],F=function(e){return{clientX:e.clientX,clientY:e.clientY,force:1,identifier:e.pointerId,pageX:e.pageX,pageY:e.pageY,radiusX:e.width/2,radiusY:e.height/2,screenX:e.screenX,screenY:e.screenY,target:e.target}},q=function(e){V.push(function(e){return{event:e,touch:F(e)}}(e))},j=function(e){for(var t=0;t<V.length;t++){if(V[t].event.pointerId===e.pointerId)return void V.splice(t,1)}},Y=function(e){e.touches=V.map((function(e){return e.touch}))},X=function(e){return"mouse"===e.pointerType||4===e.pointerType};e.registerBinding(e.container,"pointerdown",(function(e){X(e)||(e.preventDefault(),q(e),Y(e),I(e))})),e.registerBinding(e.container,"pointerup",(function(e){X(e)||(j(e),Y(e),A(e))})),e.registerBinding(e.container,"pointercancel",(function(e){X(e)||(j(e),Y(e),L())})),e.registerBinding(e.container,"pointermove",(function(e){X(e)||(e.preventDefault(),function(e){var t=V.filter((function(t){return t.event.pointerId===e.pointerId}))[0];t.event=e,t.touch=F(e)}(e),Y(e),z(e))}))}};var is={generatePolygon:function(e,t){return this.nodeShapes[e]={renderer:this,name:e,points:t,draw:function(e,t,n,r,i){this.renderer.nodeShapeImpl("polygon",e,t,n,r,i,this.points)},intersectLine:function(e,t,n,r,i,a,o){return It(i,a,this.points,e,t,n/2,r/2,o)},checkPoint:function(e,t,n,r,i,a,o){return Pt(e,t,this.points,a,o,r,i,[0,-1],n)}}}};is.generateEllipse=function(){return this.nodeShapes.ellipse={renderer:this,name:"ellipse",draw:function(e,t,n,r,i){this.renderer.nodeShapeImpl(this.name,e,t,n,r,i)},intersectLine:function(e,t,n,r,i,a,o){return function(e,t,n,r,i,a){var o=n-e,s=r-t;o/=i,s/=a;var l=Math.sqrt(o*o+s*s),u=l-1;if(u<0)return[];var c=u/l;return[(n-e)*c+e,(r-t)*c+t]}(i,a,e,t,n/2+o,r/2+o)},checkPoint:function(e,t,n,r,i,a,o){return Mt(e,t,r,i,a,o,n)}}},is.generateRoundPolygon=function(e,t){for(var n=new Array(2*t.length),r=0;r<t.length/2;r++){var i=2*r,a=void 0;a=r<t.length/2-1?2*(r+1):0,n[4*r]=t[i],n[4*r+1]=t[i+1];var o=t[a]-t[i],s=t[a+1]-t[i+1],l=Math.sqrt(o*o+s*s);n[4*r+2]=o/l,n[4*r+3]=s/l}return this.nodeShapes[e]={renderer:this,name:e,points:n,draw:function(e,t,n,r,i){this.renderer.nodeShapeImpl("round-polygon",e,t,n,r,i,this.points)},intersectLine:function(e,t,n,r,i,a,o){return function(e,t,n,r,i,a,o,s){for(var l,u=[],c=new Array(n.length),d=a/2,h=o/2,p=Vt(a,o),f=0;f<n.length/4;f++){var g,v=void 0;v=0===f?n.length-2:4*f-2,g=4*f+2;var y=r+d*n[4*f],m=i+h*n[4*f+1],b=-n[v]*n[g]-n[v+1]*n[g+1],x=p/Math.tan(Math.acos(b)/2),w=y-x*n[v],E=m-x*n[v+1],k=y+x*n[g],C=m+x*n[g+1];0===f?(c[n.length-2]=w,c[n.length-1]=E):(c[4*f-2]=w,c[4*f-1]=E),c[4*f]=k,c[4*f+1]=C;var S=n[v+1],P=-n[v];S*n[g]+P*n[g+1]<0&&(S*=-1,P*=-1),0!==(l=Bt(e,t,r,i,w+S*p,E+P*p,p)).length&&u.push(l[0],l[1])}for(var D=0;D<c.length/4;D++)0!==(l=Nt(e,t,r,i,c[4*D],c[4*D+1],c[4*D+2],c[4*D+3],!1)).length&&u.push(l[0],l[1]);if(u.length>2){for(var T=[u[0],u[1]],M=Math.pow(T[0]-e,2)+Math.pow(T[1]-t,2),B=1;B<u.length/2;B++){var _=Math.pow(u[2*B]-e,2)+Math.pow(u[2*B+1]-t,2);_<=M&&(T[0]=u[2*B],T[1]=u[2*B+1],M=_)}return T}return u}(i,a,this.points,e,t,n,r)},checkPoint:function(e,t,n,r,i,a,o){return function(e,t,n,r,i,a,o){for(var s=new Array(n.length),l=a/2,u=o/2,c=Vt(a,o),d=c*c,h=0;h<n.length/4;h++){var p,f=void 0;f=0===h?n.length-2:4*h-2,p=4*h+2;var g=r+l*n[4*h],v=i+u*n[4*h+1],y=-n[f]*n[p]-n[f+1]*n[p+1],m=c/Math.tan(Math.acos(y)/2),b=g-m*n[f],x=v-m*n[f+1],w=g+m*n[p],E=v+m*n[p+1];s[4*h]=b,s[4*h+1]=x,s[4*h+2]=w,s[4*h+3]=E;var k=n[f+1],C=-n[f];k*n[p]+C*n[p+1]<0&&(k*=-1,C*=-1);var S=b+k*c,P=x+C*c;if(Math.pow(S-e,2)+Math.pow(P-t,2)<=d)return!0}return St(e,t,s)}(e,t,this.points,a,o,r,i)}}},is.generateRoundRectangle=function(){return this.nodeShapes["round-rectangle"]=this.nodeShapes.roundrectangle={renderer:this,name:"round-rectangle",points:Lt(4,0),draw:function(e,t,n,r,i){this.renderer.nodeShapeImpl(this.name,e,t,n,r,i)},intersectLine:function(e,t,n,r,i,a,o){return xt(i,a,e,t,n,r,o)},checkPoint:function(e,t,n,r,i,a,o){var s=Rt(r,i),l=2*s;return!!Pt(e,t,this.points,a,o,r,i-l,[0,-1],n)||(!!Pt(e,t,this.points,a,o,r-l,i,[0,-1],n)||(!!Mt(e,t,l,l,a-r/2+s,o-i/2+s,n)||(!!Mt(e,t,l,l,a+r/2-s,o-i/2+s,n)||(!!Mt(e,t,l,l,a+r/2-s,o+i/2-s,n)||!!Mt(e,t,l,l,a-r/2+s,o+i/2-s,n)))))}}},is.generateCutRectangle=function(){return this.nodeShapes["cut-rectangle"]=this.nodeShapes.cutrectangle={renderer:this,name:"cut-rectangle",cornerLength:8,points:Lt(4,0),draw:function(e,t,n,r,i){this.renderer.nodeShapeImpl(this.name,e,t,n,r,i)},generateCutTrianglePts:function(e,t,n,r){var i=this.cornerLength,a=t/2,o=e/2,s=n-o,l=n+o,u=r-a,c=r+a;return{topLeft:[s,u+i,s+i,u,s+i,u+i],topRight:[l-i,u,l,u+i,l-i,u+i],bottomRight:[l,c-i,l-i,c,l-i,c-i],bottomLeft:[s+i,c,s,c-i,s+i,c-i]}},intersectLine:function(e,t,n,r,i,a,o){var s=this.generateCutTrianglePts(n+2*o,r+2*o,e,t),l=[].concat.apply([],[s.topLeft.splice(0,4),s.topRight.splice(0,4),s.bottomRight.splice(0,4),s.bottomLeft.splice(0,4)]);return It(i,a,l,e,t)},checkPoint:function(e,t,n,r,i,a,o){if(Pt(e,t,this.points,a,o,r,i-2*this.cornerLength,[0,-1],n))return!0;if(Pt(e,t,this.points,a,o,r-2*this.cornerLength,i,[0,-1],n))return!0;var s=this.generateCutTrianglePts(r,i,a,o);return St(e,t,s.topLeft)||St(e,t,s.topRight)||St(e,t,s.bottomRight)||St(e,t,s.bottomLeft)}}},is.generateBarrel=function(){return this.nodeShapes.barrel={renderer:this,name:"barrel",points:Lt(4,0),draw:function(e,t,n,r,i){this.renderer.nodeShapeImpl(this.name,e,t,n,r,i)},intersectLine:function(e,t,n,r,i,a,o){var s=this.generateBarrelBezierPts(n+2*o,r+2*o,e,t),l=function(e){var t=ct({x:e[0],y:e[1]},{x:e[2],y:e[3]},{x:e[4],y:e[5]},.15),n=ct({x:e[0],y:e[1]},{x:e[2],y:e[3]},{x:e[4],y:e[5]},.5),r=ct({x:e[0],y:e[1]},{x:e[2],y:e[3]},{x:e[4],y:e[5]},.85);return[e[0],e[1],t.x,t.y,n.x,n.y,r.x,r.y,e[4],e[5]]},u=[].concat(l(s.topLeft),l(s.topRight),l(s.bottomRight),l(s.bottomLeft));return It(i,a,u,e,t)},generateBarrelBezierPts:function(e,t,n,r){var i=t/2,a=e/2,o=n-a,s=n+a,l=r-i,u=r+i,c=Ft(e,t),d=c.heightOffset,h=c.widthOffset,p=c.ctrlPtOffsetPct*e,f={topLeft:[o,l+d,o+p,l,o+h,l],topRight:[s-h,l,s-p,l,s,l+d],bottomRight:[s,u-d,s-p,u,s-h,u],bottomLeft:[o+h,u,o+p,u,o,u-d]};return f.topLeft.isTop=!0,f.topRight.isTop=!0,f.bottomLeft.isBottom=!0,f.bottomRight.isBottom=!0,f},checkPoint:function(e,t,n,r,i,a,o){var s=Ft(r,i),l=s.heightOffset,u=s.widthOffset;if(Pt(e,t,this.points,a,o,r,i-2*l,[0,-1],n))return!0;if(Pt(e,t,this.points,a,o,r-2*u,i,[0,-1],n))return!0;for(var c=this.generateBarrelBezierPts(r,i,a,o),d=function(e,t,n){var r,i,a=n[4],o=n[2],s=n[0],l=n[5],u=n[1],c=Math.min(a,s),d=Math.max(a,s),h=Math.min(l,u),p=Math.max(l,u);if(c<=e&&e<=d&&h<=t&&t<=p){var f=[(r=a)-2*(i=o)+s,2*(i-r),r],g=function(e,t,n,r){var i=t*t-4*e*(n-=r);if(i<0)return[];var a=Math.sqrt(i),o=2*e;return[(-t+a)/o,(-t-a)/o]}(f[0],f[1],f[2],e).filter((function(e){return 0<=e&&e<=1}));if(g.length>0)return g[0]}return null},h=Object.keys(c),p=0;p<h.length;p++){var f=c[h[p]],g=d(e,t,f);if(null!=g){var v=f[5],y=f[3],m=f[1],b=ut(v,y,m,g);if(f.isTop&&b<=t)return!0;if(f.isBottom&&t<=b)return!0}}return!1}}},is.generateBottomRoundrectangle=function(){return this.nodeShapes["bottom-round-rectangle"]=this.nodeShapes.bottomroundrectangle={renderer:this,name:"bottom-round-rectangle",points:Lt(4,0),draw:function(e,t,n,r,i){this.renderer.nodeShapeImpl(this.name,e,t,n,r,i)},intersectLine:function(e,t,n,r,i,a,o){var s=t-(r/2+o),l=Nt(i,a,e,t,e-(n/2+o),s,e+(n/2+o),s,!1);return l.length>0?l:xt(i,a,e,t,n,r,o)},checkPoint:function(e,t,n,r,i,a,o){var s=Rt(r,i),l=2*s;if(Pt(e,t,this.points,a,o,r,i-l,[0,-1],n))return!0;if(Pt(e,t,this.points,a,o,r-l,i,[0,-1],n))return!0;var u=r/2+2*n,c=i/2+2*n;return!!St(e,t,[a-u,o-c,a-u,o,a+u,o,a+u,o-c])||(!!Mt(e,t,l,l,a+r/2-s,o+i/2-s,n)||!!Mt(e,t,l,l,a-r/2+s,o+i/2-s,n))}}},is.registerNodeShapes=function(){var e=this.nodeShapes={},t=this;this.generateEllipse(),this.generatePolygon("triangle",Lt(3,0)),this.generateRoundPolygon("round-triangle",Lt(3,0)),this.generatePolygon("rectangle",Lt(4,0)),e.square=e.rectangle,this.generateRoundRectangle(),this.generateCutRectangle(),this.generateBarrel(),this.generateBottomRoundrectangle();var n=[0,1,1,0,0,-1,-1,0];this.generatePolygon("diamond",n),this.generateRoundPolygon("round-diamond",n),this.generatePolygon("pentagon",Lt(5,0)),this.generateRoundPolygon("round-pentagon",Lt(5,0)),this.generatePolygon("hexagon",Lt(6,0)),this.generateRoundPolygon("round-hexagon",Lt(6,0)),this.generatePolygon("heptagon",Lt(7,0)),this.generateRoundPolygon("round-heptagon",Lt(7,0)),this.generatePolygon("octagon",Lt(8,0)),this.generateRoundPolygon("round-octagon",Lt(8,0));var r=new Array(20),i=Ot(5,0),a=Ot(5,Math.PI/5),o=.5*(3-Math.sqrt(5));o*=1.57;for(var s=0;s<a.length/2;s++)a[2*s]*=o,a[2*s+1]*=o;for(s=0;s<5;s++)r[4*s]=i[2*s],r[4*s+1]=i[2*s+1],r[4*s+2]=a[2*s],r[4*s+3]=a[2*s+1];r=At(r),this.generatePolygon("star",r),this.generatePolygon("vee",[-1,-1,0,-.333,1,-1,0,1]),this.generatePolygon("rhomboid",[-1,-1,.333,-1,1,1,-.333,1]),this.nodeShapes.concavehexagon=this.generatePolygon("concave-hexagon",[-1,-.95,-.75,0,-1,.95,1,.95,.75,0,1,-.95]);var l=[-1,-1,.25,-1,1,0,.25,1,-1,1];this.generatePolygon("tag",l),this.generateRoundPolygon("round-tag",l),e.makePolygon=function(e){var n,r="polygon-"+e.join("$");return(n=this[r])?n:t.generatePolygon(r,e)}};var as={timeToRender:function(){return this.redrawTotalTime/this.redrawCount},redraw:function(e){e=e||Te();var t=this;void 0===t.averageRedrawTime&&(t.averageRedrawTime=0),void 0===t.lastRedrawTime&&(t.lastRedrawTime=0),void 0===t.lastDrawTime&&(t.lastDrawTime=0),t.requestedFrame=!0,t.renderOptions=e},beforeRender:function(e,t){if(!this.destroyed){null==t&&Ee("Priority is not optional for beforeRender");var n=this.beforeRenderCallbacks;n.push({fn:e,priority:t}),n.sort((function(e,t){return t.priority-e.priority}))}}},os=function(e,t,n){for(var r=e.beforeRenderCallbacks,i=0;i<r.length;i++)r[i].fn(t,n)};as.startRenderLoop=function(){var e=this,t=e.cy;if(!e.renderLoopStarted){e.renderLoopStarted=!0;re((function n(r){if(!e.destroyed){if(t.batching());else if(e.requestedFrame&&!e.skipFrame){os(e,!0,r);var i=ie();e.render(e.renderOptions);var a=e.lastDrawTime=ie();void 0===e.averageRedrawTime&&(e.averageRedrawTime=a-i),void 0===e.redrawCount&&(e.redrawCount=0),e.redrawCount++,void 0===e.redrawTotalTime&&(e.redrawTotalTime=0);var o=a-i;e.redrawTotalTime+=o,e.lastRedrawTime=o,e.averageRedrawTime=e.averageRedrawTime/2+o/2,e.requestedFrame=!1}else os(e,!1,r);e.skipFrame=!1,re(n)}}))}};var ss=function(e){this.init(e)},ls=ss.prototype;ls.clientFunctions=["redrawHint","render","renderTo","matchCanvasSize","nodeShapeImpl","arrowShapeImpl"],ls.init=function(e){var t=this;t.options=e,t.cy=e.cy;var n=t.container=e.cy.container();if(o){var r=o.document,i=r.head,a="__________cytoscape_container",s=null!=r.getElementById("__________cytoscape_stylesheet");if(n.className.indexOf(a)<0&&(n.className=(n.className||"")+" "+a),!s){var l=r.createElement("style");l.id="__________cytoscape_stylesheet",l.innerHTML="."+a+" { position: relative; }",i.insertBefore(l,i.children[0])}"static"===o.getComputedStyle(n).getPropertyValue("position")&&Ce("A Cytoscape container has style position:static and so can not use UI extensions properly")}t.selection=[void 0,void 0,void 0,void 0,0],t.bezierProjPcts=[.05,.225,.4,.5,.6,.775,.95],t.hoverData={down:null,last:null,downTime:null,triggerMode:null,dragging:!1,initialPan:[null,null],capture:!1},t.dragData={possibleDragElements:[]},t.touchData={start:null,capture:!1,startPosition:[null,null,null,null,null,null],singleTouchStartTime:null,singleTouchMoved:!0,now:[null,null,null,null,null,null],earlier:[null,null,null,null,null,null]},t.redraws=0,t.showFps=e.showFps,t.debug=e.debug,t.hideEdgesOnViewport=e.hideEdgesOnViewport,t.textureOnViewport=e.textureOnViewport,t.wheelSensitivity=e.wheelSensitivity,t.motionBlurEnabled=e.motionBlur,t.forcedPixelRatio=y(e.pixelRatio)?e.pixelRatio:null,t.motionBlur=e.motionBlur,t.motionBlurOpacity=e.motionBlurOpacity,t.motionBlurTransparency=1-t.motionBlurOpacity,t.motionBlurPxRatio=1,t.mbPxRBlurry=1,t.minMbLowQualFrames=4,t.fullQualityMb=!1,t.clearedForMotionBlur=[],t.desktopTapThreshold=e.desktopTapThreshold,t.desktopTapThreshold2=e.desktopTapThreshold*e.desktopTapThreshold,t.touchTapThreshold=e.touchTapThreshold,t.touchTapThreshold2=e.touchTapThreshold*e.touchTapThreshold,t.tapholdDuration=500,t.bindings=[],t.beforeRenderCallbacks=[],t.beforeRenderPriorities={animations:400,eleCalcs:300,eleTxrDeq:200,lyrTxrDeq:150,lyrTxrSkip:100},t.registerNodeShapes(),t.registerArrowShapes(),t.registerCalculationListeners()},ls.notify=function(e,t){var n=this,r=n.cy;this.destroyed||("init"!==e?"destroy"!==e?(("add"===e||"remove"===e||"move"===e&&r.hasCompoundNodes()||"load"===e||"zorder"===e||"mount"===e)&&n.invalidateCachedZSortedEles(),"viewport"===e&&n.redrawHint("select",!0),"load"!==e&&"resize"!==e&&"mount"!==e||(n.invalidateContainerClientCoordsCache(),n.matchCanvasSize(n.container)),n.redrawHint("eles",!0),n.redrawHint("drag",!0),this.startRenderLoop(),this.redraw()):n.destroy():n.load())},ls.destroy=function(){var e=this;e.destroyed=!0,e.cy.stopAnimationLoop();for(var t=0;t<e.bindings.length;t++){var n=e.bindings[t],r=n.target;(r.off||r.removeEventListener).apply(r,n.args)}if(e.bindings=[],e.beforeRenderCallbacks=[],e.onUpdateEleCalcsFns=[],e.removeObserver&&e.removeObserver.disconnect(),e.styleObserver&&e.styleObserver.disconnect(),e.resizeObserver&&e.resizeObserver.disconnect(),e.labelCalcDiv)try{document.body.removeChild(e.labelCalcDiv)}catch(e){}},ls.isHeadless=function(){return!1},[Fo,ts,ns,rs,is,as].forEach((function(e){I(ls,e)}));var us=function(e){return function(){var t=this,n=this.renderer;if(!t.dequeueingSetup){t.dequeueingSetup=!0;var r=J((function(){n.redrawHint("eles",!0),n.redrawHint("drag",!0),n.redraw()}),e.deqRedrawThreshold),i=e.priority||we;n.beforeRender((function(i,a){var o=ie(),s=n.averageRedrawTime,l=n.lastRedrawTime,u=[],c=n.cy.extent(),d=n.getPixelRatio();for(i||n.flushRenderedStyleQueue();;){var h=ie(),p=h-o,f=h-a;if(l<1e3/60){var g=1e3/60-(i?s:0);if(f>=e.deqFastCost*g)break}else if(i){if(p>=e.deqCost*l||p>=e.deqAvgCost*s)break}else if(f>=e.deqNoDrawCost*(1e3/60))break;var v=e.deq(t,d,c);if(!(v.length>0))break;for(var y=0;y<v.length;y++)u.push(v[y])}u.length>0&&(e.onDeqd(t,u),!i&&e.shouldRedraw(t,u,d,c)&&r())}),i(t))}}},cs=function(){function e(n){var r=arguments.length>1&&void 0!==arguments[1]?arguments[1]:be;t(this,e),this.idsByKey=new ze,this.keyForId=new ze,this.cachesByLvl=new ze,this.lvls=[],this.getKey=n,this.doesEleInvalidateKey=r}return r(e,[{key:"getIdsFor",value:function(e){null==e&&Ee("Can not get id list for null key");var t=this.idsByKey,n=this.idsByKey.get(e);return n||(n=new Ae,t.set(e,n)),n}},{key:"addIdForKey",value:function(e,t){null!=e&&this.getIdsFor(e).add(t)}},{key:"deleteIdForKey",value:function(e,t){null!=e&&this.getIdsFor(e).delete(t)}},{key:"getNumberOfIdsForKey",value:function(e){return null==e?0:this.getIdsFor(e).size}},{key:"updateKeyMappingFor",value:function(e){var t=e.id(),n=this.keyForId.get(t),r=this.getKey(e);this.deleteIdForKey(n,t),this.addIdForKey(r,t),this.keyForId.set(t,r)}},{key:"deleteKeyMappingFor",value:function(e){var t=e.id(),n=this.keyForId.get(t);this.deleteIdForKey(n,t),this.keyForId.delete(t)}},{key:"keyHasChangedFor",value:function(e){var t=e.id();return this.keyForId.get(t)!==this.getKey(e)}},{key:"isInvalid",value:function(e){return this.keyHasChangedFor(e)||this.doesEleInvalidateKey(e)}},{key:"getCachesAt",value:function(e){var t=this.cachesByLvl,n=this.lvls,r=t.get(e);return r||(r=new ze,t.set(e,r),n.push(e)),r}},{key:"getCache",value:function(e,t){return this.getCachesAt(t).get(e)}},{key:"get",value:function(e,t){var n=this.getKey(e),r=this.getCache(n,t);return null!=r&&this.updateKeyMappingFor(e),r}},{key:"getForCachedKey",value:function(e,t){var n=this.keyForId.get(e.id());return this.getCache(n,t)}},{key:"hasCache",value:function(e,t){return this.getCachesAt(t).has(e)}},{key:"has",value:function(e,t){var n=this.getKey(e);return this.hasCache(n,t)}},{key:"setCache",value:function(e,t,n){n.key=e,this.getCachesAt(t).set(e,n)}},{key:"set",value:function(e,t,n){var r=this.getKey(e);this.setCache(r,t,n),this.updateKeyMappingFor(e)}},{key:"deleteCache",value:function(e,t){this.getCachesAt(t).delete(e)}},{key:"delete",value:function(e,t){var n=this.getKey(e);this.deleteCache(n,t)}},{key:"invalidateKey",value:function(e){var t=this;this.lvls.forEach((function(n){return t.deleteCache(e,n)}))}},{key:"invalidate",value:function(e){var t=e.id(),n=this.keyForId.get(t);this.deleteKeyMappingFor(e);var r=this.doesEleInvalidateKey(e);return r&&this.invalidateKey(n),r||0===this.getNumberOfIdsForKey(n)}}]),e}(),ds={dequeue:"dequeue",downscale:"downscale",highQuality:"highQuality"},hs=Me({getKey:null,doesEleInvalidateKey:be,drawElement:null,getBoundingBox:null,getRotationPoint:null,getRotationOffset:null,isVisible:me,allowEdgeTxrCaching:!0,allowParentTxrCaching:!0}),ps=function(e,t){this.renderer=e,this.onDequeues=[];var n=hs(t);I(this,n),this.lookup=new cs(n.getKey,n.doesEleInvalidateKey),this.setupDequeueing()},fs=ps.prototype;fs.reasons=ds,fs.getTextureQueue=function(e){return this.eleImgCaches=this.eleImgCaches||{},this.eleImgCaches[e]=this.eleImgCaches[e]||[]},fs.getRetiredTextureQueue=function(e){var t=this.eleImgCaches.retired=this.eleImgCaches.retired||{};return t[e]=t[e]||[]},fs.getElementQueue=function(){return this.eleCacheQueue=this.eleCacheQueue||new Fe((function(e,t){return t.reqs-e.reqs}))},fs.getElementKeyToQueue=function(){return this.eleKeyToCacheQueue=this.eleKeyToCacheQueue||{}},fs.getElement=function(e,t,n,r,i){var a=this,o=this.renderer,s=o.cy.zoom(),l=this.lookup;if(!t||0===t.w||0===t.h||isNaN(t.w)||isNaN(t.h)||!e.visible()||e.removed())return null;if(!a.allowEdgeTxrCaching&&e.isEdge()||!a.allowParentTxrCaching&&e.isParent())return null;if(null==r&&(r=Math.ceil(it(s*n))),r<-4)r=-4;else if(s>=7.99||r>3)return null;var u=Math.pow(2,r),c=t.h*u,d=t.w*u,h=o.eleTextBiggerThanMin(e,u);if(!this.isVisible(e,h))return null;var p,f=l.get(e,r);if(f&&f.invalidated&&(f.invalidated=!1,f.texture.invalidatedWidth-=f.width),f)return f;if(p=c<=25?25:c<=50?50:50*Math.ceil(c/50),c>1024||d>1024)return null;var g=a.getTextureQueue(p),v=g[g.length-2],y=function(){return a.recycleTexture(p,d)||a.addTexture(p,d)};v||(v=g[g.length-1]),v||(v=y()),v.width-v.usedWidth<d&&(v=y());for(var m,b=function(e){return e&&e.scaledLabelShown===h},x=i&&i===ds.dequeue,w=i&&i===ds.highQuality,E=i&&i===ds.downscale,k=r+1;k<=3;k++){var C=l.get(e,k);if(C){m=C;break}}var S=m&&m.level===r+1?m:null,P=function(){v.context.drawImage(S.texture.canvas,S.x,0,S.width,S.height,v.usedWidth,0,d,c)};if(v.context.setTransform(1,0,0,1,0,0),v.context.clearRect(v.usedWidth,0,d,p),b(S))P();else if(b(m)){if(!w)return a.queueElement(e,m.level-1),m;for(var D=m.level;D>r;D--)S=a.getElement(e,t,n,D,ds.downscale);P()}else{var T;if(!x&&!w&&!E)for(var M=r-1;M>=-4;M--){var B=l.get(e,M);if(B){T=B;break}}if(b(T))return a.queueElement(e,r),T;v.context.translate(v.usedWidth,0),v.context.scale(u,u),this.drawElement(v.context,e,t,h,!1),v.context.scale(1/u,1/u),v.context.translate(-v.usedWidth,0)}return f={x:v.usedWidth,texture:v,level:r,scale:u,width:d,height:c,scaledLabelShown:h},v.usedWidth+=Math.ceil(d+8),v.eleCaches.push(f),l.set(e,r,f),a.checkTextureFullness(v),f},fs.invalidateElements=function(e){for(var t=0;t<e.length;t++)this.invalidateElement(e[t])},fs.invalidateElement=function(e){var t=this.lookup,n=[];if(t.isInvalid(e)){for(var r=-4;r<=3;r++){var i=t.getForCachedKey(e,r);i&&n.push(i)}if(t.invalidate(e))for(var a=0;a<n.length;a++){var o=n[a],s=o.texture;s.invalidatedWidth+=o.width,o.invalidated=!0,this.checkTextureUtility(s)}this.removeFromQueue(e)}},fs.checkTextureUtility=function(e){e.invalidatedWidth>=.2*e.width&&this.retireTexture(e)},fs.checkTextureFullness=function(e){var t=this.getTextureQueue(e.height);e.usedWidth/e.width>.8&&e.fullnessChecks>=10?Be(t,e):e.fullnessChecks++},fs.retireTexture=function(e){var t=e.height,n=this.getTextureQueue(t),r=this.lookup;Be(n,e),e.retired=!0;for(var i=e.eleCaches,a=0;a<i.length;a++){var o=i[a];r.deleteCache(o.key,o.level)}_e(i),this.getRetiredTextureQueue(t).push(e)},fs.addTexture=function(e,t){var n={};return 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o=t.pop(),s=o.key,l=o.eles[0],u=i.hasCache(l,o.level);if(n[s]=null,!u){r.push(o);var c=this.getBoundingBox(l);this.getElement(l,c,e,o.level,ds.dequeue)}}return r},fs.removeFromQueue=function(e){var t=this.getElementQueue(),n=this.getElementKeyToQueue(),r=this.getKey(e),i=n[r];null!=i&&(1===i.eles.length?(i.reqs=ye,t.updateItem(i),t.pop(),n[r]=null):i.eles.unmerge(e))},fs.onDequeue=function(e){this.onDequeues.push(e)},fs.offDequeue=function(e){Be(this.onDequeues,e)},fs.setupDequeueing=us({deqRedrawThreshold:100,deqCost:.15,deqAvgCost:.1,deqNoDrawCost:.9,deqFastCost:.9,deq:function(e,t,n){return e.dequeue(t,n)},onDeqd:function(e,t){for(var n=0;n<e.onDequeues.length;n++){(0,e.onDequeues[n])(t)}},shouldRedraw:function(e,t,n,r){for(var i=0;i<t.length;i++)for(var a=t[i].eles,o=0;o<a.length;o++){var s=a[o].boundingBox();if(yt(s,r))return!0}return!1},priority:function(e){return e.renderer.beforeRenderPriorities.eleTxrDeq}});var gs=function(e){var 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0)},_setOptionDisabled:function(t){this._super(t),this.element.attr("aria-disabled",t),this._toggleClass(null,"ui-state-disabled",!!t),this._toggleClass(this.headers.add(this.headers.next()),null,"ui-state-disabled",!!t)},_keydown:function(e){if(!e.altKey&&!e.ctrlKey){var i=t.ui.keyCode,s=this.headers.length,n=this.headers.index(e.target),o=!1;switch(e.keyCode){case i.RIGHT:case i.DOWN:o=this.headers[(n+1)%s];break;case i.LEFT:case i.UP:o=this.headers[(n-1+s)%s];break;case i.SPACE:case i.ENTER:this._eventHandler(e);break;case i.HOME:o=this.headers[0];break;case i.END:o=this.headers[s-1]}o&&(t(e.target).attr("tabIndex",-1),t(o).attr("tabIndex",0),t(o).trigger("focus"),e.preventDefault())}},_panelKeyDown:function(e){e.keyCode===t.ui.keyCode.UP&&e.ctrlKey&&t(e.currentTarget).prev().trigger("focus")},refresh:function(){var e=this.options;this._processPanels(),e.active===!1&&e.collapsible===!0||!this.headers.length?(e.active=!1,this.active=t()):e.active===!1?this._activate(0):this.active.length&&!t.contains(this.element[0],this.active[0])?this.headers.length===this.headers.find(".ui-state-disabled").length?(e.active=!1,this.active=t()):this._activate(Math.max(0,e.active-1)):e.active=this.headers.index(this.active),this._destroyIcons(),this._refresh()},_processPanels:function(){var t=this.headers,e=this.panels;this.headers=this.element.find(this.options.header),this._addClass(this.headers,"ui-accordion-header ui-accordion-header-collapsed","ui-state-default"),this.panels=this.headers.next().filter(":not(.ui-accordion-content-active)").hide(),this._addClass(this.panels,"ui-accordion-content","ui-helper-reset ui-widget-content"),e&&(this._off(t.not(this.headers)),this._off(e.not(this.panels)))},_refresh:function(){var e,i=this.options,s=i.heightStyle,n=this.element.parent();this.active=this._findActive(i.active),this._addClass(this.active,"ui-accordion-header-active","ui-state-active")._removeClass(this.active,"ui-accordion-header-collapsed"),this._addClass(this.active.next(),"ui-accordion-content-active"),this.active.next().show(),this.headers.attr("role","tab").each(function(){var e=t(this),i=e.uniqueId().attr("id"),s=e.next(),n=s.uniqueId().attr("id");e.attr("aria-controls",n),s.attr("aria-labelledby",i)}).next().attr("role","tabpanel"),this.headers.not(this.active).attr({"aria-selected":"false","aria-expanded":"false",tabIndex:-1}).next().attr({"aria-hidden":"true"}).hide(),this.active.length?this.active.attr({"aria-selected":"true","aria-expanded":"true",tabIndex:0}).next().attr({"aria-hidden":"false"}):this.headers.eq(0).attr("tabIndex",0),this._createIcons(),this._setupEvents(i.event),"fill"===s?(e=n.height(),this.element.siblings(":visible").each(function(){var 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t.ui.keyCode.ESCAPE:this.collapse(e);break;default:a=!1,s=this.previousFilter||"",o=!1,n=e.keyCode>=96&&105>=e.keyCode?""+(e.keyCode-96):String.fromCharCode(e.keyCode),clearTimeout(this.filterTimer),n===s?o=!0:n=s+n,i=this._filterMenuItems(n),i=o&&-1!==i.index(this.active.next())?this.active.nextAll(".ui-menu-item"):i,i.length||(n=String.fromCharCode(e.keyCode),i=this._filterMenuItems(n)),i.length?(this.focus(e,i),this.previousFilter=n,this.filterTimer=this._delay(function(){delete this.previousFilter},1e3)):delete this.previousFilter}a&&e.preventDefault()},_activate:function(t){this.active&&!this.active.is(".ui-state-disabled")&&(this.active.children("[aria-haspopup='true']").length?this.expand(t):this.select(t))},refresh:function(){var e,i,s,n,o,a=this,r=this.options.icons.submenu,h=this.element.find(this.options.menus);this._toggleClass("ui-menu-icons",null,!!this.element.find(".ui-icon").length),s=h.filter(":not(.ui-menu)").hide().attr({role:this.options.role,"aria-hidden":"true","aria-expanded":"false"}).each(function(){var e=t(this),i=e.prev(),s=t("<span>").data("ui-menu-submenu-caret",!0);a._addClass(s,"ui-menu-icon","ui-icon "+r),i.attr("aria-haspopup","true").prepend(s),e.attr("aria-labelledby",i.attr("id"))}),this._addClass(s,"ui-menu","ui-widget ui-widget-content ui-front"),e=h.add(this.element),i=e.find(this.options.items),i.not(".ui-menu-item").each(function(){var e=t(this);a._isDivider(e)&&a._addClass(e,"ui-menu-divider","ui-widget-content")}),n=i.not(".ui-menu-item, .ui-menu-divider"),o=n.children().not(".ui-menu").uniqueId().attr({tabIndex:-1,role:this._itemRole()}),this._addClass(n,"ui-menu-item")._addClass(o,"ui-menu-item-wrapper"),i.filter(".ui-state-disabled").attr("aria-disabled","true"),this.active&&!t.contains(this.element[0],this.active[0])&&this.blur()},_itemRole:function(){return{menu:"menuitem",listbox:"option"}[this.options.role]},_setOption:function(t,e){if("icons"===t){var i=this.element.find(".ui-menu-icon");this._removeClass(i,null,this.options.icons.submenu)._addClass(i,null,e.submenu)}this._super(t,e)},_setOptionDisabled:function(t){this._super(t),this.element.attr("aria-disabled",t+""),this._toggleClass(null,"ui-state-disabled",!!t)},focus:function(t,e){var i,s,n;this.blur(t,t&&"focus"===t.type),this._scrollIntoView(e),this.active=e.first(),s=this.active.children(".ui-menu-item-wrapper"),this._addClass(s,null,"ui-state-active"),this.options.role&&this.element.attr("aria-activedescendant",s.attr("id")),n=this.active.parent().closest(".ui-menu-item").children(".ui-menu-item-wrapper"),this._addClass(n,null,"ui-state-active"),t&&"keydown"===t.type?this._close():this.timer=this._delay(function(){this._close()},this.delay),i=e.children(".ui-menu"),i.length&&t&&/^mouse/.test(t.type)&&this._startOpening(i),this.activeMenu=e.parent(),this._trigger("focus",t,{item:e})},_scrollIntoView:function(e){var i,s,n,o,a,r;this._hasScroll()&&(i=parseFloat(t.css(this.activeMenu[0],"borderTopWidth"))||0,s=parseFloat(t.css(this.activeMenu[0],"paddingTop"))||0,n=e.offset().top-this.activeMenu.offset().top-i-s,o=this.activeMenu.scrollTop(),a=this.activeMenu.height(),r=e.outerHeight(),0>n?this.activeMenu.scrollTop(o+n):n+r>a&&this.activeMenu.scrollTop(o+n-a+r))},blur:function(t,e){e||clearTimeout(this.timer),this.active&&(this._removeClass(this.active.children(".ui-menu-item-wrapper"),null,"ui-state-active"),this._trigger("blur",t,{item:this.active}),this.active=null)},_startOpening:function(t){clearTimeout(this.timer),"true"===t.attr("aria-hidden")&&(this.timer=this._delay(function(){this._close(),this._open(t)},this.delay))},_open:function(e){var i=t.extend({of:this.active},this.options.position);clearTimeout(this.timer),this.element.find(".ui-menu").not(e.parents(".ui-menu")).hide().attr("aria-hidden","true"),e.show().removeAttr("aria-hidden").attr("aria-expanded","true").position(i)},collapseAll:function(e,i){clearTimeout(this.timer),this.timer=this._delay(function(){var s=i?this.element:t(e&&e.target).closest(this.element.find(".ui-menu"));s.length||(s=this.element),this._close(s),this.blur(e),this._removeClass(s.find(".ui-state-active"),null,"ui-state-active"),this.activeMenu=s},this.delay)},_close:function(t){t||(t=this.active?this.active.parent():this.element),t.find(".ui-menu").hide().attr("aria-hidden","true").attr("aria-expanded","false")},_closeOnDocumentClick:function(e){return!t(e.target).closest(".ui-menu").length},_isDivider:function(t){return!/[^\-\u2014\u2013\s]/.test(t.text())},collapse:function(t){var 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this.active?(this.isLastItem()||(this._hasScroll()?(s=this.active.offset().top,n=this.element.height(),this.active.nextAll(".ui-menu-item").each(function(){return i=t(this),0>i.offset().top-s-n}),this.focus(e,i)):this.focus(e,this.activeMenu.find(this.options.items)[this.active?"last":"first"]())),void 0):(this.next(e),void 0)},previousPage:function(e){var i,s,n;return this.active?(this.isFirstItem()||(this._hasScroll()?(s=this.active.offset().top,n=this.element.height(),this.active.prevAll(".ui-menu-item").each(function(){return i=t(this),i.offset().top-s+n>0}),this.focus(e,i)):this.focus(e,this.activeMenu.find(this.options.items).first())),void 0):(this.next(e),void 0)},_hasScroll:function(){return this.element.outerHeight()<this.element.prop("scrollHeight")},select:function(e){this.active=this.active||t(e.target).closest(".ui-menu-item");var i={item:this.active};this.active.has(".ui-menu").length||this.collapseAll(e,!0),this._trigger("select",e,i)},_filterMenuItems:function(e){var i=e.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g,"\\$&"),s=RegExp("^"+i,"i");return this.activeMenu.find(this.options.items).filter(".ui-menu-item").filter(function(){return s.test(t.trim(t(this).children(".ui-menu-item-wrapper").text()))})}}),t.widget("ui.autocomplete",{version:"1.12.1",defaultElement:"<input>",options:{appendTo:null,autoFocus:!1,delay:300,minLength:1,position:{my:"left top",at:"left bottom",collision:"none"},source:null,change:null,close:null,focus:null,open:null,response:null,search:null,select:null},requestIndex:0,pending:0,_create:function(){var e,i,s,n=this.element[0].nodeName.toLowerCase(),o="textarea"===n,a="input"===n;
+this.isMultiLine=o||!a&&this._isContentEditable(this.element),this.valueMethod=this.element[o||a?"val":"text"],this.isNewMenu=!0,this._addClass("ui-autocomplete-input"),this.element.attr("autocomplete","off"),this._on(this.element,{keydown:function(n){if(this.element.prop("readOnly"))return e=!0,s=!0,i=!0,void 0;e=!1,s=!1,i=!1;var o=t.ui.keyCode;switch(n.keyCode){case o.PAGE_UP:e=!0,this._move("previousPage",n);break;case o.PAGE_DOWN:e=!0,this._move("nextPage",n);break;case o.UP:e=!0,this._keyEvent("previous",n);break;case o.DOWN:e=!0,this._keyEvent("next",n);break;case o.ENTER:this.menu.active&&(e=!0,n.preventDefault(),this.menu.select(n));break;case o.TAB:this.menu.active&&this.menu.select(n);break;case o.ESCAPE:this.menu.element.is(":visible")&&(this.isMultiLine||this._value(this.term),this.close(n),n.preventDefault());break;default:i=!0,this._searchTimeout(n)}},keypress:function(s){if(e)return e=!1,(!this.isMultiLine||this.menu.element.is(":visible"))&&s.preventDefault(),void 0;if(!i){var n=t.ui.keyCode;switch(s.keyCode){case n.PAGE_UP:this._move("previousPage",s);break;case n.PAGE_DOWN:this._move("nextPage",s);break;case n.UP:this._keyEvent("previous",s);break;case n.DOWN:this._keyEvent("next",s)}}},input:function(t){return s?(s=!1,t.preventDefault(),void 0):(this._searchTimeout(t),void 0)},focus:function(){this.selectedItem=null,this.previous=this._value()},blur:function(t){return this.cancelBlur?(delete this.cancelBlur,void 0):(clearTimeout(this.searching),this.close(t),this._change(t),void 0)}}),this._initSource(),this.menu=t("<ul>").appendTo(this._appendTo()).menu({role:null}).hide().menu("instance"),this._addClass(this.menu.element,"ui-autocomplete","ui-front"),this._on(this.menu.element,{mousedown:function(e){e.preventDefault(),this.cancelBlur=!0,this._delay(function(){delete this.cancelBlur,this.element[0]!==t.ui.safeActiveElement(this.document[0])&&this.element.trigger("focus")})},menufocus:function(e,i){var s,n;return this.isNewMenu&&(this.isNewMenu=!1,e.originalEvent&&/^mouse/.test(e.originalEvent.type))?(this.menu.blur(),this.document.one("mousemove",function(){t(e.target).trigger(e.originalEvent)}),void 0):(n=i.item.data("ui-autocomplete-item"),!1!==this._trigger("focus",e,{item:n})&&e.originalEvent&&/^key/.test(e.originalEvent.type)&&this._value(n.value),s=i.item.attr("aria-label")||n.value,s&&t.trim(s).length&&(this.liveRegion.children().hide(),t("<div>").text(s).appendTo(this.liveRegion)),void 0)},menuselect:function(e,i){var s=i.item.data("ui-autocomplete-item"),n=this.previous;this.element[0]!==t.ui.safeActiveElement(this.document[0])&&(this.element.trigger("focus"),this.previous=n,this._delay(function(){this.previous=n,this.selectedItem=s})),!1!==this._trigger("select",e,{item:s})&&this._value(s.value),this.term=this._value(),this.close(e),this.selectedItem=s}}),this.liveRegion=t("<div>",{role:"status","aria-live":"assertive","aria-relevant":"additions"}).appendTo(this.document[0].body),this._addClass(this.liveRegion,null,"ui-helper-hidden-accessible"),this._on(this.window,{beforeunload:function(){this.element.removeAttr("autocomplete")}})},_destroy:function(){clearTimeout(this.searching),this.element.removeAttr("autocomplete"),this.menu.element.remove(),this.liveRegion.remove()},_setOption:function(t,e){this._super(t,e),"source"===t&&this._initSource(),"appendTo"===t&&this.menu.element.appendTo(this._appendTo()),"disabled"===t&&e&&this.xhr&&this.xhr.abort()},_isEventTargetInWidget:function(e){var i=this.menu.element[0];return e.target===this.element[0]||e.target===i||t.contains(i,e.target)},_closeOnClickOutside:function(t){this._isEventTargetInWidget(t)||this.close()},_appendTo:function(){var e=this.options.appendTo;return e&&(e=e.jquery||e.nodeType?t(e):this.document.find(e).eq(0)),e&&e[0]||(e=this.element.closest(".ui-front, dialog")),e.length||(e=this.document[0].body),e},_initSource:function(){var e,i,s=this;t.isArray(this.options.source)?(e=this.options.source,this.source=function(i,s){s(t.ui.autocomplete.filter(e,i.term))}):"string"==typeof this.options.source?(i=this.options.source,this.source=function(e,n){s.xhr&&s.xhr.abort(),s.xhr=t.ajax({url:i,data:e,dataType:"json",success:function(t){n(t)},error:function(){n([])}})}):this.source=this.options.source},_searchTimeout:function(t){clearTimeout(this.searching),this.searching=this._delay(function(){var e=this.term===this._value(),i=this.menu.element.is(":visible"),s=t.altKey||t.ctrlKey||t.metaKey||t.shiftKey;(!e||e&&!i&&!s)&&(this.selectedItem=null,this.search(null,t))},this.options.delay)},search:function(t,e){return t=null!=t?t:this._value(),this.term=this._value(),t.length<this.options.minLength?this.close(e):this._trigger("search",e)!==!1?this._search(t):void 0},_search:function(t){this.pending++,this._addClass("ui-autocomplete-loading"),this.cancelSearch=!1,this.source({term:t},this._response())},_response:function(){var e=++this.requestIndex;return t.proxy(function(t){e===this.requestIndex&&this.__response(t),this.pending--,this.pending||this._removeClass("ui-autocomplete-loading")},this)},__response:function(t){t&&(t=this._normalize(t)),this._trigger("response",null,{content:t}),!this.options.disabled&&t&&t.length&&!this.cancelSearch?(this._suggest(t),this._trigger("open")):this._close()},close:function(t){this.cancelSearch=!0,this._close(t)},_close:function(t){this._off(this.document,"mousedown"),this.menu.element.is(":visible")&&(this.menu.element.hide(),this.menu.blur(),this.isNewMenu=!0,this._trigger("close",t))},_change:function(t){this.previous!==this._value()&&this._trigger("change",t,{item:this.selectedItem})},_normalize:function(e){return e.length&&e[0].label&&e[0].value?e:t.map(e,function(e){return"string"==typeof e?{label:e,value:e}:t.extend({},e,{label:e.label||e.value,value:e.value||e.label})})},_suggest:function(e){var i=this.menu.element.empty();this._renderMenu(i,e),this.isNewMenu=!0,this.menu.refresh(),i.show(),this._resizeMenu(),i.position(t.extend({of:this.element},this.options.position)),this.options.autoFocus&&this.menu.next(),this._on(this.document,{mousedown:"_closeOnClickOutside"})},_resizeMenu:function(){var t=this.menu.element;t.outerWidth(Math.max(t.width("").outerWidth()+1,this.element.outerWidth()))},_renderMenu:function(e,i){var s=this;t.each(i,function(t,i){s._renderItemData(e,i)})},_renderItemData:function(t,e){return this._renderItem(t,e).data("ui-autocomplete-item",e)},_renderItem:function(e,i){return t("<li>").append(t("<div>").text(i.label)).appendTo(e)},_move:function(t,e){return this.menu.element.is(":visible")?this.menu.isFirstItem()&&/^previous/.test(t)||this.menu.isLastItem()&&/^next/.test(t)?(this.isMultiLine||this._value(this.term),this.menu.blur(),void 0):(this.menu[t](e),void 0):(this.search(null,e),void 0)},widget:function(){return this.menu.element},_value:function(){return this.valueMethod.apply(this.element,arguments)},_keyEvent:function(t,e){(!this.isMultiLine||this.menu.element.is(":visible"))&&(this._move(t,e),e.preventDefault())},_isContentEditable:function(t){if(!t.length)return!1;var e=t.prop("contentEditable");return"inherit"===e?this._isContentEditable(t.parent()):"true"===e}}),t.extend(t.ui.autocomplete,{escapeRegex:function(t){return t.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g,"\\$&")},filter:function(e,i){var s=RegExp(t.ui.autocomplete.escapeRegex(i),"i");return t.grep(e,function(t){return s.test(t.label||t.value||t)})}}),t.widget("ui.autocomplete",t.ui.autocomplete,{options:{messages:{noResults:"No search results.",results:function(t){return t+(t>1?" results are":" result is")+" available, use up and down arrow keys to navigate."}}},__response:function(e){var i;this._superApply(arguments),this.options.disabled||this.cancelSearch||(i=e&&e.length?this.options.messages.results(e.length):this.options.messages.noResults,this.liveRegion.children().hide(),t("<div>").text(i).appendTo(this.liveRegion))}}),t.ui.autocomplete;var g=/ui-corner-([a-z]){2,6}/g;t.widget("ui.controlgroup",{version:"1.12.1",defaultElement:"<div>",options:{direction:"horizontal",disabled:null,onlyVisible:!0,items:{button:"input[type=button], input[type=submit], input[type=reset], button, a",controlgroupLabel:".ui-controlgroup-label",checkboxradio:"input[type='checkbox'], input[type='radio']",selectmenu:"select",spinner:".ui-spinner-input"}},_create:function(){this._enhance()},_enhance:function(){this.element.attr("role","toolbar"),this.refresh()},_destroy:function(){this._callChildMethod("destroy"),this.childWidgets.removeData("ui-controlgroup-data"),this.element.removeAttr("role"),this.options.items.controlgroupLabel&&this.element.find(this.options.items.controlgroupLabel).find(".ui-controlgroup-label-contents").contents().unwrap()},_initWidgets:function(){var e=this,i=[];t.each(this.options.items,function(s,n){var o,a={};return n?"controlgroupLabel"===s?(o=e.element.find(n),o.each(function(){var e=t(this);e.children(".ui-controlgroup-label-contents").length||e.contents().wrapAll("<span class='ui-controlgroup-label-contents'></span>")}),e._addClass(o,null,"ui-widget ui-widget-content ui-state-default"),i=i.concat(o.get()),void 0):(t.fn[s]&&(a=e["_"+s+"Options"]?e["_"+s+"Options"]("middle"):{classes:{}},e.element.find(n).each(function(){var n=t(this),o=n[s]("instance"),r=t.widget.extend({},a);if("button"!==s||!n.parent(".ui-spinner").length){o||(o=n[s]()[s]("instance")),o&&(r.classes=e._resolveClassesValues(r.classes,o)),n[s](r);var h=n[s]("widget");t.data(h[0],"ui-controlgroup-data",o?o:n[s]("instance")),i.push(h[0])}})),void 0):void 0}),this.childWidgets=t(t.unique(i)),this._addClass(this.childWidgets,"ui-controlgroup-item")},_callChildMethod:function(e){this.childWidgets.each(function(){var i=t(this),s=i.data("ui-controlgroup-data");s&&s[e]&&s[e]()})},_updateCornerClass:function(t,e){var i="ui-corner-top ui-corner-bottom ui-corner-left ui-corner-right ui-corner-all",s=this._buildSimpleOptions(e,"label").classes.label;this._removeClass(t,null,i),this._addClass(t,null,s)},_buildSimpleOptions:function(t,e){var i="vertical"===this.options.direction,s={classes:{}};return s.classes[e]={middle:"",first:"ui-corner-"+(i?"top":"left"),last:"ui-corner-"+(i?"bottom":"right"),only:"ui-corner-all"}[t],s},_spinnerOptions:function(t){var e=this._buildSimpleOptions(t,"ui-spinner");return e.classes["ui-spinner-up"]="",e.classes["ui-spinner-down"]="",e},_buttonOptions:function(t){return this._buildSimpleOptions(t,"ui-button")},_checkboxradioOptions:function(t){return this._buildSimpleOptions(t,"ui-checkboxradio-label")},_selectmenuOptions:function(t){var e="vertical"===this.options.direction;return{width:e?"auto":!1,classes:{middle:{"ui-selectmenu-button-open":"","ui-selectmenu-button-closed":""},first:{"ui-selectmenu-button-open":"ui-corner-"+(e?"top":"tl"),"ui-selectmenu-button-closed":"ui-corner-"+(e?"top":"left")},last:{"ui-selectmenu-button-open":e?"":"ui-corner-tr","ui-selectmenu-button-closed":"ui-corner-"+(e?"bottom":"right")},only:{"ui-selectmenu-button-open":"ui-corner-top","ui-selectmenu-button-closed":"ui-corner-all"}}[t]}},_resolveClassesValues:function(e,i){var s={};return t.each(e,function(n){var o=i.options.classes[n]||"";o=t.trim(o.replace(g,"")),s[n]=(o+" "+e[n]).replace(/\s+/g," ")}),s},_setOption:function(t,e){return"direction"===t&&this._removeClass("ui-controlgroup-"+this.options.direction),this._super(t,e),"disabled"===t?(this._callChildMethod(e?"disable":"enable"),void 0):(this.refresh(),void 0)},refresh:function(){var e,i=this;this._addClass("ui-controlgroup ui-controlgroup-"+this.options.direction),"horizontal"===this.options.direction&&this._addClass(null,"ui-helper-clearfix"),this._initWidgets(),e=this.childWidgets,this.options.onlyVisible&&(e=e.filter(":visible")),e.length&&(t.each(["first","last"],function(t,s){var n=e[s]().data("ui-controlgroup-data");if(n&&i["_"+n.widgetName+"Options"]){var o=i["_"+n.widgetName+"Options"](1===e.length?"only":s);o.classes=i._resolveClassesValues(o.classes,n),n.element[n.widgetName](o)}else i._updateCornerClass(e[s](),s)}),this._callChildMethod("refresh"))}}),t.widget("ui.checkboxradio",[t.ui.formResetMixin,{version:"1.12.1",options:{disabled:null,label:null,icon:!0,classes:{"ui-checkboxradio-label":"ui-corner-all","ui-checkboxradio-icon":"ui-corner-all"}},_getCreateOptions:function(){var e,i,s=this,n=this._super()||{};return this._readType(),i=this.element.labels(),this.label=t(i[i.length-1]),this.label.length||t.error("No label found for checkboxradio widget"),this.originalLabel="",this.label.contents().not(this.element[0]).each(function(){s.originalLabel+=3===this.nodeType?t(this).text():this.outerHTML}),this.originalLabel&&(n.label=this.originalLabel),e=this.element[0].disabled,null!=e&&(n.disabled=e),n},_create:function(){var t=this.element[0].checked;this._bindFormResetHandler(),null==this.options.disabled&&(this.options.disabled=this.element[0].disabled),this._setOption("disabled",this.options.disabled),this._addClass("ui-checkboxradio","ui-helper-hidden-accessible"),this._addClass(this.label,"ui-checkboxradio-label","ui-button ui-widget"),"radio"===this.type&&this._addClass(this.label,"ui-checkboxradio-radio-label"),this.options.label&&this.options.label!==this.originalLabel?this._updateLabel():this.originalLabel&&(this.options.label=this.originalLabel),this._enhance(),t&&(this._addClass(this.label,"ui-checkboxradio-checked","ui-state-active"),this.icon&&this._addClass(this.icon,null,"ui-state-hover")),this._on({change:"_toggleClasses",focus:function(){this._addClass(this.label,null,"ui-state-focus ui-visual-focus")},blur:function(){this._removeClass(this.label,null,"ui-state-focus ui-visual-focus")}})},_readType:function(){var e=this.element[0].nodeName.toLowerCase();this.type=this.element[0].type,"input"===e&&/radio|checkbox/.test(this.type)||t.error("Can't create checkboxradio on element.nodeName="+e+" and element.type="+this.type)},_enhance:function(){this._updateIcon(this.element[0].checked)},widget:function(){return this.label},_getRadioGroup:function(){var e,i=this.element[0].name,s="input[name='"+t.ui.escapeSelector(i)+"']";return i?(e=this.form.length?t(this.form[0].elements).filter(s):t(s).filter(function(){return 0===t(this).form().length}),e.not(this.element)):t([])},_toggleClasses:function(){var e=this.element[0].checked;this._toggleClass(this.label,"ui-checkboxradio-checked","ui-state-active",e),this.options.icon&&"checkbox"===this.type&&this._toggleClass(this.icon,null,"ui-icon-check ui-state-checked",e)._toggleClass(this.icon,null,"ui-icon-blank",!e),"radio"===this.type&&this._getRadioGroup().each(function(){var e=t(this).checkboxradio("instance");e&&e._removeClass(e.label,"ui-checkboxradio-checked","ui-state-active")})},_destroy:function(){this._unbindFormResetHandler(),this.icon&&(this.icon.remove(),this.iconSpace.remove())},_setOption:function(t,e){return"label"!==t||e?(this._super(t,e),"disabled"===t?(this._toggleClass(this.label,null,"ui-state-disabled",e),this.element[0].disabled=e,void 0):(this.refresh(),void 0)):void 0},_updateIcon:function(e){var i="ui-icon ui-icon-background ";this.options.icon?(this.icon||(this.icon=t("<span>"),this.iconSpace=t("<span> </span>"),this._addClass(this.iconSpace,"ui-checkboxradio-icon-space")),"checkbox"===this.type?(i+=e?"ui-icon-check ui-state-checked":"ui-icon-blank",this._removeClass(this.icon,null,e?"ui-icon-blank":"ui-icon-check")):i+="ui-icon-blank",this._addClass(this.icon,"ui-checkboxradio-icon",i),e||this._removeClass(this.icon,null,"ui-icon-check ui-state-checked"),this.icon.prependTo(this.label).after(this.iconSpace)):void 0!==this.icon&&(this.icon.remove(),this.iconSpace.remove(),delete this.icon)},_updateLabel:function(){var t=this.label.contents().not(this.element[0]);this.icon&&(t=t.not(this.icon[0])),this.iconSpace&&(t=t.not(this.iconSpace[0])),t.remove(),this.label.append(this.options.label)},refresh:function(){var t=this.element[0].checked,e=this.element[0].disabled;this._updateIcon(t),this._toggleClass(this.label,"ui-checkboxradio-checked","ui-state-active",t),null!==this.options.label&&this._updateLabel(),e!==this.options.disabled&&this._setOptions({disabled:e})}}]),t.ui.checkboxradio,t.widget("ui.button",{version:"1.12.1",defaultElement:"<button>",options:{classes:{"ui-button":"ui-corner-all"},disabled:null,icon:null,iconPosition:"beginning",label:null,showLabel:!0},_getCreateOptions:function(){var t,e=this._super()||{};return this.isInput=this.element.is("input"),t=this.element[0].disabled,null!=t&&(e.disabled=t),this.originalLabel=this.isInput?this.element.val():this.element.html(),this.originalLabel&&(e.label=this.originalLabel),e},_create:function(){!this.option.showLabel&!this.options.icon&&(this.options.showLabel=!0),null==this.options.disabled&&(this.options.disabled=this.element[0].disabled||!1),this.hasTitle=!!this.element.attr("title"),this.options.label&&this.options.label!==this.originalLabel&&(this.isInput?this.element.val(this.options.label):this.element.html(this.options.label)),this._addClass("ui-button","ui-widget"),this._setOption("disabled",this.options.disabled),this._enhance(),this.element.is("a")&&this._on({keyup:function(e){e.keyCode===t.ui.keyCode.SPACE&&(e.preventDefault(),this.element[0].click?this.element[0].click():this.element.trigger("click"))}})},_enhance:function(){this.element.is("button")||this.element.attr("role","button"),this.options.icon&&(this._updateIcon("icon",this.options.icon),this._updateTooltip())},_updateTooltip:function(){this.title=this.element.attr("title"),this.options.showLabel||this.title||this.element.attr("title",this.options.label)},_updateIcon:function(e,i){var s="iconPosition"!==e,n=s?this.options.iconPosition:i,o="top"===n||"bottom"===n;this.icon?s&&this._removeClass(this.icon,null,this.options.icon):(this.icon=t("<span>"),this._addClass(this.icon,"ui-button-icon","ui-icon"),this.options.showLabel||this._addClass("ui-button-icon-only")),s&&this._addClass(this.icon,null,i),this._attachIcon(n),o?(this._addClass(this.icon,null,"ui-widget-icon-block"),this.iconSpace&&this.iconSpace.remove()):(this.iconSpace||(this.iconSpace=t("<span> </span>"),this._addClass(this.iconSpace,"ui-button-icon-space")),this._removeClass(this.icon,null,"ui-wiget-icon-block"),this._attachIconSpace(n))},_destroy:function(){this.element.removeAttr("role"),this.icon&&this.icon.remove(),this.iconSpace&&this.iconSpace.remove(),this.hasTitle||this.element.removeAttr("title")},_attachIconSpace:function(t){this.icon[/^(?:end|bottom)/.test(t)?"before":"after"](this.iconSpace)},_attachIcon:function(t){this.element[/^(?:end|bottom)/.test(t)?"append":"prepend"](this.icon)},_setOptions:function(t){var e=void 0===t.showLabel?this.options.showLabel:t.showLabel,i=void 0===t.icon?this.options.icon:t.icon;e||i||(t.showLabel=!0),this._super(t)},_setOption:function(t,e){"icon"===t&&(e?this._updateIcon(t,e):this.icon&&(this.icon.remove(),this.iconSpace&&this.iconSpace.remove())),"iconPosition"===t&&this._updateIcon(t,e),"showLabel"===t&&(this._toggleClass("ui-button-icon-only",null,!e),this._updateTooltip()),"label"===t&&(this.isInput?this.element.val(e):(this.element.html(e),this.icon&&(this._attachIcon(this.options.iconPosition),this._attachIconSpace(this.options.iconPosition)))),this._super(t,e),"disabled"===t&&(this._toggleClass(null,"ui-state-disabled",e),this.element[0].disabled=e,e&&this.element.blur())},refresh:function(){var t=this.element.is("input, button")?this.element[0].disabled:this.element.hasClass("ui-button-disabled");t!==this.options.disabled&&this._setOptions({disabled:t}),this._updateTooltip()}}),t.uiBackCompat!==!1&&(t.widget("ui.button",t.ui.button,{options:{text:!0,icons:{primary:null,secondary:null}},_create:function(){this.options.showLabel&&!this.options.text&&(this.options.showLabel=this.options.text),!this.options.showLabel&&this.options.text&&(this.options.text=this.options.showLabel),this.options.icon||!this.options.icons.primary&&!this.options.icons.secondary?this.options.icon&&(this.options.icons.primary=this.options.icon):this.options.icons.primary?this.options.icon=this.options.icons.primary:(this.options.icon=this.options.icons.secondary,this.options.iconPosition="end"),this._super()},_setOption:function(t,e){return"text"===t?(this._super("showLabel",e),void 0):("showLabel"===t&&(this.options.text=e),"icon"===t&&(this.options.icons.primary=e),"icons"===t&&(e.primary?(this._super("icon",e.primary),this._super("iconPosition","beginning")):e.secondary&&(this._super("icon",e.secondary),this._super("iconPosition","end"))),this._superApply(arguments),void 0)}}),t.fn.button=function(e){return function(){return!this.length||this.length&&"INPUT"!==this[0].tagName||this.length&&"INPUT"===this[0].tagName&&"checkbox"!==this.attr("type")&&"radio"!==this.attr("type")?e.apply(this,arguments):(t.ui.checkboxradio||t.error("Checkboxradio widget missing"),0===arguments.length?this.checkboxradio({icon:!1}):this.checkboxradio.apply(this,arguments))}}(t.fn.button),t.fn.buttonset=function(){return t.ui.controlgroup||t.error("Controlgroup widget missing"),"option"===arguments[0]&&"items"===arguments[1]&&arguments[2]?this.controlgroup.apply(this,[arguments[0],"items.button",arguments[2]]):"option"===arguments[0]&&"items"===arguments[1]?this.controlgroup.apply(this,[arguments[0],"items.button"]):("object"==typeof arguments[0]&&arguments[0].items&&(arguments[0].items={button:arguments[0].items}),this.controlgroup.apply(this,arguments))}),t.ui.button,t.extend(t.ui,{datepicker:{version:"1.12.1"}});var m;t.extend(s.prototype,{markerClassName:"hasDatepicker",maxRows:4,_widgetDatepicker:function(){return this.dpDiv},setDefaults:function(t){return a(this._defaults,t||{}),this},_attachDatepicker:function(e,i){var s,n,o;s=e.nodeName.toLowerCase(),n="div"===s||"span"===s,e.id||(this.uuid+=1,e.id="dp"+this.uuid),o=this._newInst(t(e),n),o.settings=t.extend({},i||{}),"input"===s?this._connectDatepicker(e,o):n&&this._inlineDatepicker(e,o)},_newInst:function(e,i){var s=e[0].id.replace(/([^A-Za-z0-9_\-])/g,"\\\\$1");return{id:s,input:e,selectedDay:0,selectedMonth:0,selectedYear:0,drawMonth:0,drawYear:0,inline:i,dpDiv:i?n(t("<div class='"+this._inlineClass+" ui-datepicker ui-widget ui-widget-content ui-helper-clearfix ui-corner-all'></div>")):this.dpDiv}},_connectDatepicker:function(e,i){var s=t(e);i.append=t([]),i.trigger=t([]),s.hasClass(this.markerClassName)||(this._attachments(s,i),s.addClass(this.markerClassName).on("keydown",this._doKeyDown).on("keypress",this._doKeyPress).on("keyup",this._doKeyUp),this._autoSize(i),t.data(e,"datepicker",i),i.settings.disabled&&this._disableDatepicker(e))},_attachments:function(e,i){var s,n,o,a=this._get(i,"appendText"),r=this._get(i,"isRTL");i.append&&i.append.remove(),a&&(i.append=t("<span class='"+this._appendClass+"'>"+a+"</span>"),e[r?"before":"after"](i.append)),e.off("focus",this._showDatepicker),i.trigger&&i.trigger.remove(),s=this._get(i,"showOn"),("focus"===s||"both"===s)&&e.on("focus",this._showDatepicker),("button"===s||"both"===s)&&(n=this._get(i,"buttonText"),o=this._get(i,"buttonImage"),i.trigger=t(this._get(i,"buttonImageOnly")?t("<img/>").addClass(this._triggerClass).attr({src:o,alt:n,title:n}):t("<button type='button'></button>").addClass(this._triggerClass).html(o?t("<img/>").attr({src:o,alt:n,title:n}):n)),e[r?"before":"after"](i.trigger),i.trigger.on("click",function(){return t.datepicker._datepickerShowing&&t.datepicker._lastInput===e[0]?t.datepicker._hideDatepicker():t.datepicker._datepickerShowing&&t.datepicker._lastInput!==e[0]?(t.datepicker._hideDatepicker(),t.datepicker._showDatepicker(e[0])):t.datepicker._showDatepicker(e[0]),!1}))},_autoSize:function(t){if(this._get(t,"autoSize")&&!t.inline){var e,i,s,n,o=new Date(2009,11,20),a=this._get(t,"dateFormat");a.match(/[DM]/)&&(e=function(t){for(i=0,s=0,n=0;t.length>n;n++)t[n].length>i&&(i=t[n].length,s=n);return s},o.setMonth(e(this._get(t,a.match(/MM/)?"monthNames":"monthNamesShort"))),o.setDate(e(this._get(t,a.match(/DD/)?"dayNames":"dayNamesShort"))+20-o.getDay())),t.input.attr("size",this._formatDate(t,o).length)}},_inlineDatepicker:function(e,i){var s=t(e);s.hasClass(this.markerClassName)||(s.addClass(this.markerClassName).append(i.dpDiv),t.data(e,"datepicker",i),this._setDate(i,this._getDefaultDate(i),!0),this._updateDatepicker(i),this._updateAlternate(i),i.settings.disabled&&this._disableDatepicker(e),i.dpDiv.css("display","block"))},_dialogDatepicker:function(e,i,s,n,o){var r,h,l,c,u,d=this._dialogInst;return d||(this.uuid+=1,r="dp"+this.uuid,this._dialogInput=t("<input type='text' id='"+r+"' style='position: absolute; top: -100px; width: 0px;'/>"),this._dialogInput.on("keydown",this._doKeyDown),t("body").append(this._dialogInput),d=this._dialogInst=this._newInst(this._dialogInput,!1),d.settings={},t.data(this._dialogInput[0],"datepicker",d)),a(d.settings,n||{}),i=i&&i.constructor===Date?this._formatDate(d,i):i,this._dialogInput.val(i),this._pos=o?o.length?o:[o.pageX,o.pageY]:null,this._pos||(h=document.documentElement.clientWidth,l=document.documentElement.clientHeight,c=document.documentElement.scrollLeft||document.body.scrollLeft,u=document.documentElement.scrollTop||document.body.scrollTop,this._pos=[h/2-100+c,l/2-150+u]),this._dialogInput.css("left",this._pos[0]+20+"px").css("top",this._pos[1]+"px"),d.settings.onSelect=s,this._inDialog=!0,this.dpDiv.addClass(this._dialogClass),this._showDatepicker(this._dialogInput[0]),t.blockUI&&t.blockUI(this.dpDiv),t.data(this._dialogInput[0],"datepicker",d),this},_destroyDatepicker:function(e){var i,s=t(e),n=t.data(e,"datepicker");s.hasClass(this.markerClassName)&&(i=e.nodeName.toLowerCase(),t.removeData(e,"datepicker"),"input"===i?(n.append.remove(),n.trigger.remove(),s.removeClass(this.markerClassName).off("focus",this._showDatepicker).off("keydown",this._doKeyDown).off("keypress",this._doKeyPress).off("keyup",this._doKeyUp)):("div"===i||"span"===i)&&s.removeClass(this.markerClassName).empty(),m===n&&(m=null))},_enableDatepicker:function(e){var i,s,n=t(e),o=t.data(e,"datepicker");n.hasClass(this.markerClassName)&&(i=e.nodeName.toLowerCase(),"input"===i?(e.disabled=!1,o.trigger.filter("button").each(function(){this.disabled=!1}).end().filter("img").css({opacity:"1.0",cursor:""})):("div"===i||"span"===i)&&(s=n.children("."+this._inlineClass),s.children().removeClass("ui-state-disabled"),s.find("select.ui-datepicker-month, select.ui-datepicker-year").prop("disabled",!1)),this._disabledInputs=t.map(this._disabledInputs,function(t){return t===e?null:t}))},_disableDatepicker:function(e){var i,s,n=t(e),o=t.data(e,"datepicker");n.hasClass(this.markerClassName)&&(i=e.nodeName.toLowerCase(),"input"===i?(e.disabled=!0,o.trigger.filter("button").each(function(){this.disabled=!0}).end().filter("img").css({opacity:"0.5",cursor:"default"})):("div"===i||"span"===i)&&(s=n.children("."+this._inlineClass),s.children().addClass("ui-state-disabled"),s.find("select.ui-datepicker-month, select.ui-datepicker-year").prop("disabled",!0)),this._disabledInputs=t.map(this._disabledInputs,function(t){return t===e?null:t}),this._disabledInputs[this._disabledInputs.length]=e)},_isDisabledDatepicker:function(t){if(!t)return!1;for(var e=0;this._disabledInputs.length>e;e++)if(this._disabledInputs[e]===t)return!0;return!1},_getInst:function(e){try{return t.data(e,"datepicker")}catch(i){throw"Missing instance data for this datepicker"}},_optionDatepicker:function(e,i,s){var n,o,r,h,l=this._getInst(e);return 2===arguments.length&&"string"==typeof i?"defaults"===i?t.extend({},t.datepicker._defaults):l?"all"===i?t.extend({},l.settings):this._get(l,i):null:(n=i||{},"string"==typeof i&&(n={},n[i]=s),l&&(this._curInst===l&&this._hideDatepicker(),o=this._getDateDatepicker(e,!0),r=this._getMinMaxDate(l,"min"),h=this._getMinMaxDate(l,"max"),a(l.settings,n),null!==r&&void 0!==n.dateFormat&&void 0===n.minDate&&(l.settings.minDate=this._formatDate(l,r)),null!==h&&void 0!==n.dateFormat&&void 0===n.maxDate&&(l.settings.maxDate=this._formatDate(l,h)),"disabled"in n&&(n.disabled?this._disableDatepicker(e):this._enableDatepicker(e)),this._attachments(t(e),l),this._autoSize(l),this._setDate(l,o),this._updateAlternate(l),this._updateDatepicker(l)),void 0)},_changeDatepicker:function(t,e,i){this._optionDatepicker(t,e,i)},_refreshDatepicker:function(t){var e=this._getInst(t);e&&this._updateDatepicker(e)},_setDateDatepicker:function(t,e){var i=this._getInst(t);i&&(this._setDate(i,e),this._updateDatepicker(i),this._updateAlternate(i))},_getDateDatepicker:function(t,e){var i=this._getInst(t);return i&&!i.inline&&this._setDateFromField(i,e),i?this._getDate(i):null},_doKeyDown:function(e){var i,s,n,o=t.datepicker._getInst(e.target),a=!0,r=o.dpDiv.is(".ui-datepicker-rtl");if(o._keyEvent=!0,t.datepicker._datepickerShowing)switch(e.keyCode){case 9:t.datepicker._hideDatepicker(),a=!1;break;case 13:return n=t("td."+t.datepicker._dayOverClass+":not(."+t.datepicker._currentClass+")",o.dpDiv),n[0]&&t.datepicker._selectDay(e.target,o.selectedMonth,o.selectedYear,n[0]),i=t.datepicker._get(o,"onSelect"),i?(s=t.datepicker._formatDate(o),i.apply(o.input?o.input[0]:null,[s,o])):t.datepicker._hideDatepicker(),!1;case 27:t.datepicker._hideDatepicker();break;case 33:t.datepicker._adjustDate(e.target,e.ctrlKey?-t.datepicker._get(o,"stepBigMonths"):-t.datepicker._get(o,"stepMonths"),"M");break;case 34:t.datepicker._adjustDate(e.target,e.ctrlKey?+t.datepicker._get(o,"stepBigMonths"):+t.datepicker._get(o,"stepMonths"),"M");break;case 35:(e.ctrlKey||e.metaKey)&&t.datepicker._clearDate(e.target),a=e.ctrlKey||e.metaKey;break;case 36:(e.ctrlKey||e.metaKey)&&t.datepicker._gotoToday(e.target),a=e.ctrlKey||e.metaKey;break;case 37:(e.ctrlKey||e.metaKey)&&t.datepicker._adjustDate(e.target,r?1:-1,"D"),a=e.ctrlKey||e.metaKey,e.originalEvent.altKey&&t.datepicker._adjustDate(e.target,e.ctrlKey?-t.datepicker._get(o,"stepBigMonths"):-t.datepicker._get(o,"stepMonths"),"M");break;case 38:(e.ctrlKey||e.metaKey)&&t.datepicker._adjustDate(e.target,-7,"D"),a=e.ctrlKey||e.metaKey;break;case 39:(e.ctrlKey||e.metaKey)&&t.datepicker._adjustDate(e.target,r?-1:1,"D"),a=e.ctrlKey||e.metaKey,e.originalEvent.altKey&&t.datepicker._adjustDate(e.target,e.ctrlKey?+t.datepicker._get(o,"stepBigMonths"):+t.datepicker._get(o,"stepMonths"),"M");break;case 40:(e.ctrlKey||e.metaKey)&&t.datepicker._adjustDate(e.target,7,"D"),a=e.ctrlKey||e.metaKey;break;default:a=!1}else 36===e.keyCode&&e.ctrlKey?t.datepicker._showDatepicker(this):a=!1;a&&(e.preventDefault(),e.stopPropagation())},_doKeyPress:function(e){var i,s,n=t.datepicker._getInst(e.target);return t.datepicker._get(n,"constrainInput")?(i=t.datepicker._possibleChars(t.datepicker._get(n,"dateFormat")),s=String.fromCharCode(null==e.charCode?e.keyCode:e.charCode),e.ctrlKey||e.metaKey||" ">s||!i||i.indexOf(s)>-1):void 0},_doKeyUp:function(e){var i,s=t.datepicker._getInst(e.target);if(s.input.val()!==s.lastVal)try{i=t.datepicker.parseDate(t.datepicker._get(s,"dateFormat"),s.input?s.input.val():null,t.datepicker._getFormatConfig(s)),i&&(t.datepicker._setDateFromField(s),t.datepicker._updateAlternate(s),t.datepicker._updateDatepicker(s))}catch(n){}return!0},_showDatepicker:function(e){if(e=e.target||e,"input"!==e.nodeName.toLowerCase()&&(e=t("input",e.parentNode)[0]),!t.datepicker._isDisabledDatepicker(e)&&t.datepicker._lastInput!==e){var s,n,o,r,h,l,c;s=t.datepicker._getInst(e),t.datepicker._curInst&&t.datepicker._curInst!==s&&(t.datepicker._curInst.dpDiv.stop(!0,!0),s&&t.datepicker._datepickerShowing&&t.datepicker._hideDatepicker(t.datepicker._curInst.input[0])),n=t.datepicker._get(s,"beforeShow"),o=n?n.apply(e,[e,s]):{},o!==!1&&(a(s.settings,o),s.lastVal=null,t.datepicker._lastInput=e,t.datepicker._setDateFromField(s),t.datepicker._inDialog&&(e.value=""),t.datepicker._pos||(t.datepicker._pos=t.datepicker._findPos(e),t.datepicker._pos[1]+=e.offsetHeight),r=!1,t(e).parents().each(function(){return r|="fixed"===t(this).css("position"),!r}),h={left:t.datepicker._pos[0],top:t.datepicker._pos[1]},t.datepicker._pos=null,s.dpDiv.empty(),s.dpDiv.css({position:"absolute",display:"block",top:"-1000px"}),t.datepicker._updateDatepicker(s),h=t.datepicker._checkOffset(s,h,r),s.dpDiv.css({position:t.datepicker._inDialog&&t.blockUI?"static":r?"fixed":"absolute",display:"none",left:h.left+"px",top:h.top+"px"}),s.inline||(l=t.datepicker._get(s,"showAnim"),c=t.datepicker._get(s,"duration"),s.dpDiv.css("z-index",i(t(e))+1),t.datepicker._datepickerShowing=!0,t.effects&&t.effects.effect[l]?s.dpDiv.show(l,t.datepicker._get(s,"showOptions"),c):s.dpDiv[l||"show"](l?c:null),t.datepicker._shouldFocusInput(s)&&s.input.trigger("focus"),t.datepicker._curInst=s))
+}},_updateDatepicker:function(e){this.maxRows=4,m=e,e.dpDiv.empty().append(this._generateHTML(e)),this._attachHandlers(e);var i,s=this._getNumberOfMonths(e),n=s[1],a=17,r=e.dpDiv.find("."+this._dayOverClass+" a");r.length>0&&o.apply(r.get(0)),e.dpDiv.removeClass("ui-datepicker-multi-2 ui-datepicker-multi-3 ui-datepicker-multi-4").width(""),n>1&&e.dpDiv.addClass("ui-datepicker-multi-"+n).css("width",a*n+"em"),e.dpDiv[(1!==s[0]||1!==s[1]?"add":"remove")+"Class"]("ui-datepicker-multi"),e.dpDiv[(this._get(e,"isRTL")?"add":"remove")+"Class"]("ui-datepicker-rtl"),e===t.datepicker._curInst&&t.datepicker._datepickerShowing&&t.datepicker._shouldFocusInput(e)&&e.input.trigger("focus"),e.yearshtml&&(i=e.yearshtml,setTimeout(function(){i===e.yearshtml&&e.yearshtml&&e.dpDiv.find("select.ui-datepicker-year:first").replaceWith(e.yearshtml),i=e.yearshtml=null},0))},_shouldFocusInput:function(t){return t.input&&t.input.is(":visible")&&!t.input.is(":disabled")&&!t.input.is(":focus")},_checkOffset:function(e,i,s){var n=e.dpDiv.outerWidth(),o=e.dpDiv.outerHeight(),a=e.input?e.input.outerWidth():0,r=e.input?e.input.outerHeight():0,h=document.documentElement.clientWidth+(s?0:t(document).scrollLeft()),l=document.documentElement.clientHeight+(s?0:t(document).scrollTop());return i.left-=this._get(e,"isRTL")?n-a:0,i.left-=s&&i.left===e.input.offset().left?t(document).scrollLeft():0,i.top-=s&&i.top===e.input.offset().top+r?t(document).scrollTop():0,i.left-=Math.min(i.left,i.left+n>h&&h>n?Math.abs(i.left+n-h):0),i.top-=Math.min(i.top,i.top+o>l&&l>o?Math.abs(o+r):0),i},_findPos:function(e){for(var i,s=this._getInst(e),n=this._get(s,"isRTL");e&&("hidden"===e.type||1!==e.nodeType||t.expr.filters.hidden(e));)e=e[n?"previousSibling":"nextSibling"];return i=t(e).offset(),[i.left,i.top]},_hideDatepicker:function(e){var i,s,n,o,a=this._curInst;!a||e&&a!==t.data(e,"datepicker")||this._datepickerShowing&&(i=this._get(a,"showAnim"),s=this._get(a,"duration"),n=function(){t.datepicker._tidyDialog(a)},t.effects&&(t.effects.effect[i]||t.effects[i])?a.dpDiv.hide(i,t.datepicker._get(a,"showOptions"),s,n):a.dpDiv["slideDown"===i?"slideUp":"fadeIn"===i?"fadeOut":"hide"](i?s:null,n),i||n(),this._datepickerShowing=!1,o=this._get(a,"onClose"),o&&o.apply(a.input?a.input[0]:null,[a.input?a.input.val():"",a]),this._lastInput=null,this._inDialog&&(this._dialogInput.css({position:"absolute",left:"0",top:"-100px"}),t.blockUI&&(t.unblockUI(),t("body").append(this.dpDiv))),this._inDialog=!1)},_tidyDialog:function(t){t.dpDiv.removeClass(this._dialogClass).off(".ui-datepicker-calendar")},_checkExternalClick:function(e){if(t.datepicker._curInst){var i=t(e.target),s=t.datepicker._getInst(i[0]);(i[0].id!==t.datepicker._mainDivId&&0===i.parents("#"+t.datepicker._mainDivId).length&&!i.hasClass(t.datepicker.markerClassName)&&!i.closest("."+t.datepicker._triggerClass).length&&t.datepicker._datepickerShowing&&(!t.datepicker._inDialog||!t.blockUI)||i.hasClass(t.datepicker.markerClassName)&&t.datepicker._curInst!==s)&&t.datepicker._hideDatepicker()}},_adjustDate:function(e,i,s){var n=t(e),o=this._getInst(n[0]);this._isDisabledDatepicker(n[0])||(this._adjustInstDate(o,i+("M"===s?this._get(o,"showCurrentAtPos"):0),s),this._updateDatepicker(o))},_gotoToday:function(e){var i,s=t(e),n=this._getInst(s[0]);this._get(n,"gotoCurrent")&&n.currentDay?(n.selectedDay=n.currentDay,n.drawMonth=n.selectedMonth=n.currentMonth,n.drawYear=n.selectedYear=n.currentYear):(i=new Date,n.selectedDay=i.getDate(),n.drawMonth=n.selectedMonth=i.getMonth(),n.drawYear=n.selectedYear=i.getFullYear()),this._notifyChange(n),this._adjustDate(s)},_selectMonthYear:function(e,i,s){var n=t(e),o=this._getInst(n[0]);o["selected"+("M"===s?"Month":"Year")]=o["draw"+("M"===s?"Month":"Year")]=parseInt(i.options[i.selectedIndex].value,10),this._notifyChange(o),this._adjustDate(n)},_selectDay:function(e,i,s,n){var o,a=t(e);t(n).hasClass(this._unselectableClass)||this._isDisabledDatepicker(a[0])||(o=this._getInst(a[0]),o.selectedDay=o.currentDay=t("a",n).html(),o.selectedMonth=o.currentMonth=i,o.selectedYear=o.currentYear=s,this._selectDate(e,this._formatDate(o,o.currentDay,o.currentMonth,o.currentYear)))},_clearDate:function(e){var i=t(e);this._selectDate(i,"")},_selectDate:function(e,i){var s,n=t(e),o=this._getInst(n[0]);i=null!=i?i:this._formatDate(o),o.input&&o.input.val(i),this._updateAlternate(o),s=this._get(o,"onSelect"),s?s.apply(o.input?o.input[0]:null,[i,o]):o.input&&o.input.trigger("change"),o.inline?this._updateDatepicker(o):(this._hideDatepicker(),this._lastInput=o.input[0],"object"!=typeof o.input[0]&&o.input.trigger("focus"),this._lastInput=null)},_updateAlternate:function(e){var i,s,n,o=this._get(e,"altField");o&&(i=this._get(e,"altFormat")||this._get(e,"dateFormat"),s=this._getDate(e),n=this.formatDate(i,s,this._getFormatConfig(e)),t(o).val(n))},noWeekends:function(t){var e=t.getDay();return[e>0&&6>e,""]},iso8601Week:function(t){var e,i=new Date(t.getTime());return i.setDate(i.getDate()+4-(i.getDay()||7)),e=i.getTime(),i.setMonth(0),i.setDate(1),Math.floor(Math.round((e-i)/864e5)/7)+1},parseDate:function(e,i,s){if(null==e||null==i)throw"Invalid arguments";if(i="object"==typeof i?""+i:i+"",""===i)return null;var n,o,a,r,h=0,l=(s?s.shortYearCutoff:null)||this._defaults.shortYearCutoff,c="string"!=typeof l?l:(new Date).getFullYear()%100+parseInt(l,10),u=(s?s.dayNamesShort:null)||this._defaults.dayNamesShort,d=(s?s.dayNames:null)||this._defaults.dayNames,p=(s?s.monthNamesShort:null)||this._defaults.monthNamesShort,f=(s?s.monthNames:null)||this._defaults.monthNames,g=-1,m=-1,_=-1,v=-1,b=!1,y=function(t){var i=e.length>n+1&&e.charAt(n+1)===t;return i&&n++,i},w=function(t){var e=y(t),s="@"===t?14:"!"===t?20:"y"===t&&e?4:"o"===t?3:2,n="y"===t?s:1,o=RegExp("^\\d{"+n+","+s+"}"),a=i.substring(h).match(o);if(!a)throw"Missing number at position "+h;return h+=a[0].length,parseInt(a[0],10)},k=function(e,s,n){var o=-1,a=t.map(y(e)?n:s,function(t,e){return[[e,t]]}).sort(function(t,e){return-(t[1].length-e[1].length)});if(t.each(a,function(t,e){var s=e[1];return i.substr(h,s.length).toLowerCase()===s.toLowerCase()?(o=e[0],h+=s.length,!1):void 0}),-1!==o)return o+1;throw"Unknown name at position "+h},x=function(){if(i.charAt(h)!==e.charAt(n))throw"Unexpected literal at position "+h;h++};for(n=0;e.length>n;n++)if(b)"'"!==e.charAt(n)||y("'")?x():b=!1;else switch(e.charAt(n)){case"d":_=w("d");break;case"D":k("D",u,d);break;case"o":v=w("o");break;case"m":m=w("m");break;case"M":m=k("M",p,f);break;case"y":g=w("y");break;case"@":r=new Date(w("@")),g=r.getFullYear(),m=r.getMonth()+1,_=r.getDate();break;case"!":r=new Date((w("!")-this._ticksTo1970)/1e4),g=r.getFullYear(),m=r.getMonth()+1,_=r.getDate();break;case"'":y("'")?x():b=!0;break;default:x()}if(i.length>h&&(a=i.substr(h),!/^\s+/.test(a)))throw"Extra/unparsed characters found in date: "+a;if(-1===g?g=(new Date).getFullYear():100>g&&(g+=(new Date).getFullYear()-(new Date).getFullYear()%100+(c>=g?0:-100)),v>-1)for(m=1,_=v;;){if(o=this._getDaysInMonth(g,m-1),o>=_)break;m++,_-=o}if(r=this._daylightSavingAdjust(new Date(g,m-1,_)),r.getFullYear()!==g||r.getMonth()+1!==m||r.getDate()!==_)throw"Invalid date";return r},ATOM:"yy-mm-dd",COOKIE:"D, dd M yy",ISO_8601:"yy-mm-dd",RFC_822:"D, d M y",RFC_850:"DD, dd-M-y",RFC_1036:"D, d M y",RFC_1123:"D, d M yy",RFC_2822:"D, d M yy",RSS:"D, d M y",TICKS:"!",TIMESTAMP:"@",W3C:"yy-mm-dd",_ticksTo1970:1e7*60*60*24*(718685+Math.floor(492.5)-Math.floor(19.7)+Math.floor(4.925)),formatDate:function(t,e,i){if(!e)return"";var s,n=(i?i.dayNamesShort:null)||this._defaults.dayNamesShort,o=(i?i.dayNames:null)||this._defaults.dayNames,a=(i?i.monthNamesShort:null)||this._defaults.monthNamesShort,r=(i?i.monthNames:null)||this._defaults.monthNames,h=function(e){var i=t.length>s+1&&t.charAt(s+1)===e;return i&&s++,i},l=function(t,e,i){var s=""+e;if(h(t))for(;i>s.length;)s="0"+s;return s},c=function(t,e,i,s){return h(t)?s[e]:i[e]},u="",d=!1;if(e)for(s=0;t.length>s;s++)if(d)"'"!==t.charAt(s)||h("'")?u+=t.charAt(s):d=!1;else switch(t.charAt(s)){case"d":u+=l("d",e.getDate(),2);break;case"D":u+=c("D",e.getDay(),n,o);break;case"o":u+=l("o",Math.round((new Date(e.getFullYear(),e.getMonth(),e.getDate()).getTime()-new Date(e.getFullYear(),0,0).getTime())/864e5),3);break;case"m":u+=l("m",e.getMonth()+1,2);break;case"M":u+=c("M",e.getMonth(),a,r);break;case"y":u+=h("y")?e.getFullYear():(10>e.getFullYear()%100?"0":"")+e.getFullYear()%100;break;case"@":u+=e.getTime();break;case"!":u+=1e4*e.getTime()+this._ticksTo1970;break;case"'":h("'")?u+="'":d=!0;break;default:u+=t.charAt(s)}return u},_possibleChars:function(t){var e,i="",s=!1,n=function(i){var s=t.length>e+1&&t.charAt(e+1)===i;return s&&e++,s};for(e=0;t.length>e;e++)if(s)"'"!==t.charAt(e)||n("'")?i+=t.charAt(e):s=!1;else switch(t.charAt(e)){case"d":case"m":case"y":case"@":i+="0123456789";break;case"D":case"M":return null;case"'":n("'")?i+="'":s=!0;break;default:i+=t.charAt(e)}return i},_get:function(t,e){return void 0!==t.settings[e]?t.settings[e]:this._defaults[e]},_setDateFromField:function(t,e){if(t.input.val()!==t.lastVal){var i=this._get(t,"dateFormat"),s=t.lastVal=t.input?t.input.val():null,n=this._getDefaultDate(t),o=n,a=this._getFormatConfig(t);try{o=this.parseDate(i,s,a)||n}catch(r){s=e?"":s}t.selectedDay=o.getDate(),t.drawMonth=t.selectedMonth=o.getMonth(),t.drawYear=t.selectedYear=o.getFullYear(),t.currentDay=s?o.getDate():0,t.currentMonth=s?o.getMonth():0,t.currentYear=s?o.getFullYear():0,this._adjustInstDate(t)}},_getDefaultDate:function(t){return this._restrictMinMax(t,this._determineDate(t,this._get(t,"defaultDate"),new Date))},_determineDate:function(e,i,s){var n=function(t){var e=new Date;return e.setDate(e.getDate()+t),e},o=function(i){try{return t.datepicker.parseDate(t.datepicker._get(e,"dateFormat"),i,t.datepicker._getFormatConfig(e))}catch(s){}for(var n=(i.toLowerCase().match(/^c/)?t.datepicker._getDate(e):null)||new Date,o=n.getFullYear(),a=n.getMonth(),r=n.getDate(),h=/([+\-]?[0-9]+)\s*(d|D|w|W|m|M|y|Y)?/g,l=h.exec(i);l;){switch(l[2]||"d"){case"d":case"D":r+=parseInt(l[1],10);break;case"w":case"W":r+=7*parseInt(l[1],10);break;case"m":case"M":a+=parseInt(l[1],10),r=Math.min(r,t.datepicker._getDaysInMonth(o,a));break;case"y":case"Y":o+=parseInt(l[1],10),r=Math.min(r,t.datepicker._getDaysInMonth(o,a))}l=h.exec(i)}return new Date(o,a,r)},a=null==i||""===i?s:"string"==typeof i?o(i):"number"==typeof i?isNaN(i)?s:n(i):new Date(i.getTime());return a=a&&"Invalid Date"==""+a?s:a,a&&(a.setHours(0),a.setMinutes(0),a.setSeconds(0),a.setMilliseconds(0)),this._daylightSavingAdjust(a)},_daylightSavingAdjust:function(t){return t?(t.setHours(t.getHours()>12?t.getHours()+2:0),t):null},_setDate:function(t,e,i){var s=!e,n=t.selectedMonth,o=t.selectedYear,a=this._restrictMinMax(t,this._determineDate(t,e,new Date));t.selectedDay=t.currentDay=a.getDate(),t.drawMonth=t.selectedMonth=t.currentMonth=a.getMonth(),t.drawYear=t.selectedYear=t.currentYear=a.getFullYear(),n===t.selectedMonth&&o===t.selectedYear||i||this._notifyChange(t),this._adjustInstDate(t),t.input&&t.input.val(s?"":this._formatDate(t))},_getDate:function(t){var e=!t.currentYear||t.input&&""===t.input.val()?null:this._daylightSavingAdjust(new Date(t.currentYear,t.currentMonth,t.currentDay));return e},_attachHandlers:function(e){var i=this._get(e,"stepMonths"),s="#"+e.id.replace(/\\\\/g,"\\");e.dpDiv.find("[data-handler]").map(function(){var e={prev:function(){t.datepicker._adjustDate(s,-i,"M")},next:function(){t.datepicker._adjustDate(s,+i,"M")},hide:function(){t.datepicker._hideDatepicker()},today:function(){t.datepicker._gotoToday(s)},selectDay:function(){return t.datepicker._selectDay(s,+this.getAttribute("data-month"),+this.getAttribute("data-year"),this),!1},selectMonth:function(){return t.datepicker._selectMonthYear(s,this,"M"),!1},selectYear:function(){return t.datepicker._selectMonthYear(s,this,"Y"),!1}};t(this).on(this.getAttribute("data-event"),e[this.getAttribute("data-handler")])})},_generateHTML:function(t){var e,i,s,n,o,a,r,h,l,c,u,d,p,f,g,m,_,v,b,y,w,k,x,C,D,I,T,P,M,S,H,z,O,A,N,W,E,F,L,R=new Date,B=this._daylightSavingAdjust(new Date(R.getFullYear(),R.getMonth(),R.getDate())),Y=this._get(t,"isRTL"),j=this._get(t,"showButtonPanel"),q=this._get(t,"hideIfNoPrevNext"),K=this._get(t,"navigationAsDateFormat"),U=this._getNumberOfMonths(t),V=this._get(t,"showCurrentAtPos"),$=this._get(t,"stepMonths"),X=1!==U[0]||1!==U[1],G=this._daylightSavingAdjust(t.currentDay?new Date(t.currentYear,t.currentMonth,t.currentDay):new Date(9999,9,9)),Q=this._getMinMaxDate(t,"min"),J=this._getMinMaxDate(t,"max"),Z=t.drawMonth-V,te=t.drawYear;if(0>Z&&(Z+=12,te--),J)for(e=this._daylightSavingAdjust(new Date(J.getFullYear(),J.getMonth()-U[0]*U[1]+1,J.getDate())),e=Q&&Q>e?Q:e;this._daylightSavingAdjust(new Date(te,Z,1))>e;)Z--,0>Z&&(Z=11,te--);for(t.drawMonth=Z,t.drawYear=te,i=this._get(t,"prevText"),i=K?this.formatDate(i,this._daylightSavingAdjust(new Date(te,Z-$,1)),this._getFormatConfig(t)):i,s=this._canAdjustMonth(t,-1,te,Z)?"<a class='ui-datepicker-prev ui-corner-all' data-handler='prev' data-event='click' title='"+i+"'><span class='ui-icon ui-icon-circle-triangle-"+(Y?"e":"w")+"'>"+i+"</span></a>":q?"":"<a class='ui-datepicker-prev ui-corner-all ui-state-disabled' title='"+i+"'><span class='ui-icon ui-icon-circle-triangle-"+(Y?"e":"w")+"'>"+i+"</span></a>",n=this._get(t,"nextText"),n=K?this.formatDate(n,this._daylightSavingAdjust(new Date(te,Z+$,1)),this._getFormatConfig(t)):n,o=this._canAdjustMonth(t,1,te,Z)?"<a class='ui-datepicker-next ui-corner-all' data-handler='next' data-event='click' title='"+n+"'><span class='ui-icon ui-icon-circle-triangle-"+(Y?"w":"e")+"'>"+n+"</span></a>":q?"":"<a class='ui-datepicker-next ui-corner-all ui-state-disabled' title='"+n+"'><span class='ui-icon ui-icon-circle-triangle-"+(Y?"w":"e")+"'>"+n+"</span></a>",a=this._get(t,"currentText"),r=this._get(t,"gotoCurrent")&&t.currentDay?G:B,a=K?this.formatDate(a,r,this._getFormatConfig(t)):a,h=t.inline?"":"<button type='button' class='ui-datepicker-close ui-state-default ui-priority-primary ui-corner-all' data-handler='hide' data-event='click'>"+this._get(t,"closeText")+"</button>",l=j?"<div class='ui-datepicker-buttonpane ui-widget-content'>"+(Y?h:"")+(this._isInRange(t,r)?"<button type='button' class='ui-datepicker-current ui-state-default ui-priority-secondary ui-corner-all' data-handler='today' data-event='click'>"+a+"</button>":"")+(Y?"":h)+"</div>":"",c=parseInt(this._get(t,"firstDay"),10),c=isNaN(c)?0:c,u=this._get(t,"showWeek"),d=this._get(t,"dayNames"),p=this._get(t,"dayNamesMin"),f=this._get(t,"monthNames"),g=this._get(t,"monthNamesShort"),m=this._get(t,"beforeShowDay"),_=this._get(t,"showOtherMonths"),v=this._get(t,"selectOtherMonths"),b=this._getDefaultDate(t),y="",k=0;U[0]>k;k++){for(x="",this.maxRows=4,C=0;U[1]>C;C++){if(D=this._daylightSavingAdjust(new Date(te,Z,t.selectedDay)),I=" ui-corner-all",T="",X){if(T+="<div class='ui-datepicker-group",U[1]>1)switch(C){case 0:T+=" ui-datepicker-group-first",I=" ui-corner-"+(Y?"right":"left");break;case U[1]-1:T+=" ui-datepicker-group-last",I=" ui-corner-"+(Y?"left":"right");break;default:T+=" ui-datepicker-group-middle",I=""}T+="'>"}for(T+="<div class='ui-datepicker-header ui-widget-header ui-helper-clearfix"+I+"'>"+(/all|left/.test(I)&&0===k?Y?o:s:"")+(/all|right/.test(I)&&0===k?Y?s:o:"")+this._generateMonthYearHeader(t,Z,te,Q,J,k>0||C>0,f,g)+"</div><table class='ui-datepicker-calendar'><thead>"+"<tr>",P=u?"<th class='ui-datepicker-week-col'>"+this._get(t,"weekHeader")+"</th>":"",w=0;7>w;w++)M=(w+c)%7,P+="<th scope='col'"+((w+c+6)%7>=5?" class='ui-datepicker-week-end'":"")+">"+"<span title='"+d[M]+"'>"+p[M]+"</span></th>";for(T+=P+"</tr></thead><tbody>",S=this._getDaysInMonth(te,Z),te===t.selectedYear&&Z===t.selectedMonth&&(t.selectedDay=Math.min(t.selectedDay,S)),H=(this._getFirstDayOfMonth(te,Z)-c+7)%7,z=Math.ceil((H+S)/7),O=X?this.maxRows>z?this.maxRows:z:z,this.maxRows=O,A=this._daylightSavingAdjust(new Date(te,Z,1-H)),N=0;O>N;N++){for(T+="<tr>",W=u?"<td class='ui-datepicker-week-col'>"+this._get(t,"calculateWeek")(A)+"</td>":"",w=0;7>w;w++)E=m?m.apply(t.input?t.input[0]:null,[A]):[!0,""],F=A.getMonth()!==Z,L=F&&!v||!E[0]||Q&&Q>A||J&&A>J,W+="<td class='"+((w+c+6)%7>=5?" ui-datepicker-week-end":"")+(F?" ui-datepicker-other-month":"")+(A.getTime()===D.getTime()&&Z===t.selectedMonth&&t._keyEvent||b.getTime()===A.getTime()&&b.getTime()===D.getTime()?" "+this._dayOverClass:"")+(L?" "+this._unselectableClass+" ui-state-disabled":"")+(F&&!_?"":" "+E[1]+(A.getTime()===G.getTime()?" "+this._currentClass:"")+(A.getTime()===B.getTime()?" ui-datepicker-today":""))+"'"+(F&&!_||!E[2]?"":" title='"+E[2].replace(/'/g,"&#39;")+"'")+(L?"":" data-handler='selectDay' data-event='click' data-month='"+A.getMonth()+"' data-year='"+A.getFullYear()+"'")+">"+(F&&!_?"&#xa0;":L?"<span class='ui-state-default'>"+A.getDate()+"</span>":"<a class='ui-state-default"+(A.getTime()===B.getTime()?" ui-state-highlight":"")+(A.getTime()===G.getTime()?" ui-state-active":"")+(F?" ui-priority-secondary":"")+"' href='#'>"+A.getDate()+"</a>")+"</td>",A.setDate(A.getDate()+1),A=this._daylightSavingAdjust(A);T+=W+"</tr>"}Z++,Z>11&&(Z=0,te++),T+="</tbody></table>"+(X?"</div>"+(U[0]>0&&C===U[1]-1?"<div class='ui-datepicker-row-break'></div>":""):""),x+=T}y+=x}return y+=l,t._keyEvent=!1,y},_generateMonthYearHeader:function(t,e,i,s,n,o,a,r){var h,l,c,u,d,p,f,g,m=this._get(t,"changeMonth"),_=this._get(t,"changeYear"),v=this._get(t,"showMonthAfterYear"),b="<div class='ui-datepicker-title'>",y="";if(o||!m)y+="<span class='ui-datepicker-month'>"+a[e]+"</span>";else{for(h=s&&s.getFullYear()===i,l=n&&n.getFullYear()===i,y+="<select class='ui-datepicker-month' data-handler='selectMonth' data-event='change'>",c=0;12>c;c++)(!h||c>=s.getMonth())&&(!l||n.getMonth()>=c)&&(y+="<option value='"+c+"'"+(c===e?" selected='selected'":"")+">"+r[c]+"</option>");y+="</select>"}if(v||(b+=y+(!o&&m&&_?"":"&#xa0;")),!t.yearshtml)if(t.yearshtml="",o||!_)b+="<span class='ui-datepicker-year'>"+i+"</span>";else{for(u=this._get(t,"yearRange").split(":"),d=(new Date).getFullYear(),p=function(t){var e=t.match(/c[+\-].*/)?i+parseInt(t.substring(1),10):t.match(/[+\-].*/)?d+parseInt(t,10):parseInt(t,10);return isNaN(e)?d:e},f=p(u[0]),g=Math.max(f,p(u[1]||"")),f=s?Math.max(f,s.getFullYear()):f,g=n?Math.min(g,n.getFullYear()):g,t.yearshtml+="<select class='ui-datepicker-year' data-handler='selectYear' data-event='change'>";g>=f;f++)t.yearshtml+="<option value='"+f+"'"+(f===i?" selected='selected'":"")+">"+f+"</option>";t.yearshtml+="</select>",b+=t.yearshtml,t.yearshtml=null}return b+=this._get(t,"yearSuffix"),v&&(b+=(!o&&m&&_?"":"&#xa0;")+y),b+="</div>"},_adjustInstDate:function(t,e,i){var s=t.selectedYear+("Y"===i?e:0),n=t.selectedMonth+("M"===i?e:0),o=Math.min(t.selectedDay,this._getDaysInMonth(s,n))+("D"===i?e:0),a=this._restrictMinMax(t,this._daylightSavingAdjust(new Date(s,n,o)));t.selectedDay=a.getDate(),t.drawMonth=t.selectedMonth=a.getMonth(),t.drawYear=t.selectedYear=a.getFullYear(),("M"===i||"Y"===i)&&this._notifyChange(t)},_restrictMinMax:function(t,e){var i=this._getMinMaxDate(t,"min"),s=this._getMinMaxDate(t,"max"),n=i&&i>e?i:e;return s&&n>s?s:n},_notifyChange:function(t){var e=this._get(t,"onChangeMonthYear");e&&e.apply(t.input?t.input[0]:null,[t.selectedYear,t.selectedMonth+1,t])},_getNumberOfMonths:function(t){var e=this._get(t,"numberOfMonths");return null==e?[1,1]:"number"==typeof e?[1,e]:e},_getMinMaxDate:function(t,e){return this._determineDate(t,this._get(t,e+"Date"),null)},_getDaysInMonth:function(t,e){return 32-this._daylightSavingAdjust(new Date(t,e,32)).getDate()},_getFirstDayOfMonth:function(t,e){return new Date(t,e,1).getDay()},_canAdjustMonth:function(t,e,i,s){var n=this._getNumberOfMonths(t),o=this._daylightSavingAdjust(new Date(i,s+(0>e?e:n[0]*n[1]),1));return 0>e&&o.setDate(this._getDaysInMonth(o.getFullYear(),o.getMonth())),this._isInRange(t,o)},_isInRange:function(t,e){var i,s,n=this._getMinMaxDate(t,"min"),o=this._getMinMaxDate(t,"max"),a=null,r=null,h=this._get(t,"yearRange");return h&&(i=h.split(":"),s=(new Date).getFullYear(),a=parseInt(i[0],10),r=parseInt(i[1],10),i[0].match(/[+\-].*/)&&(a+=s),i[1].match(/[+\-].*/)&&(r+=s)),(!n||e.getTime()>=n.getTime())&&(!o||e.getTime()<=o.getTime())&&(!a||e.getFullYear()>=a)&&(!r||r>=e.getFullYear())},_getFormatConfig:function(t){var e=this._get(t,"shortYearCutoff");return e="string"!=typeof e?e:(new Date).getFullYear()%100+parseInt(e,10),{shortYearCutoff:e,dayNamesShort:this._get(t,"dayNamesShort"),dayNames:this._get(t,"dayNames"),monthNamesShort:this._get(t,"monthNamesShort"),monthNames:this._get(t,"monthNames")}},_formatDate:function(t,e,i,s){e||(t.currentDay=t.selectedDay,t.currentMonth=t.selectedMonth,t.currentYear=t.selectedYear);var n=e?"object"==typeof e?e:this._daylightSavingAdjust(new Date(s,i,e)):this._daylightSavingAdjust(new Date(t.currentYear,t.currentMonth,t.currentDay));return this.formatDate(this._get(t,"dateFormat"),n,this._getFormatConfig(t))}}),t.fn.datepicker=function(e){if(!this.length)return this;t.datepicker.initialized||(t(document).on("mousedown",t.datepicker._checkExternalClick),t.datepicker.initialized=!0),0===t("#"+t.datepicker._mainDivId).length&&t("body").append(t.datepicker.dpDiv);var i=Array.prototype.slice.call(arguments,1);return"string"!=typeof e||"isDisabled"!==e&&"getDate"!==e&&"widget"!==e?"option"===e&&2===arguments.length&&"string"==typeof arguments[1]?t.datepicker["_"+e+"Datepicker"].apply(t.datepicker,[this[0]].concat(i)):this.each(function(){"string"==typeof e?t.datepicker["_"+e+"Datepicker"].apply(t.datepicker,[this].concat(i)):t.datepicker._attachDatepicker(this,e)}):t.datepicker["_"+e+"Datepicker"].apply(t.datepicker,[this[0]].concat(i))},t.datepicker=new s,t.datepicker.initialized=!1,t.datepicker.uuid=(new Date).getTime(),t.datepicker.version="1.12.1",t.datepicker,t.ui.ie=!!/msie [\w.]+/.exec(navigator.userAgent.toLowerCase());var _=!1;t(document).on("mouseup",function(){_=!1}),t.widget("ui.mouse",{version:"1.12.1",options:{cancel:"input, textarea, button, select, option",distance:1,delay:0},_mouseInit:function(){var e=this;this.element.on("mousedown."+this.widgetName,function(t){return e._mouseDown(t)}).on("click."+this.widgetName,function(i){return!0===t.data(i.target,e.widgetName+".preventClickEvent")?(t.removeData(i.target,e.widgetName+".preventClickEvent"),i.stopImmediatePropagation(),!1):void 0}),this.started=!1},_mouseDestroy:function(){this.element.off("."+this.widgetName),this._mouseMoveDelegate&&this.document.off("mousemove."+this.widgetName,this._mouseMoveDelegate).off("mouseup."+this.widgetName,this._mouseUpDelegate)},_mouseDown:function(e){if(!_){this._mouseMoved=!1,this._mouseStarted&&this._mouseUp(e),this._mouseDownEvent=e;var i=this,s=1===e.which,n="string"==typeof this.options.cancel&&e.target.nodeName?t(e.target).closest(this.options.cancel).length:!1;return s&&!n&&this._mouseCapture(e)?(this.mouseDelayMet=!this.options.delay,this.mouseDelayMet||(this._mouseDelayTimer=setTimeout(function(){i.mouseDelayMet=!0},this.options.delay)),this._mouseDistanceMet(e)&&this._mouseDelayMet(e)&&(this._mouseStarted=this._mouseStart(e)!==!1,!this._mouseStarted)?(e.preventDefault(),!0):(!0===t.data(e.target,this.widgetName+".preventClickEvent")&&t.removeData(e.target,this.widgetName+".preventClickEvent"),this._mouseMoveDelegate=function(t){return i._mouseMove(t)},this._mouseUpDelegate=function(t){return i._mouseUp(t)},this.document.on("mousemove."+this.widgetName,this._mouseMoveDelegate).on("mouseup."+this.widgetName,this._mouseUpDelegate),e.preventDefault(),_=!0,!0)):!0}},_mouseMove:function(e){if(this._mouseMoved){if(t.ui.ie&&(!document.documentMode||9>document.documentMode)&&!e.button)return this._mouseUp(e);if(!e.which)if(e.originalEvent.altKey||e.originalEvent.ctrlKey||e.originalEvent.metaKey||e.originalEvent.shiftKey)this.ignoreMissingWhich=!0;else if(!this.ignoreMissingWhich)return this._mouseUp(e)}return(e.which||e.button)&&(this._mouseMoved=!0),this._mouseStarted?(this._mouseDrag(e),e.preventDefault()):(this._mouseDistanceMet(e)&&this._mouseDelayMet(e)&&(this._mouseStarted=this._mouseStart(this._mouseDownEvent,e)!==!1,this._mouseStarted?this._mouseDrag(e):this._mouseUp(e)),!this._mouseStarted)},_mouseUp:function(e){this.document.off("mousemove."+this.widgetName,this._mouseMoveDelegate).off("mouseup."+this.widgetName,this._mouseUpDelegate),this._mouseStarted&&(this._mouseStarted=!1,e.target===this._mouseDownEvent.target&&t.data(e.target,this.widgetName+".preventClickEvent",!0),this._mouseStop(e)),this._mouseDelayTimer&&(clearTimeout(this._mouseDelayTimer),delete this._mouseDelayTimer),this.ignoreMissingWhich=!1,_=!1,e.preventDefault()},_mouseDistanceMet:function(t){return Math.max(Math.abs(this._mouseDownEvent.pageX-t.pageX),Math.abs(this._mouseDownEvent.pageY-t.pageY))>=this.options.distance},_mouseDelayMet:function(){return this.mouseDelayMet},_mouseStart:function(){},_mouseDrag:function(){},_mouseStop:function(){},_mouseCapture:function(){return!0}}),t.ui.plugin={add:function(e,i,s){var n,o=t.ui[e].prototype;for(n in s)o.plugins[n]=o.plugins[n]||[],o.plugins[n].push([i,s[n]])},call:function(t,e,i,s){var n,o=t.plugins[e];if(o&&(s||t.element[0].parentNode&&11!==t.element[0].parentNode.nodeType))for(n=0;o.length>n;n++)t.options[o[n][0]]&&o[n][1].apply(t.element,i)}},t.ui.safeBlur=function(e){e&&"body"!==e.nodeName.toLowerCase()&&t(e).trigger("blur")},t.widget("ui.draggable",t.ui.mouse,{version:"1.12.1",widgetEventPrefix:"drag",options:{addClasses:!0,appendTo:"parent",axis:!1,connectToSortable:!1,containment:!1,cursor:"auto",cursorAt:!1,grid:!1,handle:!1,helper:"original",iframeFix:!1,opacity:!1,refreshPositions:!1,revert:!1,revertDuration:500,scope:"default",scroll:!0,scrollSensitivity:20,scrollSpeed:20,snap:!1,snapMode:"both",snapTolerance:20,stack:!1,zIndex:!1,drag:null,start:null,stop:null},_create:function(){"original"===this.options.helper&&this._setPositionRelative(),this.options.addClasses&&this._addClass("ui-draggable"),this._setHandleClassName(),this._mouseInit()},_setOption:function(t,e){this._super(t,e),"handle"===t&&(this._removeHandleClassName(),this._setHandleClassName())},_destroy:function(){return(this.helper||this.element).is(".ui-draggable-dragging")?(this.destroyOnClear=!0,void 0):(this._removeHandleClassName(),this._mouseDestroy(),void 0)},_mouseCapture:function(e){var i=this.options;return this.helper||i.disabled||t(e.target).closest(".ui-resizable-handle").length>0?!1:(this.handle=this._getHandle(e),this.handle?(this._blurActiveElement(e),this._blockFrames(i.iframeFix===!0?"iframe":i.iframeFix),!0):!1)},_blockFrames:function(e){this.iframeBlocks=this.document.find(e).map(function(){var e=t(this);return t("<div>").css("position","absolute").appendTo(e.parent()).outerWidth(e.outerWidth()).outerHeight(e.outerHeight()).offset(e.offset())[0]})},_unblockFrames:function(){this.iframeBlocks&&(this.iframeBlocks.remove(),delete this.iframeBlocks)},_blurActiveElement:function(e){var i=t.ui.safeActiveElement(this.document[0]),s=t(e.target);s.closest(i).length||t.ui.safeBlur(i)},_mouseStart:function(e){var i=this.options;return this.helper=this._createHelper(e),this._addClass(this.helper,"ui-draggable-dragging"),this._cacheHelperProportions(),t.ui.ddmanager&&(t.ui.ddmanager.current=this),this._cacheMargins(),this.cssPosition=this.helper.css("position"),this.scrollParent=this.helper.scrollParent(!0),this.offsetParent=this.helper.offsetParent(),this.hasFixedAncestor=this.helper.parents().filter(function(){return"fixed"===t(this).css("position")}).length>0,this.positionAbs=this.element.offset(),this._refreshOffsets(e),this.originalPosition=this.position=this._generatePosition(e,!1),this.originalPageX=e.pageX,this.originalPageY=e.pageY,i.cursorAt&&this._adjustOffsetFromHelper(i.cursorAt),this._setContainment(),this._trigger("start",e)===!1?(this._clear(),!1):(this._cacheHelperProportions(),t.ui.ddmanager&&!i.dropBehaviour&&t.ui.ddmanager.prepareOffsets(this,e),this._mouseDrag(e,!0),t.ui.ddmanager&&t.ui.ddmanager.dragStart(this,e),!0)},_refreshOffsets:function(t){this.offset={top:this.positionAbs.top-this.margins.top,left:this.positionAbs.left-this.margins.left,scroll:!1,parent:this._getParentOffset(),relative:this._getRelativeOffset()},this.offset.click={left:t.pageX-this.offset.left,top:t.pageY-this.offset.top}},_mouseDrag:function(e,i){if(this.hasFixedAncestor&&(this.offset.parent=this._getParentOffset()),this.position=this._generatePosition(e,!0),this.positionAbs=this._convertPositionTo("absolute"),!i){var s=this._uiHash();if(this._trigger("drag",e,s)===!1)return this._mouseUp(new t.Event("mouseup",e)),!1;this.position=s.position}return this.helper[0].style.left=this.position.left+"px",this.helper[0].style.top=this.position.top+"px",t.ui.ddmanager&&t.ui.ddmanager.drag(this,e),!1},_mouseStop:function(e){var i=this,s=!1;return t.ui.ddmanager&&!this.options.dropBehaviour&&(s=t.ui.ddmanager.drop(this,e)),this.dropped&&(s=this.dropped,this.dropped=!1),"invalid"===this.options.revert&&!s||"valid"===this.options.revert&&s||this.options.revert===!0||t.isFunction(this.options.revert)&&this.options.revert.call(this.element,s)?t(this.helper).animate(this.originalPosition,parseInt(this.options.revertDuration,10),function(){i._trigger("stop",e)!==!1&&i._clear()}):this._trigger("stop",e)!==!1&&this._clear(),!1},_mouseUp:function(e){return this._unblockFrames(),t.ui.ddmanager&&t.ui.ddmanager.dragStop(this,e),this.handleElement.is(e.target)&&this.element.trigger("focus"),t.ui.mouse.prototype._mouseUp.call(this,e)},cancel:function(){return this.helper.is(".ui-draggable-dragging")?this._mouseUp(new t.Event("mouseup",{target:this.element[0]})):this._clear(),this},_getHandle:function(e){return this.options.handle?!!t(e.target).closest(this.element.find(this.options.handle)).length:!0},_setHandleClassName:function(){this.handleElement=this.options.handle?this.element.find(this.options.handle):this.element,this._addClass(this.handleElement,"ui-draggable-handle")},_removeHandleClassName:function(){this._removeClass(this.handleElement,"ui-draggable-handle")},_createHelper:function(e){var i=this.options,s=t.isFunction(i.helper),n=s?t(i.helper.apply(this.element[0],[e])):"clone"===i.helper?this.element.clone().removeAttr("id"):this.element;return n.parents("body").length||n.appendTo("parent"===i.appendTo?this.element[0].parentNode:i.appendTo),s&&n[0]===this.element[0]&&this._setPositionRelative(),n[0]===this.element[0]||/(fixed|absolute)/.test(n.css("position"))||n.css("position","absolute"),n},_setPositionRelative:function(){/^(?:r|a|f)/.test(this.element.css("position"))||(this.element[0].style.position="relative")},_adjustOffsetFromHelper:function(e){"string"==typeof e&&(e=e.split(" ")),t.isArray(e)&&(e={left:+e[0],top:+e[1]||0}),"left"in e&&(this.offset.click.left=e.left+this.margins.left),"right"in e&&(this.offset.click.left=this.helperProportions.width-e.right+this.margins.left),"top"in e&&(this.offset.click.top=e.top+this.margins.top),"bottom"in e&&(this.offset.click.top=this.helperProportions.height-e.bottom+this.margins.top)},_isRootNode:function(t){return/(html|body)/i.test(t.tagName)||t===this.document[0]},_getParentOffset:function(){var e=this.offsetParent.offset(),i=this.document[0];return"absolute"===this.cssPosition&&this.scrollParent[0]!==i&&t.contains(this.scrollParent[0],this.offsetParent[0])&&(e.left+=this.scrollParent.scrollLeft(),e.top+=this.scrollParent.scrollTop()),this._isRootNode(this.offsetParent[0])&&(e={top:0,left:0}),{top:e.top+(parseInt(this.offsetParent.css("borderTopWidth"),10)||0),left:e.left+(parseInt(this.offsetParent.css("borderLeftWidth"),10)||0)}},_getRelativeOffset:function(){if("relative"!==this.cssPosition)return{top:0,left:0};var t=this.element.position(),e=this._isRootNode(this.scrollParent[0]);return{top:t.top-(parseInt(this.helper.css("top"),10)||0)+(e?0:this.scrollParent.scrollTop()),left:t.left-(parseInt(this.helper.css("left"),10)||0)+(e?0:this.scrollParent.scrollLeft())}
+},_cacheMargins:function(){this.margins={left:parseInt(this.element.css("marginLeft"),10)||0,top:parseInt(this.element.css("marginTop"),10)||0,right:parseInt(this.element.css("marginRight"),10)||0,bottom:parseInt(this.element.css("marginBottom"),10)||0}},_cacheHelperProportions:function(){this.helperProportions={width:this.helper.outerWidth(),height:this.helper.outerHeight()}},_setContainment:function(){var e,i,s,n=this.options,o=this.document[0];return this.relativeContainer=null,n.containment?"window"===n.containment?(this.containment=[t(window).scrollLeft()-this.offset.relative.left-this.offset.parent.left,t(window).scrollTop()-this.offset.relative.top-this.offset.parent.top,t(window).scrollLeft()+t(window).width()-this.helperProportions.width-this.margins.left,t(window).scrollTop()+(t(window).height()||o.body.parentNode.scrollHeight)-this.helperProportions.height-this.margins.top],void 0):"document"===n.containment?(this.containment=[0,0,t(o).width()-this.helperProportions.width-this.margins.left,(t(o).height()||o.body.parentNode.scrollHeight)-this.helperProportions.height-this.margins.top],void 0):n.containment.constructor===Array?(this.containment=n.containment,void 0):("parent"===n.containment&&(n.containment=this.helper[0].parentNode),i=t(n.containment),s=i[0],s&&(e=/(scroll|auto)/.test(i.css("overflow")),this.containment=[(parseInt(i.css("borderLeftWidth"),10)||0)+(parseInt(i.css("paddingLeft"),10)||0),(parseInt(i.css("borderTopWidth"),10)||0)+(parseInt(i.css("paddingTop"),10)||0),(e?Math.max(s.scrollWidth,s.offsetWidth):s.offsetWidth)-(parseInt(i.css("borderRightWidth"),10)||0)-(parseInt(i.css("paddingRight"),10)||0)-this.helperProportions.width-this.margins.left-this.margins.right,(e?Math.max(s.scrollHeight,s.offsetHeight):s.offsetHeight)-(parseInt(i.css("borderBottomWidth"),10)||0)-(parseInt(i.css("paddingBottom"),10)||0)-this.helperProportions.height-this.margins.top-this.margins.bottom],this.relativeContainer=i),void 0):(this.containment=null,void 0)},_convertPositionTo:function(t,e){e||(e=this.position);var i="absolute"===t?1:-1,s=this._isRootNode(this.scrollParent[0]);return{top:e.top+this.offset.relative.top*i+this.offset.parent.top*i-("fixed"===this.cssPosition?-this.offset.scroll.top:s?0:this.offset.scroll.top)*i,left:e.left+this.offset.relative.left*i+this.offset.parent.left*i-("fixed"===this.cssPosition?-this.offset.scroll.left:s?0:this.offset.scroll.left)*i}},_generatePosition:function(t,e){var i,s,n,o,a=this.options,r=this._isRootNode(this.scrollParent[0]),h=t.pageX,l=t.pageY;return r&&this.offset.scroll||(this.offset.scroll={top:this.scrollParent.scrollTop(),left:this.scrollParent.scrollLeft()}),e&&(this.containment&&(this.relativeContainer?(s=this.relativeContainer.offset(),i=[this.containment[0]+s.left,this.containment[1]+s.top,this.containment[2]+s.left,this.containment[3]+s.top]):i=this.containment,t.pageX-this.offset.click.left<i[0]&&(h=i[0]+this.offset.click.left),t.pageY-this.offset.click.top<i[1]&&(l=i[1]+this.offset.click.top),t.pageX-this.offset.click.left>i[2]&&(h=i[2]+this.offset.click.left),t.pageY-this.offset.click.top>i[3]&&(l=i[3]+this.offset.click.top)),a.grid&&(n=a.grid[1]?this.originalPageY+Math.round((l-this.originalPageY)/a.grid[1])*a.grid[1]:this.originalPageY,l=i?n-this.offset.click.top>=i[1]||n-this.offset.click.top>i[3]?n:n-this.offset.click.top>=i[1]?n-a.grid[1]:n+a.grid[1]:n,o=a.grid[0]?this.originalPageX+Math.round((h-this.originalPageX)/a.grid[0])*a.grid[0]:this.originalPageX,h=i?o-this.offset.click.left>=i[0]||o-this.offset.click.left>i[2]?o:o-this.offset.click.left>=i[0]?o-a.grid[0]:o+a.grid[0]:o),"y"===a.axis&&(h=this.originalPageX),"x"===a.axis&&(l=this.originalPageY)),{top:l-this.offset.click.top-this.offset.relative.top-this.offset.parent.top+("fixed"===this.cssPosition?-this.offset.scroll.top:r?0:this.offset.scroll.top),left:h-this.offset.click.left-this.offset.relative.left-this.offset.parent.left+("fixed"===this.cssPosition?-this.offset.scroll.left:r?0:this.offset.scroll.left)}},_clear:function(){this._removeClass(this.helper,"ui-draggable-dragging"),this.helper[0]===this.element[0]||this.cancelHelperRemoval||this.helper.remove(),this.helper=null,this.cancelHelperRemoval=!1,this.destroyOnClear&&this.destroy()},_trigger:function(e,i,s){return s=s||this._uiHash(),t.ui.plugin.call(this,e,[i,s,this],!0),/^(drag|start|stop)/.test(e)&&(this.positionAbs=this._convertPositionTo("absolute"),s.offset=this.positionAbs),t.Widget.prototype._trigger.call(this,e,i,s)},plugins:{},_uiHash:function(){return{helper:this.helper,position:this.position,originalPosition:this.originalPosition,offset:this.positionAbs}}}),t.ui.plugin.add("draggable","connectToSortable",{start:function(e,i,s){var n=t.extend({},i,{item:s.element});s.sortables=[],t(s.options.connectToSortable).each(function(){var i=t(this).sortable("instance");i&&!i.options.disabled&&(s.sortables.push(i),i.refreshPositions(),i._trigger("activate",e,n))})},stop:function(e,i,s){var n=t.extend({},i,{item:s.element});s.cancelHelperRemoval=!1,t.each(s.sortables,function(){var t=this;t.isOver?(t.isOver=0,s.cancelHelperRemoval=!0,t.cancelHelperRemoval=!1,t._storedCSS={position:t.placeholder.css("position"),top:t.placeholder.css("top"),left:t.placeholder.css("left")},t._mouseStop(e),t.options.helper=t.options._helper):(t.cancelHelperRemoval=!0,t._trigger("deactivate",e,n))})},drag:function(e,i,s){t.each(s.sortables,function(){var n=!1,o=this;o.positionAbs=s.positionAbs,o.helperProportions=s.helperProportions,o.offset.click=s.offset.click,o._intersectsWith(o.containerCache)&&(n=!0,t.each(s.sortables,function(){return this.positionAbs=s.positionAbs,this.helperProportions=s.helperProportions,this.offset.click=s.offset.click,this!==o&&this._intersectsWith(this.containerCache)&&t.contains(o.element[0],this.element[0])&&(n=!1),n})),n?(o.isOver||(o.isOver=1,s._parent=i.helper.parent(),o.currentItem=i.helper.appendTo(o.element).data("ui-sortable-item",!0),o.options._helper=o.options.helper,o.options.helper=function(){return i.helper[0]},e.target=o.currentItem[0],o._mouseCapture(e,!0),o._mouseStart(e,!0,!0),o.offset.click.top=s.offset.click.top,o.offset.click.left=s.offset.click.left,o.offset.parent.left-=s.offset.parent.left-o.offset.parent.left,o.offset.parent.top-=s.offset.parent.top-o.offset.parent.top,s._trigger("toSortable",e),s.dropped=o.element,t.each(s.sortables,function(){this.refreshPositions()}),s.currentItem=s.element,o.fromOutside=s),o.currentItem&&(o._mouseDrag(e),i.position=o.position)):o.isOver&&(o.isOver=0,o.cancelHelperRemoval=!0,o.options._revert=o.options.revert,o.options.revert=!1,o._trigger("out",e,o._uiHash(o)),o._mouseStop(e,!0),o.options.revert=o.options._revert,o.options.helper=o.options._helper,o.placeholder&&o.placeholder.remove(),i.helper.appendTo(s._parent),s._refreshOffsets(e),i.position=s._generatePosition(e,!0),s._trigger("fromSortable",e),s.dropped=!1,t.each(s.sortables,function(){this.refreshPositions()}))})}}),t.ui.plugin.add("draggable","cursor",{start:function(e,i,s){var n=t("body"),o=s.options;n.css("cursor")&&(o._cursor=n.css("cursor")),n.css("cursor",o.cursor)},stop:function(e,i,s){var n=s.options;n._cursor&&t("body").css("cursor",n._cursor)}}),t.ui.plugin.add("draggable","opacity",{start:function(e,i,s){var n=t(i.helper),o=s.options;n.css("opacity")&&(o._opacity=n.css("opacity")),n.css("opacity",o.opacity)},stop:function(e,i,s){var n=s.options;n._opacity&&t(i.helper).css("opacity",n._opacity)}}),t.ui.plugin.add("draggable","scroll",{start:function(t,e,i){i.scrollParentNotHidden||(i.scrollParentNotHidden=i.helper.scrollParent(!1)),i.scrollParentNotHidden[0]!==i.document[0]&&"HTML"!==i.scrollParentNotHidden[0].tagName&&(i.overflowOffset=i.scrollParentNotHidden.offset())},drag:function(e,i,s){var n=s.options,o=!1,a=s.scrollParentNotHidden[0],r=s.document[0];a!==r&&"HTML"!==a.tagName?(n.axis&&"x"===n.axis||(s.overflowOffset.top+a.offsetHeight-e.pageY<n.scrollSensitivity?a.scrollTop=o=a.scrollTop+n.scrollSpeed:e.pageY-s.overflowOffset.top<n.scrollSensitivity&&(a.scrollTop=o=a.scrollTop-n.scrollSpeed)),n.axis&&"y"===n.axis||(s.overflowOffset.left+a.offsetWidth-e.pageX<n.scrollSensitivity?a.scrollLeft=o=a.scrollLeft+n.scrollSpeed:e.pageX-s.overflowOffset.left<n.scrollSensitivity&&(a.scrollLeft=o=a.scrollLeft-n.scrollSpeed))):(n.axis&&"x"===n.axis||(e.pageY-t(r).scrollTop()<n.scrollSensitivity?o=t(r).scrollTop(t(r).scrollTop()-n.scrollSpeed):t(window).height()-(e.pageY-t(r).scrollTop())<n.scrollSensitivity&&(o=t(r).scrollTop(t(r).scrollTop()+n.scrollSpeed))),n.axis&&"y"===n.axis||(e.pageX-t(r).scrollLeft()<n.scrollSensitivity?o=t(r).scrollLeft(t(r).scrollLeft()-n.scrollSpeed):t(window).width()-(e.pageX-t(r).scrollLeft())<n.scrollSensitivity&&(o=t(r).scrollLeft(t(r).scrollLeft()+n.scrollSpeed)))),o!==!1&&t.ui.ddmanager&&!n.dropBehaviour&&t.ui.ddmanager.prepareOffsets(s,e)}}),t.ui.plugin.add("draggable","snap",{start:function(e,i,s){var n=s.options;s.snapElements=[],t(n.snap.constructor!==String?n.snap.items||":data(ui-draggable)":n.snap).each(function(){var e=t(this),i=e.offset();this!==s.element[0]&&s.snapElements.push({item:this,width:e.outerWidth(),height:e.outerHeight(),top:i.top,left:i.left})})},drag:function(e,i,s){var n,o,a,r,h,l,c,u,d,p,f=s.options,g=f.snapTolerance,m=i.offset.left,_=m+s.helperProportions.width,v=i.offset.top,b=v+s.helperProportions.height;for(d=s.snapElements.length-1;d>=0;d--)h=s.snapElements[d].left-s.margins.left,l=h+s.snapElements[d].width,c=s.snapElements[d].top-s.margins.top,u=c+s.snapElements[d].height,h-g>_||m>l+g||c-g>b||v>u+g||!t.contains(s.snapElements[d].item.ownerDocument,s.snapElements[d].item)?(s.snapElements[d].snapping&&s.options.snap.release&&s.options.snap.release.call(s.element,e,t.extend(s._uiHash(),{snapItem:s.snapElements[d].item})),s.snapElements[d].snapping=!1):("inner"!==f.snapMode&&(n=g>=Math.abs(c-b),o=g>=Math.abs(u-v),a=g>=Math.abs(h-_),r=g>=Math.abs(l-m),n&&(i.position.top=s._convertPositionTo("relative",{top:c-s.helperProportions.height,left:0}).top),o&&(i.position.top=s._convertPositionTo("relative",{top:u,left:0}).top),a&&(i.position.left=s._convertPositionTo("relative",{top:0,left:h-s.helperProportions.width}).left),r&&(i.position.left=s._convertPositionTo("relative",{top:0,left:l}).left)),p=n||o||a||r,"outer"!==f.snapMode&&(n=g>=Math.abs(c-v),o=g>=Math.abs(u-b),a=g>=Math.abs(h-m),r=g>=Math.abs(l-_),n&&(i.position.top=s._convertPositionTo("relative",{top:c,left:0}).top),o&&(i.position.top=s._convertPositionTo("relative",{top:u-s.helperProportions.height,left:0}).top),a&&(i.position.left=s._convertPositionTo("relative",{top:0,left:h}).left),r&&(i.position.left=s._convertPositionTo("relative",{top:0,left:l-s.helperProportions.width}).left)),!s.snapElements[d].snapping&&(n||o||a||r||p)&&s.options.snap.snap&&s.options.snap.snap.call(s.element,e,t.extend(s._uiHash(),{snapItem:s.snapElements[d].item})),s.snapElements[d].snapping=n||o||a||r||p)}}),t.ui.plugin.add("draggable","stack",{start:function(e,i,s){var 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s.grid?[s.grid,s.grid]:s.grid,l=h[0]||1,c=h[1]||1,u=Math.round((n.width-o.width)/l)*l,d=Math.round((n.height-o.height)/c)*c,p=o.width+u,f=o.height+d,g=s.maxWidth&&p>s.maxWidth,m=s.maxHeight&&f>s.maxHeight,_=s.minWidth&&s.minWidth>p,v=s.minHeight&&s.minHeight>f;s.grid=h,_&&(p+=l),v&&(f+=c),g&&(p-=l),m&&(f-=c),/^(se|s|e)$/.test(r)?(i.size.width=p,i.size.height=f):/^(ne)$/.test(r)?(i.size.width=p,i.size.height=f,i.position.top=a.top-d):/^(sw)$/.test(r)?(i.size.width=p,i.size.height=f,i.position.left=a.left-u):((0>=f-c||0>=p-l)&&(e=i._getPaddingPlusBorderDimensions(this)),f-c>0?(i.size.height=f,i.position.top=a.top-d):(f=c-e.height,i.size.height=f,i.position.top=a.top+o.height-f),p-l>0?(i.size.width=p,i.position.left=a.left-u):(p=l-e.width,i.size.width=p,i.position.left=a.left+o.width-p))}}),t.ui.resizable,t.widget("ui.dialog",{version:"1.12.1",options:{appendTo:"body",autoOpen:!0,buttons:[],classes:{"ui-dialog":"ui-corner-all","ui-dialog-titlebar":"ui-corner-all"},closeOnEscape:!0,closeText:"Close",draggable:!0,hide:null,height:"auto",maxHeight:null,maxWidth:null,minHeight:150,minWidth:150,modal:!1,position:{my:"center",at:"center",of:window,collision:"fit",using:function(e){var i=t(this).css(e).offset().top;0>i&&t(this).css("top",e.top-i)}},resizable:!0,show:null,title:null,width:300,beforeClose:null,close:null,drag:null,dragStart:null,dragStop:null,focus:null,open:null,resize:null,resizeStart:null,resizeStop:null},sizeRelatedOptions:{buttons:!0,height:!0,maxHeight:!0,maxWidth:!0,minHeight:!0,minWidth:!0,width:!0},resizableRelatedOptions:{maxHeight:!0,maxWidth:!0,minHeight:!0,minWidth:!0},_create:function(){this.originalCss={display:this.element[0].style.display,width:this.element[0].style.width,minHeight:this.element[0].style.minHeight,maxHeight:this.element[0].style.maxHeight,height:this.element[0].style.height},this.originalPosition={parent:this.element.parent(),index:this.element.parent().children().index(this.element)},this.originalTitle=this.element.attr("title"),null==this.options.title&&null!=this.originalTitle&&(this.options.title=this.originalTitle),this.options.disabled&&(this.options.disabled=!1),this._createWrapper(),this.element.show().removeAttr("title").appendTo(this.uiDialog),this._addClass("ui-dialog-content","ui-widget-content"),this._createTitlebar(),this._createButtonPane(),this.options.draggable&&t.fn.draggable&&this._makeDraggable(),this.options.resizable&&t.fn.resizable&&this._makeResizable(),this._isOpen=!1,this._trackFocus()},_init:function(){this.options.autoOpen&&this.open()},_appendTo:function(){var e=this.options.appendTo;return e&&(e.jquery||e.nodeType)?t(e):this.document.find(e||"body").eq(0)},_destroy:function(){var t,e=this.originalPosition;this._untrackInstance(),this._destroyOverlay(),this.element.removeUniqueId().css(this.originalCss).detach(),this.uiDialog.remove(),this.originalTitle&&this.element.attr("title",this.originalTitle),t=e.parent.children().eq(e.index),t.length&&t[0]!==this.element[0]?t.before(this.element):e.parent.append(this.element)},widget:function(){return this.uiDialog
+},disable:t.noop,enable:t.noop,close:function(e){var i=this;this._isOpen&&this._trigger("beforeClose",e)!==!1&&(this._isOpen=!1,this._focusedElement=null,this._destroyOverlay(),this._untrackInstance(),this.opener.filter(":focusable").trigger("focus").length||t.ui.safeBlur(t.ui.safeActiveElement(this.document[0])),this._hide(this.uiDialog,this.options.hide,function(){i._trigger("close",e)}))},isOpen:function(){return this._isOpen},moveToTop:function(){this._moveToTop()},_moveToTop:function(e,i){var s=!1,n=this.uiDialog.siblings(".ui-front:visible").map(function(){return+t(this).css("z-index")}).get(),o=Math.max.apply(null,n);return o>=+this.uiDialog.css("z-index")&&(this.uiDialog.css("z-index",o+1),s=!0),s&&!i&&this._trigger("focus",e),s},open:function(){var e=this;return this._isOpen?(this._moveToTop()&&this._focusTabbable(),void 0):(this._isOpen=!0,this.opener=t(t.ui.safeActiveElement(this.document[0])),this._size(),this._position(),this._createOverlay(),this._moveToTop(null,!0),this.overlay&&this.overlay.css("z-index",this.uiDialog.css("z-index")-1),this._show(this.uiDialog,this.options.show,function(){e._focusTabbable(),e._trigger("focus")}),this._makeFocusTarget(),this._trigger("open"),void 0)},_focusTabbable:function(){var t=this._focusedElement;t||(t=this.element.find("[autofocus]")),t.length||(t=this.element.find(":tabbable")),t.length||(t=this.uiDialogButtonPane.find(":tabbable")),t.length||(t=this.uiDialogTitlebarClose.filter(":tabbable")),t.length||(t=this.uiDialog),t.eq(0).trigger("focus")},_keepFocus:function(e){function i(){var e=t.ui.safeActiveElement(this.document[0]),i=this.uiDialog[0]===e||t.contains(this.uiDialog[0],e);i||this._focusTabbable()}e.preventDefault(),i.call(this),this._delay(i)},_createWrapper:function(){this.uiDialog=t("<div>").hide().attr({tabIndex:-1,role:"dialog"}).appendTo(this._appendTo()),this._addClass(this.uiDialog,"ui-dialog","ui-widget ui-widget-content ui-front"),this._on(this.uiDialog,{keydown:function(e){if(this.options.closeOnEscape&&!e.isDefaultPrevented()&&e.keyCode&&e.keyCode===t.ui.keyCode.ESCAPE)return e.preventDefault(),this.close(e),void 0;if(e.keyCode===t.ui.keyCode.TAB&&!e.isDefaultPrevented()){var i=this.uiDialog.find(":tabbable"),s=i.filter(":first"),n=i.filter(":last");e.target!==n[0]&&e.target!==this.uiDialog[0]||e.shiftKey?e.target!==s[0]&&e.target!==this.uiDialog[0]||!e.shiftKey||(this._delay(function(){n.trigger("focus")}),e.preventDefault()):(this._delay(function(){s.trigger("focus")}),e.preventDefault())}},mousedown:function(t){this._moveToTop(t)&&this._focusTabbable()}}),this.element.find("[aria-describedby]").length||this.uiDialog.attr({"aria-describedby":this.element.uniqueId().attr("id")})},_createTitlebar:function(){var e;this.uiDialogTitlebar=t("<div>"),this._addClass(this.uiDialogTitlebar,"ui-dialog-titlebar","ui-widget-header ui-helper-clearfix"),this._on(this.uiDialogTitlebar,{mousedown:function(e){t(e.target).closest(".ui-dialog-titlebar-close")||this.uiDialog.trigger("focus")}}),this.uiDialogTitlebarClose=t("<button type='button'></button>").button({label:t("<a>").text(this.options.closeText).html(),icon:"ui-icon-closethick",showLabel:!1}).appendTo(this.uiDialogTitlebar),this._addClass(this.uiDialogTitlebarClose,"ui-dialog-titlebar-close"),this._on(this.uiDialogTitlebarClose,{click:function(t){t.preventDefault(),this.close(t)}}),e=t("<span>").uniqueId().prependTo(this.uiDialogTitlebar),this._addClass(e,"ui-dialog-title"),this._title(e),this.uiDialogTitlebar.prependTo(this.uiDialog),this.uiDialog.attr({"aria-labelledby":e.attr("id")})},_title:function(t){this.options.title?t.text(this.options.title):t.html("&#160;")},_createButtonPane:function(){this.uiDialogButtonPane=t("<div>"),this._addClass(this.uiDialogButtonPane,"ui-dialog-buttonpane","ui-widget-content ui-helper-clearfix"),this.uiButtonSet=t("<div>").appendTo(this.uiDialogButtonPane),this._addClass(this.uiButtonSet,"ui-dialog-buttonset"),this._createButtons()},_createButtons:function(){var e=this,i=this.options.buttons;return this.uiDialogButtonPane.remove(),this.uiButtonSet.empty(),t.isEmptyObject(i)||t.isArray(i)&&!i.length?(this._removeClass(this.uiDialog,"ui-dialog-buttons"),void 0):(t.each(i,function(i,s){var n,o;s=t.isFunction(s)?{click:s,text:i}:s,s=t.extend({type:"button"},s),n=s.click,o={icon:s.icon,iconPosition:s.iconPosition,showLabel:s.showLabel,icons:s.icons,text:s.text},delete s.click,delete s.icon,delete s.iconPosition,delete s.showLabel,delete s.icons,"boolean"==typeof s.text&&delete s.text,t("<button></button>",s).button(o).appendTo(e.uiButtonSet).on("click",function(){n.apply(e.element[0],arguments)})}),this._addClass(this.uiDialog,"ui-dialog-buttons"),this.uiDialogButtonPane.appendTo(this.uiDialog),void 0)},_makeDraggable:function(){function e(t){return{position:t.position,offset:t.offset}}var i=this,s=this.options;this.uiDialog.draggable({cancel:".ui-dialog-content, .ui-dialog-titlebar-close",handle:".ui-dialog-titlebar",containment:"document",start:function(s,n){i._addClass(t(this),"ui-dialog-dragging"),i._blockFrames(),i._trigger("dragStart",s,e(n))},drag:function(t,s){i._trigger("drag",t,e(s))},stop:function(n,o){var a=o.offset.left-i.document.scrollLeft(),r=o.offset.top-i.document.scrollTop();s.position={my:"left top",at:"left"+(a>=0?"+":"")+a+" "+"top"+(r>=0?"+":"")+r,of:i.window},i._removeClass(t(this),"ui-dialog-dragging"),i._unblockFrames(),i._trigger("dragStop",n,e(o))}})},_makeResizable:function(){function e(t){return{originalPosition:t.originalPosition,originalSize:t.originalSize,position:t.position,size:t.size}}var i=this,s=this.options,n=s.resizable,o=this.uiDialog.css("position"),a="string"==typeof n?n:"n,e,s,w,se,sw,ne,nw";this.uiDialog.resizable({cancel:".ui-dialog-content",containment:"document",alsoResize:this.element,maxWidth:s.maxWidth,maxHeight:s.maxHeight,minWidth:s.minWidth,minHeight:this._minHeight(),handles:a,start:function(s,n){i._addClass(t(this),"ui-dialog-resizing"),i._blockFrames(),i._trigger("resizeStart",s,e(n))},resize:function(t,s){i._trigger("resize",t,e(s))},stop:function(n,o){var a=i.uiDialog.offset(),r=a.left-i.document.scrollLeft(),h=a.top-i.document.scrollTop();s.height=i.uiDialog.height(),s.width=i.uiDialog.width(),s.position={my:"left top",at:"left"+(r>=0?"+":"")+r+" "+"top"+(h>=0?"+":"")+h,of:i.window},i._removeClass(t(this),"ui-dialog-resizing"),i._unblockFrames(),i._trigger("resizeStop",n,e(o))}}).css("position",o)},_trackFocus:function(){this._on(this.widget(),{focusin:function(e){this._makeFocusTarget(),this._focusedElement=t(e.target)}})},_makeFocusTarget:function(){this._untrackInstance(),this._trackingInstances().unshift(this)},_untrackInstance:function(){var e=this._trackingInstances(),i=t.inArray(this,e);-1!==i&&e.splice(i,1)},_trackingInstances:function(){var t=this.document.data("ui-dialog-instances");return t||(t=[],this.document.data("ui-dialog-instances",t)),t},_minHeight:function(){var t=this.options;return"auto"===t.height?t.minHeight:Math.min(t.minHeight,t.height)},_position:function(){var t=this.uiDialog.is(":visible");t||this.uiDialog.show(),this.uiDialog.position(this.options.position),t||this.uiDialog.hide()},_setOptions:function(e){var i=this,s=!1,n={};t.each(e,function(t,e){i._setOption(t,e),t in i.sizeRelatedOptions&&(s=!0),t in i.resizableRelatedOptions&&(n[t]=e)}),s&&(this._size(),this._position()),this.uiDialog.is(":data(ui-resizable)")&&this.uiDialog.resizable("option",n)},_setOption:function(e,i){var s,n,o=this.uiDialog;"disabled"!==e&&(this._super(e,i),"appendTo"===e&&this.uiDialog.appendTo(this._appendTo()),"buttons"===e&&this._createButtons(),"closeText"===e&&this.uiDialogTitlebarClose.button({label:t("<a>").text(""+this.options.closeText).html()}),"draggable"===e&&(s=o.is(":data(ui-draggable)"),s&&!i&&o.draggable("destroy"),!s&&i&&this._makeDraggable()),"position"===e&&this._position(),"resizable"===e&&(n=o.is(":data(ui-resizable)"),n&&!i&&o.resizable("destroy"),n&&"string"==typeof i&&o.resizable("option","handles",i),n||i===!1||this._makeResizable()),"title"===e&&this._title(this.uiDialogTitlebar.find(".ui-dialog-title")))},_size:function(){var t,e,i,s=this.options;this.element.show().css({width:"auto",minHeight:0,maxHeight:"none",height:0}),s.minWidth>s.width&&(s.width=s.minWidth),t=this.uiDialog.css({height:"auto",width:s.width}).outerHeight(),e=Math.max(0,s.minHeight-t),i="number"==typeof s.maxHeight?Math.max(0,s.maxHeight-t):"none","auto"===s.height?this.element.css({minHeight:e,maxHeight:i,height:"auto"}):this.element.height(Math.max(0,s.height-t)),this.uiDialog.is(":data(ui-resizable)")&&this.uiDialog.resizable("option","minHeight",this._minHeight())},_blockFrames:function(){this.iframeBlocks=this.document.find("iframe").map(function(){var e=t(this);return t("<div>").css({position:"absolute",width:e.outerWidth(),height:e.outerHeight()}).appendTo(e.parent()).offset(e.offset())[0]})},_unblockFrames:function(){this.iframeBlocks&&(this.iframeBlocks.remove(),delete this.iframeBlocks)},_allowInteraction:function(e){return t(e.target).closest(".ui-dialog").length?!0:!!t(e.target).closest(".ui-datepicker").length},_createOverlay:function(){if(this.options.modal){var e=!0;this._delay(function(){e=!1}),this.document.data("ui-dialog-overlays")||this._on(this.document,{focusin:function(t){e||this._allowInteraction(t)||(t.preventDefault(),this._trackingInstances()[0]._focusTabbable())}}),this.overlay=t("<div>").appendTo(this._appendTo()),this._addClass(this.overlay,null,"ui-widget-overlay ui-front"),this._on(this.overlay,{mousedown:"_keepFocus"}),this.document.data("ui-dialog-overlays",(this.document.data("ui-dialog-overlays")||0)+1)}},_destroyOverlay:function(){if(this.options.modal&&this.overlay){var t=this.document.data("ui-dialog-overlays")-1;t?this.document.data("ui-dialog-overlays",t):(this._off(this.document,"focusin"),this.document.removeData("ui-dialog-overlays")),this.overlay.remove(),this.overlay=null}}}),t.uiBackCompat!==!1&&t.widget("ui.dialog",t.ui.dialog,{options:{dialogClass:""},_createWrapper:function(){this._super(),this.uiDialog.addClass(this.options.dialogClass)},_setOption:function(t,e){"dialogClass"===t&&this.uiDialog.removeClass(this.options.dialogClass).addClass(e),this._superApply(arguments)}}),t.ui.dialog,t.widget("ui.droppable",{version:"1.12.1",widgetEventPrefix:"drop",options:{accept:"*",addClasses:!0,greedy:!1,scope:"default",tolerance:"intersect",activate:null,deactivate:null,drop:null,out:null,over:null},_create:function(){var e,i=this.options,s=i.accept;this.isover=!1,this.isout=!0,this.accept=t.isFunction(s)?s:function(t){return t.is(s)},this.proportions=function(){return arguments.length?(e=arguments[0],void 0):e?e:e={width:this.element[0].offsetWidth,height:this.element[0].offsetHeight}},this._addToManager(i.scope),i.addClasses&&this._addClass("ui-droppable")},_addToManager:function(e){t.ui.ddmanager.droppables[e]=t.ui.ddmanager.droppables[e]||[],t.ui.ddmanager.droppables[e].push(this)},_splice:function(t){for(var e=0;t.length>e;e++)t[e]===this&&t.splice(e,1)},_destroy:function(){var e=t.ui.ddmanager.droppables[this.options.scope];this._splice(e)},_setOption:function(e,i){if("accept"===e)this.accept=t.isFunction(i)?i:function(t){return t.is(i)};else if("scope"===e){var s=t.ui.ddmanager.droppables[this.options.scope];this._splice(s),this._addToManager(i)}this._super(e,i)},_activate:function(e){var i=t.ui.ddmanager.current;this._addActiveClass(),i&&this._trigger("activate",e,this.ui(i))},_deactivate:function(e){var i=t.ui.ddmanager.current;this._removeActiveClass(),i&&this._trigger("deactivate",e,this.ui(i))},_over:function(e){var i=t.ui.ddmanager.current;i&&(i.currentItem||i.element)[0]!==this.element[0]&&this.accept.call(this.element[0],i.currentItem||i.element)&&(this._addHoverClass(),this._trigger("over",e,this.ui(i)))},_out:function(e){var i=t.ui.ddmanager.current;i&&(i.currentItem||i.element)[0]!==this.element[0]&&this.accept.call(this.element[0],i.currentItem||i.element)&&(this._removeHoverClass(),this._trigger("out",e,this.ui(i)))},_drop:function(e,i){var s=i||t.ui.ddmanager.current,n=!1;return s&&(s.currentItem||s.element)[0]!==this.element[0]?(this.element.find(":data(ui-droppable)").not(".ui-draggable-dragging").each(function(){var i=t(this).droppable("instance");return i.options.greedy&&!i.options.disabled&&i.options.scope===s.options.scope&&i.accept.call(i.element[0],s.currentItem||s.element)&&v(s,t.extend(i,{offset:i.element.offset()}),i.options.tolerance,e)?(n=!0,!1):void 0}),n?!1:this.accept.call(this.element[0],s.currentItem||s.element)?(this._removeActiveClass(),this._removeHoverClass(),this._trigger("drop",e,this.ui(s)),this.element):!1):!1},ui:function(t){return{draggable:t.currentItem||t.element,helper:t.helper,position:t.position,offset:t.positionAbs}},_addHoverClass:function(){this._addClass("ui-droppable-hover")},_removeHoverClass:function(){this._removeClass("ui-droppable-hover")},_addActiveClass:function(){this._addClass("ui-droppable-active")},_removeActiveClass:function(){this._removeClass("ui-droppable-active")}});var v=t.ui.intersect=function(){function t(t,e,i){return t>=e&&e+i>t}return function(e,i,s,n){if(!i.offset)return!1;var o=(e.positionAbs||e.position.absolute).left+e.margins.left,a=(e.positionAbs||e.position.absolute).top+e.margins.top,r=o+e.helperProportions.width,h=a+e.helperProportions.height,l=i.offset.left,c=i.offset.top,u=l+i.proportions().width,d=c+i.proportions().height;switch(s){case"fit":return o>=l&&u>=r&&a>=c&&d>=h;case"intersect":return o+e.helperProportions.width/2>l&&u>r-e.helperProportions.width/2&&a+e.helperProportions.height/2>c&&d>h-e.helperProportions.height/2;case"pointer":return t(n.pageY,c,i.proportions().height)&&t(n.pageX,l,i.proportions().width);case"touch":return(a>=c&&d>=a||h>=c&&d>=h||c>a&&h>d)&&(o>=l&&u>=o||r>=l&&u>=r||l>o&&r>u);default:return!1}}}();t.ui.ddmanager={current:null,droppables:{"default":[]},prepareOffsets:function(e,i){var s,n,o=t.ui.ddmanager.droppables[e.options.scope]||[],a=i?i.type:null,r=(e.currentItem||e.element).find(":data(ui-droppable)").addBack();t:for(s=0;o.length>s;s++)if(!(o[s].options.disabled||e&&!o[s].accept.call(o[s].element[0],e.currentItem||e.element))){for(n=0;r.length>n;n++)if(r[n]===o[s].element[0]){o[s].proportions().height=0;continue t}o[s].visible="none"!==o[s].element.css("display"),o[s].visible&&("mousedown"===a&&o[s]._activate.call(o[s],i),o[s].offset=o[s].element.offset(),o[s].proportions({width:o[s].element[0].offsetWidth,height:o[s].element[0].offsetHeight}))}},drop:function(e,i){var s=!1;return t.each((t.ui.ddmanager.droppables[e.options.scope]||[]).slice(),function(){this.options&&(!this.options.disabled&&this.visible&&v(e,this,this.options.tolerance,i)&&(s=this._drop.call(this,i)||s),!this.options.disabled&&this.visible&&this.accept.call(this.element[0],e.currentItem||e.element)&&(this.isout=!0,this.isover=!1,this._deactivate.call(this,i)))}),s},dragStart:function(e,i){e.element.parentsUntil("body").on("scroll.droppable",function(){e.options.refreshPositions||t.ui.ddmanager.prepareOffsets(e,i)})},drag:function(e,i){e.options.refreshPositions&&t.ui.ddmanager.prepareOffsets(e,i),t.each(t.ui.ddmanager.droppables[e.options.scope]||[],function(){if(!this.options.disabled&&!this.greedyChild&&this.visible){var s,n,o,a=v(e,this,this.options.tolerance,i),r=!a&&this.isover?"isout":a&&!this.isover?"isover":null;r&&(this.options.greedy&&(n=this.options.scope,o=this.element.parents(":data(ui-droppable)").filter(function(){return t(this).droppable("instance").options.scope===n}),o.length&&(s=t(o[0]).droppable("instance"),s.greedyChild="isover"===r)),s&&"isover"===r&&(s.isover=!1,s.isout=!0,s._out.call(s,i)),this[r]=!0,this["isout"===r?"isover":"isout"]=!1,this["isover"===r?"_over":"_out"].call(this,i),s&&"isout"===r&&(s.isout=!1,s.isover=!0,s._over.call(s,i)))}})},dragStop:function(e,i){e.element.parentsUntil("body").off("scroll.droppable"),e.options.refreshPositions||t.ui.ddmanager.prepareOffsets(e,i)}},t.uiBackCompat!==!1&&t.widget("ui.droppable",t.ui.droppable,{options:{hoverClass:!1,activeClass:!1},_addActiveClass:function(){this._super(),this.options.activeClass&&this.element.addClass(this.options.activeClass)},_removeActiveClass:function(){this._super(),this.options.activeClass&&this.element.removeClass(this.options.activeClass)},_addHoverClass:function(){this._super(),this.options.hoverClass&&this.element.addClass(this.options.hoverClass)},_removeHoverClass:function(){this._super(),this.options.hoverClass&&this.element.removeClass(this.options.hoverClass)}}),t.ui.droppable,t.widget("ui.progressbar",{version:"1.12.1",options:{classes:{"ui-progressbar":"ui-corner-all","ui-progressbar-value":"ui-corner-left","ui-progressbar-complete":"ui-corner-right"},max:100,value:0,change:null,complete:null},min:0,_create:function(){this.oldValue=this.options.value=this._constrainedValue(),this.element.attr({role:"progressbar","aria-valuemin":this.min}),this._addClass("ui-progressbar","ui-widget ui-widget-content"),this.valueDiv=t("<div>").appendTo(this.element),this._addClass(this.valueDiv,"ui-progressbar-value","ui-widget-header"),this._refreshValue()},_destroy:function(){this.element.removeAttr("role aria-valuemin aria-valuemax aria-valuenow"),this.valueDiv.remove()},value:function(t){return void 0===t?this.options.value:(this.options.value=this._constrainedValue(t),this._refreshValue(),void 0)},_constrainedValue:function(t){return void 0===t&&(t=this.options.value),this.indeterminate=t===!1,"number"!=typeof t&&(t=0),this.indeterminate?!1:Math.min(this.options.max,Math.max(this.min,t))},_setOptions:function(t){var e=t.value;delete t.value,this._super(t),this.options.value=this._constrainedValue(e),this._refreshValue()},_setOption:function(t,e){"max"===t&&(e=Math.max(this.min,e)),this._super(t,e)},_setOptionDisabled:function(t){this._super(t),this.element.attr("aria-disabled",t),this._toggleClass(null,"ui-state-disabled",!!t)},_percentage:function(){return this.indeterminate?100:100*(this.options.value-this.min)/(this.options.max-this.min)},_refreshValue:function(){var e=this.options.value,i=this._percentage();this.valueDiv.toggle(this.indeterminate||e>this.min).width(i.toFixed(0)+"%"),this._toggleClass(this.valueDiv,"ui-progressbar-complete",null,e===this.options.max)._toggleClass("ui-progressbar-indeterminate",null,this.indeterminate),this.indeterminate?(this.element.removeAttr("aria-valuenow"),this.overlayDiv||(this.overlayDiv=t("<div>").appendTo(this.valueDiv),this._addClass(this.overlayDiv,"ui-progressbar-overlay"))):(this.element.attr({"aria-valuemax":this.options.max,"aria-valuenow":e}),this.overlayDiv&&(this.overlayDiv.remove(),this.overlayDiv=null)),this.oldValue!==e&&(this.oldValue=e,this._trigger("change")),e===this.options.max&&this._trigger("complete")}}),t.widget("ui.selectable",t.ui.mouse,{version:"1.12.1",options:{appendTo:"body",autoRefresh:!0,distance:0,filter:"*",tolerance:"touch",selected:null,selecting:null,start:null,stop:null,unselected:null,unselecting:null},_create:function(){var e=this;this._addClass("ui-selectable"),this.dragged=!1,this.refresh=function(){e.elementPos=t(e.element[0]).offset(),e.selectees=t(e.options.filter,e.element[0]),e._addClass(e.selectees,"ui-selectee"),e.selectees.each(function(){var i=t(this),s=i.offset(),n={left:s.left-e.elementPos.left,top:s.top-e.elementPos.top};t.data(this,"selectable-item",{element:this,$element:i,left:n.left,top:n.top,right:n.left+i.outerWidth(),bottom:n.top+i.outerHeight(),startselected:!1,selected:i.hasClass("ui-selected"),selecting:i.hasClass("ui-selecting"),unselecting:i.hasClass("ui-unselecting")})})},this.refresh(),this._mouseInit(),this.helper=t("<div>"),this._addClass(this.helper,"ui-selectable-helper")},_destroy:function(){this.selectees.removeData("selectable-item"),this._mouseDestroy()},_mouseStart:function(e){var i=this,s=this.options;this.opos=[e.pageX,e.pageY],this.elementPos=t(this.element[0]).offset(),this.options.disabled||(this.selectees=t(s.filter,this.element[0]),this._trigger("start",e),t(s.appendTo).append(this.helper),this.helper.css({left:e.pageX,top:e.pageY,width:0,height:0}),s.autoRefresh&&this.refresh(),this.selectees.filter(".ui-selected").each(function(){var s=t.data(this,"selectable-item");s.startselected=!0,e.metaKey||e.ctrlKey||(i._removeClass(s.$element,"ui-selected"),s.selected=!1,i._addClass(s.$element,"ui-unselecting"),s.unselecting=!0,i._trigger("unselecting",e,{unselecting:s.element}))}),t(e.target).parents().addBack().each(function(){var s,n=t.data(this,"selectable-item");return n?(s=!e.metaKey&&!e.ctrlKey||!n.$element.hasClass("ui-selected"),i._removeClass(n.$element,s?"ui-unselecting":"ui-selected")._addClass(n.$element,s?"ui-selecting":"ui-unselecting"),n.unselecting=!s,n.selecting=s,n.selected=s,s?i._trigger("selecting",e,{selecting:n.element}):i._trigger("unselecting",e,{unselecting:n.element}),!1):void 0}))},_mouseDrag:function(e){if(this.dragged=!0,!this.options.disabled){var i,s=this,n=this.options,o=this.opos[0],a=this.opos[1],r=e.pageX,h=e.pageY;return o>r&&(i=r,r=o,o=i),a>h&&(i=h,h=a,a=i),this.helper.css({left:o,top:a,width:r-o,height:h-a}),this.selectees.each(function(){var i=t.data(this,"selectable-item"),l=!1,c={};i&&i.element!==s.element[0]&&(c.left=i.left+s.elementPos.left,c.right=i.right+s.elementPos.left,c.top=i.top+s.elementPos.top,c.bottom=i.bottom+s.elementPos.top,"touch"===n.tolerance?l=!(c.left>r||o>c.right||c.top>h||a>c.bottom):"fit"===n.tolerance&&(l=c.left>o&&r>c.right&&c.top>a&&h>c.bottom),l?(i.selected&&(s._removeClass(i.$element,"ui-selected"),i.selected=!1),i.unselecting&&(s._removeClass(i.$element,"ui-unselecting"),i.unselecting=!1),i.selecting||(s._addClass(i.$element,"ui-selecting"),i.selecting=!0,s._trigger("selecting",e,{selecting:i.element}))):(i.selecting&&((e.metaKey||e.ctrlKey)&&i.startselected?(s._removeClass(i.$element,"ui-selecting"),i.selecting=!1,s._addClass(i.$element,"ui-selected"),i.selected=!0):(s._removeClass(i.$element,"ui-selecting"),i.selecting=!1,i.startselected&&(s._addClass(i.$element,"ui-unselecting"),i.unselecting=!0),s._trigger("unselecting",e,{unselecting:i.element}))),i.selected&&(e.metaKey||e.ctrlKey||i.startselected||(s._removeClass(i.$element,"ui-selected"),i.selected=!1,s._addClass(i.$element,"ui-unselecting"),i.unselecting=!0,s._trigger("unselecting",e,{unselecting:i.element})))))}),!1}},_mouseStop:function(e){var i=this;return this.dragged=!1,t(".ui-unselecting",this.element[0]).each(function(){var s=t.data(this,"selectable-item");i._removeClass(s.$element,"ui-unselecting"),s.unselecting=!1,s.startselected=!1,i._trigger("unselected",e,{unselected:s.element})}),t(".ui-selecting",this.element[0]).each(function(){var s=t.data(this,"selectable-item");i._removeClass(s.$element,"ui-selecting")._addClass(s.$element,"ui-selected"),s.selecting=!1,s.selected=!0,s.startselected=!0,i._trigger("selected",e,{selected:s.element})}),this._trigger("stop",e),this.helper.remove(),!1}}),t.widget("ui.selectmenu",[t.ui.formResetMixin,{version:"1.12.1",defaultElement:"<select>",options:{appendTo:null,classes:{"ui-selectmenu-button-open":"ui-corner-top","ui-selectmenu-button-closed":"ui-corner-all"},disabled:null,icons:{button:"ui-icon-triangle-1-s"},position:{my:"left top",at:"left bottom",collision:"none"},width:!1,change:null,close:null,focus:null,open:null,select:null},_create:function(){var e=this.element.uniqueId().attr("id");this.ids={element:e,button:e+"-button",menu:e+"-menu"},this._drawButton(),this._drawMenu(),this._bindFormResetHandler(),this._rendered=!1,this.menuItems=t()},_drawButton:function(){var e,i=this,s=this._parseOption(this.element.find("option:selected"),this.element[0].selectedIndex);this.labels=this.element.labels().attr("for",this.ids.button),this._on(this.labels,{click:function(t){this.button.focus(),t.preventDefault()}}),this.element.hide(),this.button=t("<span>",{tabindex:this.options.disabled?-1:0,id:this.ids.button,role:"combobox","aria-expanded":"false","aria-autocomplete":"list","aria-owns":this.ids.menu,"aria-haspopup":"true",title:this.element.attr("title")}).insertAfter(this.element),this._addClass(this.button,"ui-selectmenu-button ui-selectmenu-button-closed","ui-button ui-widget"),e=t("<span>").appendTo(this.button),this._addClass(e,"ui-selectmenu-icon","ui-icon "+this.options.icons.button),this.buttonItem=this._renderButtonItem(s).appendTo(this.button),this.options.width!==!1&&this._resizeButton(),this._on(this.button,this._buttonEvents),this.button.one("focusin",function(){i._rendered||i._refreshMenu()})},_drawMenu:function(){var e=this;this.menu=t("<ul>",{"aria-hidden":"true","aria-labelledby":this.ids.button,id:this.ids.menu}),this.menuWrap=t("<div>").append(this.menu),this._addClass(this.menuWrap,"ui-selectmenu-menu","ui-front"),this.menuWrap.appendTo(this._appendTo()),this.menuInstance=this.menu.menu({classes:{"ui-menu":"ui-corner-bottom"},role:"listbox",select:function(t,i){t.preventDefault(),e._setSelection(),e._select(i.item.data("ui-selectmenu-item"),t)},focus:function(t,i){var s=i.item.data("ui-selectmenu-item");null!=e.focusIndex&&s.index!==e.focusIndex&&(e._trigger("focus",t,{item:s}),e.isOpen||e._select(s,t)),e.focusIndex=s.index,e.button.attr("aria-activedescendant",e.menuItems.eq(s.index).attr("id"))}}).menu("instance"),this.menuInstance._off(this.menu,"mouseleave"),this.menuInstance._closeOnDocumentClick=function(){return!1},this.menuInstance._isDivider=function(){return!1}},refresh:function(){this._refreshMenu(),this.buttonItem.replaceWith(this.buttonItem=this._renderButtonItem(this._getSelectedItem().data("ui-selectmenu-item")||{})),null===this.options.width&&this._resizeButton()},_refreshMenu:function(){var t,e=this.element.find("option");this.menu.empty(),this._parseOptions(e),this._renderMenu(this.menu,this.items),this.menuInstance.refresh(),this.menuItems=this.menu.find("li").not(".ui-selectmenu-optgroup").find(".ui-menu-item-wrapper"),this._rendered=!0,e.length&&(t=this._getSelectedItem(),this.menuInstance.focus(null,t),this._setAria(t.data("ui-selectmenu-item")),this._setOption("disabled",this.element.prop("disabled")))},open:function(t){this.options.disabled||(this._rendered?(this._removeClass(this.menu.find(".ui-state-active"),null,"ui-state-active"),this.menuInstance.focus(null,this._getSelectedItem())):this._refreshMenu(),this.menuItems.length&&(this.isOpen=!0,this._toggleAttr(),this._resizeMenu(),this._position(),this._on(this.document,this._documentClick),this._trigger("open",t)))},_position:function(){this.menuWrap.position(t.extend({of:this.button},this.options.position))},close:function(t){this.isOpen&&(this.isOpen=!1,this._toggleAttr(),this.range=null,this._off(this.document),this._trigger("close",t))},widget:function(){return this.button},menuWidget:function(){return this.menu},_renderButtonItem:function(e){var i=t("<span>");return this._setText(i,e.label),this._addClass(i,"ui-selectmenu-text"),i},_renderMenu:function(e,i){var s=this,n="";t.each(i,function(i,o){var a;o.optgroup!==n&&(a=t("<li>",{text:o.optgroup}),s._addClass(a,"ui-selectmenu-optgroup","ui-menu-divider"+(o.element.parent("optgroup").prop("disabled")?" ui-state-disabled":"")),a.appendTo(e),n=o.optgroup),s._renderItemData(e,o)})},_renderItemData:function(t,e){return this._renderItem(t,e).data("ui-selectmenu-item",e)},_renderItem:function(e,i){var s=t("<li>"),n=t("<div>",{title:i.element.attr("title")});return i.disabled&&this._addClass(s,null,"ui-state-disabled"),this._setText(n,i.label),s.append(n).appendTo(e)},_setText:function(t,e){e?t.text(e):t.html("&#160;")},_move:function(t,e){var i,s,n=".ui-menu-item";this.isOpen?i=this.menuItems.eq(this.focusIndex).parent("li"):(i=this.menuItems.eq(this.element[0].selectedIndex).parent("li"),n+=":not(.ui-state-disabled)"),s="first"===t||"last"===t?i["first"===t?"prevAll":"nextAll"](n).eq(-1):i[t+"All"](n).eq(0),s.length&&this.menuInstance.focus(e,s)},_getSelectedItem:function(){return this.menuItems.eq(this.element[0].selectedIndex).parent("li")},_toggle:function(t){this[this.isOpen?"close":"open"](t)},_setSelection:function(){var t;this.range&&(window.getSelection?(t=window.getSelection(),t.removeAllRanges(),t.addRange(this.range)):this.range.select(),this.button.focus())},_documentClick:{mousedown:function(e){this.isOpen&&(t(e.target).closest(".ui-selectmenu-menu, #"+t.ui.escapeSelector(this.ids.button)).length||this.close(e))}},_buttonEvents:{mousedown:function(){var t;window.getSelection?(t=window.getSelection(),t.rangeCount&&(this.range=t.getRangeAt(0))):this.range=document.selection.createRange()},click:function(t){this._setSelection(),this._toggle(t)},keydown:function(e){var i=!0;switch(e.keyCode){case t.ui.keyCode.TAB:case t.ui.keyCode.ESCAPE:this.close(e),i=!1;break;case t.ui.keyCode.ENTER:this.isOpen&&this._selectFocusedItem(e);break;case t.ui.keyCode.UP:e.altKey?this._toggle(e):this._move("prev",e);break;case t.ui.keyCode.DOWN:e.altKey?this._toggle(e):this._move("next",e);break;case t.ui.keyCode.SPACE:this.isOpen?this._selectFocusedItem(e):this._toggle(e);break;case t.ui.keyCode.LEFT:this._move("prev",e);break;case t.ui.keyCode.RIGHT:this._move("next",e);break;case t.ui.keyCode.HOME:case t.ui.keyCode.PAGE_UP:this._move("first",e);break;case t.ui.keyCode.END:case t.ui.keyCode.PAGE_DOWN:this._move("last",e);break;default:this.menu.trigger(e),i=!1}i&&e.preventDefault()}},_selectFocusedItem:function(t){var e=this.menuItems.eq(this.focusIndex).parent("li");e.hasClass("ui-state-disabled")||this._select(e.data("ui-selectmenu-item"),t)},_select:function(t,e){var i=this.element[0].selectedIndex;this.element[0].selectedIndex=t.index,this.buttonItem.replaceWith(this.buttonItem=this._renderButtonItem(t)),this._setAria(t),this._trigger("select",e,{item:t}),t.index!==i&&this._trigger("change",e,{item:t}),this.close(e)},_setAria:function(t){var e=this.menuItems.eq(t.index).attr("id");this.button.attr({"aria-labelledby":e,"aria-activedescendant":e}),this.menu.attr("aria-activedescendant",e)},_setOption:function(t,e){if("icons"===t){var i=this.button.find("span.ui-icon");this._removeClass(i,null,this.options.icons.button)._addClass(i,null,e.button)}this._super(t,e),"appendTo"===t&&this.menuWrap.appendTo(this._appendTo()),"width"===t&&this._resizeButton()},_setOptionDisabled:function(t){this._super(t),this.menuInstance.option("disabled",t),this.button.attr("aria-disabled",t),this._toggleClass(this.button,null,"ui-state-disabled",t),this.element.prop("disabled",t),t?(this.button.attr("tabindex",-1),this.close()):this.button.attr("tabindex",0)},_appendTo:function(){var e=this.options.appendTo;return e&&(e=e.jquery||e.nodeType?t(e):this.document.find(e).eq(0)),e&&e[0]||(e=this.element.closest(".ui-front, dialog")),e.length||(e=this.document[0].body),e},_toggleAttr:function(){this.button.attr("aria-expanded",this.isOpen),this._removeClass(this.button,"ui-selectmenu-button-"+(this.isOpen?"closed":"open"))._addClass(this.button,"ui-selectmenu-button-"+(this.isOpen?"open":"closed"))._toggleClass(this.menuWrap,"ui-selectmenu-open",null,this.isOpen),this.menu.attr("aria-hidden",!this.isOpen)},_resizeButton:function(){var t=this.options.width;return t===!1?(this.button.css("width",""),void 0):(null===t&&(t=this.element.show().outerWidth(),this.element.hide()),this.button.outerWidth(t),void 0)},_resizeMenu:function(){this.menu.outerWidth(Math.max(this.button.outerWidth(),this.menu.width("").outerWidth()+1))},_getCreateOptions:function(){var t=this._super();return t.disabled=this.element.prop("disabled"),t},_parseOptions:function(e){var i=this,s=[];e.each(function(e,n){s.push(i._parseOption(t(n),e))}),this.items=s},_parseOption:function(t,e){var i=t.parent("optgroup");return{element:t,index:e,value:t.val(),label:t.text(),optgroup:i.attr("label")||"",disabled:i.prop("disabled")||t.prop("disabled")}},_destroy:function(){this._unbindFormResetHandler(),this.menuWrap.remove(),this.button.remove(),this.element.show(),this.element.removeUniqueId(),this.labels.attr("for",this.ids.element)}}]),t.widget("ui.slider",t.ui.mouse,{version:"1.12.1",widgetEventPrefix:"slide",options:{animate:!1,classes:{"ui-slider":"ui-corner-all","ui-slider-handle":"ui-corner-all","ui-slider-range":"ui-corner-all ui-widget-header"},distance:0,max:100,min:0,orientation:"horizontal",range:!1,step:1,value:0,values:null,change:null,slide:null,start:null,stop:null},numPages:5,_create:function(){this._keySliding=!1,this._mouseSliding=!1,this._animateOff=!0,this._handleIndex=null,this._detectOrientation(),this._mouseInit(),this._calculateNewMax(),this._addClass("ui-slider ui-slider-"+this.orientation,"ui-widget ui-widget-content"),this._refresh(),this._animateOff=!1
+},_refresh:function(){this._createRange(),this._createHandles(),this._setupEvents(),this._refreshValue()},_createHandles:function(){var e,i,s=this.options,n=this.element.find(".ui-slider-handle"),o="<span tabindex='0'></span>",a=[];for(i=s.values&&s.values.length||1,n.length>i&&(n.slice(i).remove(),n=n.slice(0,i)),e=n.length;i>e;e++)a.push(o);this.handles=n.add(t(a.join("")).appendTo(this.element)),this._addClass(this.handles,"ui-slider-handle","ui-state-default"),this.handle=this.handles.eq(0),this.handles.each(function(e){t(this).data("ui-slider-handle-index",e).attr("tabIndex",0)})},_createRange:function(){var e=this.options;e.range?(e.range===!0&&(e.values?e.values.length&&2!==e.values.length?e.values=[e.values[0],e.values[0]]:t.isArray(e.values)&&(e.values=e.values.slice(0)):e.values=[this._valueMin(),this._valueMin()]),this.range&&this.range.length?(this._removeClass(this.range,"ui-slider-range-min ui-slider-range-max"),this.range.css({left:"",bottom:""})):(this.range=t("<div>").appendTo(this.element),this._addClass(this.range,"ui-slider-range")),("min"===e.range||"max"===e.range)&&this._addClass(this.range,"ui-slider-range-"+e.range)):(this.range&&this.range.remove(),this.range=null)},_setupEvents:function(){this._off(this.handles),this._on(this.handles,this._handleEvents),this._hoverable(this.handles),this._focusable(this.handles)},_destroy:function(){this.handles.remove(),this.range&&this.range.remove(),this._mouseDestroy()},_mouseCapture:function(e){var i,s,n,o,a,r,h,l,c=this,u=this.options;return u.disabled?!1:(this.elementSize={width:this.element.outerWidth(),height:this.element.outerHeight()},this.elementOffset=this.element.offset(),i={x:e.pageX,y:e.pageY},s=this._normValueFromMouse(i),n=this._valueMax()-this._valueMin()+1,this.handles.each(function(e){var i=Math.abs(s-c.values(e));(n>i||n===i&&(e===c._lastChangedValue||c.values(e)===u.min))&&(n=i,o=t(this),a=e)}),r=this._start(e,a),r===!1?!1:(this._mouseSliding=!0,this._handleIndex=a,this._addClass(o,null,"ui-state-active"),o.trigger("focus"),h=o.offset(),l=!t(e.target).parents().addBack().is(".ui-slider-handle"),this._clickOffset=l?{left:0,top:0}:{left:e.pageX-h.left-o.width()/2,top:e.pageY-h.top-o.height()/2-(parseInt(o.css("borderTopWidth"),10)||0)-(parseInt(o.css("borderBottomWidth"),10)||0)+(parseInt(o.css("marginTop"),10)||0)},this.handles.hasClass("ui-state-hover")||this._slide(e,a,s),this._animateOff=!0,!0))},_mouseStart:function(){return!0},_mouseDrag:function(t){var e={x:t.pageX,y:t.pageY},i=this._normValueFromMouse(e);return this._slide(t,this._handleIndex,i),!1},_mouseStop:function(t){return this._removeClass(this.handles,null,"ui-state-active"),this._mouseSliding=!1,this._stop(t,this._handleIndex),this._change(t,this._handleIndex),this._handleIndex=null,this._clickOffset=null,this._animateOff=!1,!1},_detectOrientation:function(){this.orientation="vertical"===this.options.orientation?"vertical":"horizontal"},_normValueFromMouse:function(t){var e,i,s,n,o;return"horizontal"===this.orientation?(e=this.elementSize.width,i=t.x-this.elementOffset.left-(this._clickOffset?this._clickOffset.left:0)):(e=this.elementSize.height,i=t.y-this.elementOffset.top-(this._clickOffset?this._clickOffset.top:0)),s=i/e,s>1&&(s=1),0>s&&(s=0),"vertical"===this.orientation&&(s=1-s),n=this._valueMax()-this._valueMin(),o=this._valueMin()+s*n,this._trimAlignValue(o)},_uiHash:function(t,e,i){var s={handle:this.handles[t],handleIndex:t,value:void 0!==e?e:this.value()};return this._hasMultipleValues()&&(s.value=void 0!==e?e:this.values(t),s.values=i||this.values()),s},_hasMultipleValues:function(){return this.options.values&&this.options.values.length},_start:function(t,e){return this._trigger("start",t,this._uiHash(e))},_slide:function(t,e,i){var s,n,o=this.value(),a=this.values();this._hasMultipleValues()&&(n=this.values(e?0:1),o=this.values(e),2===this.options.values.length&&this.options.range===!0&&(i=0===e?Math.min(n,i):Math.max(n,i)),a[e]=i),i!==o&&(s=this._trigger("slide",t,this._uiHash(e,i,a)),s!==!1&&(this._hasMultipleValues()?this.values(e,i):this.value(i)))},_stop:function(t,e){this._trigger("stop",t,this._uiHash(e))},_change:function(t,e){this._keySliding||this._mouseSliding||(this._lastChangedValue=e,this._trigger("change",t,this._uiHash(e)))},value:function(t){return arguments.length?(this.options.value=this._trimAlignValue(t),this._refreshValue(),this._change(null,0),void 0):this._value()},values:function(e,i){var s,n,o;if(arguments.length>1)return this.options.values[e]=this._trimAlignValue(i),this._refreshValue(),this._change(null,e),void 0;if(!arguments.length)return this._values();if(!t.isArray(arguments[0]))return this._hasMultipleValues()?this._values(e):this.value();for(s=this.options.values,n=arguments[0],o=0;s.length>o;o+=1)s[o]=this._trimAlignValue(n[o]),this._change(null,o);this._refreshValue()},_setOption:function(e,i){var s,n=0;switch("range"===e&&this.options.range===!0&&("min"===i?(this.options.value=this._values(0),this.options.values=null):"max"===i&&(this.options.value=this._values(this.options.values.length-1),this.options.values=null)),t.isArray(this.options.values)&&(n=this.options.values.length),this._super(e,i),e){case"orientation":this._detectOrientation(),this._removeClass("ui-slider-horizontal ui-slider-vertical")._addClass("ui-slider-"+this.orientation),this._refreshValue(),this.options.range&&this._refreshRange(i),this.handles.css("horizontal"===i?"bottom":"left","");break;case"value":this._animateOff=!0,this._refreshValue(),this._change(null,0),this._animateOff=!1;break;case"values":for(this._animateOff=!0,this._refreshValue(),s=n-1;s>=0;s--)this._change(null,s);this._animateOff=!1;break;case"step":case"min":case"max":this._animateOff=!0,this._calculateNewMax(),this._refreshValue(),this._animateOff=!1;break;case"range":this._animateOff=!0,this._refresh(),this._animateOff=!1}},_setOptionDisabled:function(t){this._super(t),this._toggleClass(null,"ui-state-disabled",!!t)},_value:function(){var t=this.options.value;return t=this._trimAlignValue(t)},_values:function(t){var e,i,s;if(arguments.length)return e=this.options.values[t],e=this._trimAlignValue(e);if(this._hasMultipleValues()){for(i=this.options.values.slice(),s=0;i.length>s;s+=1)i[s]=this._trimAlignValue(i[s]);return i}return[]},_trimAlignValue:function(t){if(this._valueMin()>=t)return this._valueMin();if(t>=this._valueMax())return this._valueMax();var e=this.options.step>0?this.options.step:1,i=(t-this._valueMin())%e,s=t-i;return 2*Math.abs(i)>=e&&(s+=i>0?e:-e),parseFloat(s.toFixed(5))},_calculateNewMax:function(){var t=this.options.max,e=this._valueMin(),i=this.options.step,s=Math.round((t-e)/i)*i;t=s+e,t>this.options.max&&(t-=i),this.max=parseFloat(t.toFixed(this._precision()))},_precision:function(){var t=this._precisionOf(this.options.step);return null!==this.options.min&&(t=Math.max(t,this._precisionOf(this.options.min))),t},_precisionOf:function(t){var e=""+t,i=e.indexOf(".");return-1===i?0:e.length-i-1},_valueMin:function(){return this.options.min},_valueMax:function(){return this.max},_refreshRange:function(t){"vertical"===t&&this.range.css({width:"",left:""}),"horizontal"===t&&this.range.css({height:"",bottom:""})},_refreshValue:function(){var e,i,s,n,o,a=this.options.range,r=this.options,h=this,l=this._animateOff?!1:r.animate,c={};this._hasMultipleValues()?this.handles.each(function(s){i=100*((h.values(s)-h._valueMin())/(h._valueMax()-h._valueMin())),c["horizontal"===h.orientation?"left":"bottom"]=i+"%",t(this).stop(1,1)[l?"animate":"css"](c,r.animate),h.options.range===!0&&("horizontal"===h.orientation?(0===s&&h.range.stop(1,1)[l?"animate":"css"]({left:i+"%"},r.animate),1===s&&h.range[l?"animate":"css"]({width:i-e+"%"},{queue:!1,duration:r.animate})):(0===s&&h.range.stop(1,1)[l?"animate":"css"]({bottom:i+"%"},r.animate),1===s&&h.range[l?"animate":"css"]({height:i-e+"%"},{queue:!1,duration:r.animate}))),e=i}):(s=this.value(),n=this._valueMin(),o=this._valueMax(),i=o!==n?100*((s-n)/(o-n)):0,c["horizontal"===this.orientation?"left":"bottom"]=i+"%",this.handle.stop(1,1)[l?"animate":"css"](c,r.animate),"min"===a&&"horizontal"===this.orientation&&this.range.stop(1,1)[l?"animate":"css"]({width:i+"%"},r.animate),"max"===a&&"horizontal"===this.orientation&&this.range.stop(1,1)[l?"animate":"css"]({width:100-i+"%"},r.animate),"min"===a&&"vertical"===this.orientation&&this.range.stop(1,1)[l?"animate":"css"]({height:i+"%"},r.animate),"max"===a&&"vertical"===this.orientation&&this.range.stop(1,1)[l?"animate":"css"]({height:100-i+"%"},r.animate))},_handleEvents:{keydown:function(e){var i,s,n,o,a=t(e.target).data("ui-slider-handle-index");switch(e.keyCode){case t.ui.keyCode.HOME:case t.ui.keyCode.END:case t.ui.keyCode.PAGE_UP:case t.ui.keyCode.PAGE_DOWN:case t.ui.keyCode.UP:case t.ui.keyCode.RIGHT:case t.ui.keyCode.DOWN:case t.ui.keyCode.LEFT:if(e.preventDefault(),!this._keySliding&&(this._keySliding=!0,this._addClass(t(e.target),null,"ui-state-active"),i=this._start(e,a),i===!1))return}switch(o=this.options.step,s=n=this._hasMultipleValues()?this.values(a):this.value(),e.keyCode){case t.ui.keyCode.HOME:n=this._valueMin();break;case t.ui.keyCode.END:n=this._valueMax();break;case t.ui.keyCode.PAGE_UP:n=this._trimAlignValue(s+(this._valueMax()-this._valueMin())/this.numPages);break;case t.ui.keyCode.PAGE_DOWN:n=this._trimAlignValue(s-(this._valueMax()-this._valueMin())/this.numPages);break;case t.ui.keyCode.UP:case t.ui.keyCode.RIGHT:if(s===this._valueMax())return;n=this._trimAlignValue(s+o);break;case t.ui.keyCode.DOWN:case t.ui.keyCode.LEFT:if(s===this._valueMin())return;n=this._trimAlignValue(s-o)}this._slide(e,a,n)},keyup:function(e){var i=t(e.target).data("ui-slider-handle-index");this._keySliding&&(this._keySliding=!1,this._stop(e,i),this._change(e,i),this._removeClass(t(e.target),null,"ui-state-active"))}}}),t.widget("ui.sortable",t.ui.mouse,{version:"1.12.1",widgetEventPrefix:"sort",ready:!1,options:{appendTo:"parent",axis:!1,connectWith:!1,containment:!1,cursor:"auto",cursorAt:!1,dropOnEmpty:!0,forcePlaceholderSize:!1,forceHelperSize:!1,grid:!1,handle:!1,helper:"original",items:"> *",opacity:!1,placeholder:!1,revert:!1,scroll:!0,scrollSensitivity:20,scrollSpeed:20,scope:"default",tolerance:"intersect",zIndex:1e3,activate:null,beforeStop:null,change:null,deactivate:null,out:null,over:null,receive:null,remove:null,sort:null,start:null,stop:null,update:null},_isOverAxis:function(t,e,i){return t>=e&&e+i>t},_isFloating:function(t){return/left|right/.test(t.css("float"))||/inline|table-cell/.test(t.css("display"))},_create:function(){this.containerCache={},this._addClass("ui-sortable"),this.refresh(),this.offset=this.element.offset(),this._mouseInit(),this._setHandleClassName(),this.ready=!0},_setOption:function(t,e){this._super(t,e),"handle"===t&&this._setHandleClassName()},_setHandleClassName:function(){var e=this;this._removeClass(this.element.find(".ui-sortable-handle"),"ui-sortable-handle"),t.each(this.items,function(){e._addClass(this.instance.options.handle?this.item.find(this.instance.options.handle):this.item,"ui-sortable-handle")})},_destroy:function(){this._mouseDestroy();for(var t=this.items.length-1;t>=0;t--)this.items[t].item.removeData(this.widgetName+"-item");return this},_mouseCapture:function(e,i){var s=null,n=!1,o=this;return this.reverting?!1:this.options.disabled||"static"===this.options.type?!1:(this._refreshItems(e),t(e.target).parents().each(function(){return t.data(this,o.widgetName+"-item")===o?(s=t(this),!1):void 0}),t.data(e.target,o.widgetName+"-item")===o&&(s=t(e.target)),s?!this.options.handle||i||(t(this.options.handle,s).find("*").addBack().each(function(){this===e.target&&(n=!0)}),n)?(this.currentItem=s,this._removeCurrentsFromItems(),!0):!1:!1)},_mouseStart:function(e,i,s){var n,o,a=this.options;if(this.currentContainer=this,this.refreshPositions(),this.helper=this._createHelper(e),this._cacheHelperProportions(),this._cacheMargins(),this.scrollParent=this.helper.scrollParent(),this.offset=this.currentItem.offset(),this.offset={top:this.offset.top-this.margins.top,left:this.offset.left-this.margins.left},t.extend(this.offset,{click:{left:e.pageX-this.offset.left,top:e.pageY-this.offset.top},parent:this._getParentOffset(),relative:this._getRelativeOffset()}),this.helper.css("position","absolute"),this.cssPosition=this.helper.css("position"),this.originalPosition=this._generatePosition(e),this.originalPageX=e.pageX,this.originalPageY=e.pageY,a.cursorAt&&this._adjustOffsetFromHelper(a.cursorAt),this.domPosition={prev:this.currentItem.prev()[0],parent:this.currentItem.parent()[0]},this.helper[0]!==this.currentItem[0]&&this.currentItem.hide(),this._createPlaceholder(),a.containment&&this._setContainment(),a.cursor&&"auto"!==a.cursor&&(o=this.document.find("body"),this.storedCursor=o.css("cursor"),o.css("cursor",a.cursor),this.storedStylesheet=t("<style>*{ cursor: "+a.cursor+" !important; }</style>").appendTo(o)),a.opacity&&(this.helper.css("opacity")&&(this._storedOpacity=this.helper.css("opacity")),this.helper.css("opacity",a.opacity)),a.zIndex&&(this.helper.css("zIndex")&&(this._storedZIndex=this.helper.css("zIndex")),this.helper.css("zIndex",a.zIndex)),this.scrollParent[0]!==this.document[0]&&"HTML"!==this.scrollParent[0].tagName&&(this.overflowOffset=this.scrollParent.offset()),this._trigger("start",e,this._uiHash()),this._preserveHelperProportions||this._cacheHelperProportions(),!s)for(n=this.containers.length-1;n>=0;n--)this.containers[n]._trigger("activate",e,this._uiHash(this));return t.ui.ddmanager&&(t.ui.ddmanager.current=this),t.ui.ddmanager&&!a.dropBehaviour&&t.ui.ddmanager.prepareOffsets(this,e),this.dragging=!0,this._addClass(this.helper,"ui-sortable-helper"),this._mouseDrag(e),!0},_mouseDrag:function(e){var i,s,n,o,a=this.options,r=!1;for(this.position=this._generatePosition(e),this.positionAbs=this._convertPositionTo("absolute"),this.lastPositionAbs||(this.lastPositionAbs=this.positionAbs),this.options.scroll&&(this.scrollParent[0]!==this.document[0]&&"HTML"!==this.scrollParent[0].tagName?(this.overflowOffset.top+this.scrollParent[0].offsetHeight-e.pageY<a.scrollSensitivity?this.scrollParent[0].scrollTop=r=this.scrollParent[0].scrollTop+a.scrollSpeed:e.pageY-this.overflowOffset.top<a.scrollSensitivity&&(this.scrollParent[0].scrollTop=r=this.scrollParent[0].scrollTop-a.scrollSpeed),this.overflowOffset.left+this.scrollParent[0].offsetWidth-e.pageX<a.scrollSensitivity?this.scrollParent[0].scrollLeft=r=this.scrollParent[0].scrollLeft+a.scrollSpeed:e.pageX-this.overflowOffset.left<a.scrollSensitivity&&(this.scrollParent[0].scrollLeft=r=this.scrollParent[0].scrollLeft-a.scrollSpeed)):(e.pageY-this.document.scrollTop()<a.scrollSensitivity?r=this.document.scrollTop(this.document.scrollTop()-a.scrollSpeed):this.window.height()-(e.pageY-this.document.scrollTop())<a.scrollSensitivity&&(r=this.document.scrollTop(this.document.scrollTop()+a.scrollSpeed)),e.pageX-this.document.scrollLeft()<a.scrollSensitivity?r=this.document.scrollLeft(this.document.scrollLeft()-a.scrollSpeed):this.window.width()-(e.pageX-this.document.scrollLeft())<a.scrollSensitivity&&(r=this.document.scrollLeft(this.document.scrollLeft()+a.scrollSpeed))),r!==!1&&t.ui.ddmanager&&!a.dropBehaviour&&t.ui.ddmanager.prepareOffsets(this,e)),this.positionAbs=this._convertPositionTo("absolute"),this.options.axis&&"y"===this.options.axis||(this.helper[0].style.left=this.position.left+"px"),this.options.axis&&"x"===this.options.axis||(this.helper[0].style.top=this.position.top+"px"),i=this.items.length-1;i>=0;i--)if(s=this.items[i],n=s.item[0],o=this._intersectsWithPointer(s),o&&s.instance===this.currentContainer&&n!==this.currentItem[0]&&this.placeholder[1===o?"next":"prev"]()[0]!==n&&!t.contains(this.placeholder[0],n)&&("semi-dynamic"===this.options.type?!t.contains(this.element[0],n):!0)){if(this.direction=1===o?"down":"up","pointer"!==this.options.tolerance&&!this._intersectsWithSides(s))break;this._rearrange(e,s),this._trigger("change",e,this._uiHash());break}return this._contactContainers(e),t.ui.ddmanager&&t.ui.ddmanager.drag(this,e),this._trigger("sort",e,this._uiHash()),this.lastPositionAbs=this.positionAbs,!1},_mouseStop:function(e,i){if(e){if(t.ui.ddmanager&&!this.options.dropBehaviour&&t.ui.ddmanager.drop(this,e),this.options.revert){var s=this,n=this.placeholder.offset(),o=this.options.axis,a={};o&&"x"!==o||(a.left=n.left-this.offset.parent.left-this.margins.left+(this.offsetParent[0]===this.document[0].body?0:this.offsetParent[0].scrollLeft)),o&&"y"!==o||(a.top=n.top-this.offset.parent.top-this.margins.top+(this.offsetParent[0]===this.document[0].body?0:this.offsetParent[0].scrollTop)),this.reverting=!0,t(this.helper).animate(a,parseInt(this.options.revert,10)||500,function(){s._clear(e)})}else this._clear(e,i);return!1}},cancel:function(){if(this.dragging){this._mouseUp(new t.Event("mouseup",{target:null})),"original"===this.options.helper?(this.currentItem.css(this._storedCSS),this._removeClass(this.currentItem,"ui-sortable-helper")):this.currentItem.show();for(var e=this.containers.length-1;e>=0;e--)this.containers[e]._trigger("deactivate",null,this._uiHash(this)),this.containers[e].containerCache.over&&(this.containers[e]._trigger("out",null,this._uiHash(this)),this.containers[e].containerCache.over=0)}return this.placeholder&&(this.placeholder[0].parentNode&&this.placeholder[0].parentNode.removeChild(this.placeholder[0]),"original"!==this.options.helper&&this.helper&&this.helper[0].parentNode&&this.helper.remove(),t.extend(this,{helper:null,dragging:!1,reverting:!1,_noFinalSort:null}),this.domPosition.prev?t(this.domPosition.prev).after(this.currentItem):t(this.domPosition.parent).prepend(this.currentItem)),this},serialize:function(e){var i=this._getItemsAsjQuery(e&&e.connected),s=[];return e=e||{},t(i).each(function(){var i=(t(e.item||this).attr(e.attribute||"id")||"").match(e.expression||/(.+)[\-=_](.+)/);i&&s.push((e.key||i[1]+"[]")+"="+(e.key&&e.expression?i[1]:i[2]))}),!s.length&&e.key&&s.push(e.key+"="),s.join("&")},toArray:function(e){var i=this._getItemsAsjQuery(e&&e.connected),s=[];return e=e||{},i.each(function(){s.push(t(e.item||this).attr(e.attribute||"id")||"")}),s},_intersectsWith:function(t){var e=this.positionAbs.left,i=e+this.helperProportions.width,s=this.positionAbs.top,n=s+this.helperProportions.height,o=t.left,a=o+t.width,r=t.top,h=r+t.height,l=this.offset.click.top,c=this.offset.click.left,u="x"===this.options.axis||s+l>r&&h>s+l,d="y"===this.options.axis||e+c>o&&a>e+c,p=u&&d;return"pointer"===this.options.tolerance||this.options.forcePointerForContainers||"pointer"!==this.options.tolerance&&this.helperProportions[this.floating?"width":"height"]>t[this.floating?"width":"height"]?p:e+this.helperProportions.width/2>o&&a>i-this.helperProportions.width/2&&s+this.helperProportions.height/2>r&&h>n-this.helperProportions.height/2},_intersectsWithPointer:function(t){var e,i,s="x"===this.options.axis||this._isOverAxis(this.positionAbs.top+this.offset.click.top,t.top,t.height),n="y"===this.options.axis||this._isOverAxis(this.positionAbs.left+this.offset.click.left,t.left,t.width),o=s&&n;return o?(e=this._getDragVerticalDirection(),i=this._getDragHorizontalDirection(),this.floating?"right"===i||"down"===e?2:1:e&&("down"===e?2:1)):!1},_intersectsWithSides:function(t){var e=this._isOverAxis(this.positionAbs.top+this.offset.click.top,t.top+t.height/2,t.height),i=this._isOverAxis(this.positionAbs.left+this.offset.click.left,t.left+t.width/2,t.width),s=this._getDragVerticalDirection(),n=this._getDragHorizontalDirection();return this.floating&&n?"right"===n&&i||"left"===n&&!i:s&&("down"===s&&e||"up"===s&&!e)},_getDragVerticalDirection:function(){var t=this.positionAbs.top-this.lastPositionAbs.top;return 0!==t&&(t>0?"down":"up")},_getDragHorizontalDirection:function(){var t=this.positionAbs.left-this.lastPositionAbs.left;return 0!==t&&(t>0?"right":"left")},refresh:function(t){return this._refreshItems(t),this._setHandleClassName(),this.refreshPositions(),this},_connectWith:function(){var t=this.options;return t.connectWith.constructor===String?[t.connectWith]:t.connectWith},_getItemsAsjQuery:function(e){function i(){r.push(this)}var s,n,o,a,r=[],h=[],l=this._connectWith();if(l&&e)for(s=l.length-1;s>=0;s--)for(o=t(l[s],this.document[0]),n=o.length-1;n>=0;n--)a=t.data(o[n],this.widgetFullName),a&&a!==this&&!a.options.disabled&&h.push([t.isFunction(a.options.items)?a.options.items.call(a.element):t(a.options.items,a.element).not(".ui-sortable-helper").not(".ui-sortable-placeholder"),a]);for(h.push([t.isFunction(this.options.items)?this.options.items.call(this.element,null,{options:this.options,item:this.currentItem}):t(this.options.items,this.element).not(".ui-sortable-helper").not(".ui-sortable-placeholder"),this]),s=h.length-1;s>=0;s--)h[s][0].each(i);return t(r)},_removeCurrentsFromItems:function(){var e=this.currentItem.find(":data("+this.widgetName+"-item)");this.items=t.grep(this.items,function(t){for(var i=0;e.length>i;i++)if(e[i]===t.item[0])return!1;return!0})},_refreshItems:function(e){this.items=[],this.containers=[this];var i,s,n,o,a,r,h,l,c=this.items,u=[[t.isFunction(this.options.items)?this.options.items.call(this.element[0],e,{item:this.currentItem}):t(this.options.items,this.element),this]],d=this._connectWith();if(d&&this.ready)for(i=d.length-1;i>=0;i--)for(n=t(d[i],this.document[0]),s=n.length-1;s>=0;s--)o=t.data(n[s],this.widgetFullName),o&&o!==this&&!o.options.disabled&&(u.push([t.isFunction(o.options.items)?o.options.items.call(o.element[0],e,{item:this.currentItem}):t(o.options.items,o.element),o]),this.containers.push(o));for(i=u.length-1;i>=0;i--)for(a=u[i][1],r=u[i][0],s=0,l=r.length;l>s;s++)h=t(r[s]),h.data(this.widgetName+"-item",a),c.push({item:h,instance:a,width:0,height:0,left:0,top:0})},refreshPositions:function(e){this.floating=this.items.length?"x"===this.options.axis||this._isFloating(this.items[0].item):!1,this.offsetParent&&this.helper&&(this.offset.parent=this._getParentOffset());var i,s,n,o;for(i=this.items.length-1;i>=0;i--)s=this.items[i],s.instance!==this.currentContainer&&this.currentContainer&&s.item[0]!==this.currentItem[0]||(n=this.options.toleranceElement?t(this.options.toleranceElement,s.item):s.item,e||(s.width=n.outerWidth(),s.height=n.outerHeight()),o=n.offset(),s.left=o.left,s.top=o.top);if(this.options.custom&&this.options.custom.refreshContainers)this.options.custom.refreshContainers.call(this);else for(i=this.containers.length-1;i>=0;i--)o=this.containers[i].element.offset(),this.containers[i].containerCache.left=o.left,this.containers[i].containerCache.top=o.top,this.containers[i].containerCache.width=this.containers[i].element.outerWidth(),this.containers[i].containerCache.height=this.containers[i].element.outerHeight();return this},_createPlaceholder:function(e){e=e||this;var i,s=e.options;s.placeholder&&s.placeholder.constructor!==String||(i=s.placeholder,s.placeholder={element:function(){var s=e.currentItem[0].nodeName.toLowerCase(),n=t("<"+s+">",e.document[0]);return e._addClass(n,"ui-sortable-placeholder",i||e.currentItem[0].className)._removeClass(n,"ui-sortable-helper"),"tbody"===s?e._createTrPlaceholder(e.currentItem.find("tr").eq(0),t("<tr>",e.document[0]).appendTo(n)):"tr"===s?e._createTrPlaceholder(e.currentItem,n):"img"===s&&n.attr("src",e.currentItem.attr("src")),i||n.css("visibility","hidden"),n},update:function(t,n){(!i||s.forcePlaceholderSize)&&(n.height()||n.height(e.currentItem.innerHeight()-parseInt(e.currentItem.css("paddingTop")||0,10)-parseInt(e.currentItem.css("paddingBottom")||0,10)),n.width()||n.width(e.currentItem.innerWidth()-parseInt(e.currentItem.css("paddingLeft")||0,10)-parseInt(e.currentItem.css("paddingRight")||0,10)))}}),e.placeholder=t(s.placeholder.element.call(e.element,e.currentItem)),e.currentItem.after(e.placeholder),s.placeholder.update(e,e.placeholder)},_createTrPlaceholder:function(e,i){var s=this;e.children().each(function(){t("<td>&#160;</td>",s.document[0]).attr("colspan",t(this).attr("colspan")||1).appendTo(i)})},_contactContainers:function(e){var i,s,n,o,a,r,h,l,c,u,d=null,p=null;for(i=this.containers.length-1;i>=0;i--)if(!t.contains(this.currentItem[0],this.containers[i].element[0]))if(this._intersectsWith(this.containers[i].containerCache)){if(d&&t.contains(this.containers[i].element[0],d.element[0]))continue;d=this.containers[i],p=i}else this.containers[i].containerCache.over&&(this.containers[i]._trigger("out",e,this._uiHash(this)),this.containers[i].containerCache.over=0);if(d)if(1===this.containers.length)this.containers[p].containerCache.over||(this.containers[p]._trigger("over",e,this._uiHash(this)),this.containers[p].containerCache.over=1);else{for(n=1e4,o=null,c=d.floating||this._isFloating(this.currentItem),a=c?"left":"top",r=c?"width":"height",u=c?"pageX":"pageY",s=this.items.length-1;s>=0;s--)t.contains(this.containers[p].element[0],this.items[s].item[0])&&this.items[s].item[0]!==this.currentItem[0]&&(h=this.items[s].item.offset()[a],l=!1,e[u]-h>this.items[s][r]/2&&(l=!0),n>Math.abs(e[u]-h)&&(n=Math.abs(e[u]-h),o=this.items[s],this.direction=l?"up":"down"));if(!o&&!this.options.dropOnEmpty)return;if(this.currentContainer===this.containers[p])return this.currentContainer.containerCache.over||(this.containers[p]._trigger("over",e,this._uiHash()),this.currentContainer.containerCache.over=1),void 0;o?this._rearrange(e,o,null,!0):this._rearrange(e,null,this.containers[p].element,!0),this._trigger("change",e,this._uiHash()),this.containers[p]._trigger("change",e,this._uiHash(this)),this.currentContainer=this.containers[p],this.options.placeholder.update(this.currentContainer,this.placeholder),this.containers[p]._trigger("over",e,this._uiHash(this)),this.containers[p].containerCache.over=1}},_createHelper:function(e){var i=this.options,s=t.isFunction(i.helper)?t(i.helper.apply(this.element[0],[e,this.currentItem])):"clone"===i.helper?this.currentItem.clone():this.currentItem;return s.parents("body").length||t("parent"!==i.appendTo?i.appendTo:this.currentItem[0].parentNode)[0].appendChild(s[0]),s[0]===this.currentItem[0]&&(this._storedCSS={width:this.currentItem[0].style.width,height:this.currentItem[0].style.height,position:this.currentItem.css("position"),top:this.currentItem.css("top"),left:this.currentItem.css("left")}),(!s[0].style.width||i.forceHelperSize)&&s.width(this.currentItem.width()),(!s[0].style.height||i.forceHelperSize)&&s.height(this.currentItem.height()),s},_adjustOffsetFromHelper:function(e){"string"==typeof e&&(e=e.split(" ")),t.isArray(e)&&(e={left:+e[0],top:+e[1]||0}),"left"in e&&(this.offset.click.left=e.left+this.margins.left),"right"in e&&(this.offset.click.left=this.helperProportions.width-e.right+this.margins.left),"top"in e&&(this.offset.click.top=e.top+this.margins.top),"bottom"in e&&(this.offset.click.top=this.helperProportions.height-e.bottom+this.margins.top)},_getParentOffset:function(){this.offsetParent=this.helper.offsetParent();var e=this.offsetParent.offset();return"absolute"===this.cssPosition&&this.scrollParent[0]!==this.document[0]&&t.contains(this.scrollParent[0],this.offsetParent[0])&&(e.left+=this.scrollParent.scrollLeft(),e.top+=this.scrollParent.scrollTop()),(this.offsetParent[0]===this.document[0].body||this.offsetParent[0].tagName&&"html"===this.offsetParent[0].tagName.toLowerCase()&&t.ui.ie)&&(e={top:0,left:0}),{top:e.top+(parseInt(this.offsetParent.css("borderTopWidth"),10)||0),left:e.left+(parseInt(this.offsetParent.css("borderLeftWidth"),10)||0)}},_getRelativeOffset:function(){if("relative"===this.cssPosition){var t=this.currentItem.position();return{top:t.top-(parseInt(this.helper.css("top"),10)||0)+this.scrollParent.scrollTop(),left:t.left-(parseInt(this.helper.css("left"),10)||0)+this.scrollParent.scrollLeft()}}return{top:0,left:0}},_cacheMargins:function(){this.margins={left:parseInt(this.currentItem.css("marginLeft"),10)||0,top:parseInt(this.currentItem.css("marginTop"),10)||0}},_cacheHelperProportions:function(){this.helperProportions={width:this.helper.outerWidth(),height:this.helper.outerHeight()}},_setContainment:function(){var e,i,s,n=this.options;"parent"===n.containment&&(n.containment=this.helper[0].parentNode),("document"===n.containment||"window"===n.containment)&&(this.containment=[0-this.offset.relative.left-this.offset.parent.left,0-this.offset.relative.top-this.offset.parent.top,"document"===n.containment?this.document.width():this.window.width()-this.helperProportions.width-this.margins.left,("document"===n.containment?this.document.height()||document.body.parentNode.scrollHeight:this.window.height()||this.document[0].body.parentNode.scrollHeight)-this.helperProportions.height-this.margins.top]),/^(document|window|parent)$/.test(n.containment)||(e=t(n.containment)[0],i=t(n.containment).offset(),s="hidden"!==t(e).css("overflow"),this.containment=[i.left+(parseInt(t(e).css("borderLeftWidth"),10)||0)+(parseInt(t(e).css("paddingLeft"),10)||0)-this.margins.left,i.top+(parseInt(t(e).css("borderTopWidth"),10)||0)+(parseInt(t(e).css("paddingTop"),10)||0)-this.margins.top,i.left+(s?Math.max(e.scrollWidth,e.offsetWidth):e.offsetWidth)-(parseInt(t(e).css("borderLeftWidth"),10)||0)-(parseInt(t(e).css("paddingRight"),10)||0)-this.helperProportions.width-this.margins.left,i.top+(s?Math.max(e.scrollHeight,e.offsetHeight):e.offsetHeight)-(parseInt(t(e).css("borderTopWidth"),10)||0)-(parseInt(t(e).css("paddingBottom"),10)||0)-this.helperProportions.height-this.margins.top])},_convertPositionTo:function(e,i){i||(i=this.position);var s="absolute"===e?1:-1,n="absolute"!==this.cssPosition||this.scrollParent[0]!==this.document[0]&&t.contains(this.scrollParent[0],this.offsetParent[0])?this.scrollParent:this.offsetParent,o=/(html|body)/i.test(n[0].tagName);return{top:i.top+this.offset.relative.top*s+this.offset.parent.top*s-("fixed"===this.cssPosition?-this.scrollParent.scrollTop():o?0:n.scrollTop())*s,left:i.left+this.offset.relative.left*s+this.offset.parent.left*s-("fixed"===this.cssPosition?-this.scrollParent.scrollLeft():o?0:n.scrollLeft())*s}},_generatePosition:function(e){var i,s,n=this.options,o=e.pageX,a=e.pageY,r="absolute"!==this.cssPosition||this.scrollParent[0]!==this.document[0]&&t.contains(this.scrollParent[0],this.offsetParent[0])?this.scrollParent:this.offsetParent,h=/(html|body)/i.test(r[0].tagName);return"relative"!==this.cssPosition||this.scrollParent[0]!==this.document[0]&&this.scrollParent[0]!==this.offsetParent[0]||(this.offset.relative=this._getRelativeOffset()),this.originalPosition&&(this.containment&&(e.pageX-this.offset.click.left<this.containment[0]&&(o=this.containment[0]+this.offset.click.left),e.pageY-this.offset.click.top<this.containment[1]&&(a=this.containment[1]+this.offset.click.top),e.pageX-this.offset.click.left>this.containment[2]&&(o=this.containment[2]+this.offset.click.left),e.pageY-this.offset.click.top>this.containment[3]&&(a=this.containment[3]+this.offset.click.top)),n.grid&&(i=this.originalPageY+Math.round((a-this.originalPageY)/n.grid[1])*n.grid[1],a=this.containment?i-this.offset.click.top>=this.containment[1]&&i-this.offset.click.top<=this.containment[3]?i:i-this.offset.click.top>=this.containment[1]?i-n.grid[1]:i+n.grid[1]:i,s=this.originalPageX+Math.round((o-this.originalPageX)/n.grid[0])*n.grid[0],o=this.containment?s-this.offset.click.left>=this.containment[0]&&s-this.offset.click.left<=this.containment[2]?s:s-this.offset.click.left>=this.containment[0]?s-n.grid[0]:s+n.grid[0]:s)),{top:a-this.offset.click.top-this.offset.relative.top-this.offset.parent.top+("fixed"===this.cssPosition?-this.scrollParent.scrollTop():h?0:r.scrollTop()),left:o-this.offset.click.left-this.offset.relative.left-this.offset.parent.left+("fixed"===this.cssPosition?-this.scrollParent.scrollLeft():h?0:r.scrollLeft())}},_rearrange:function(t,e,i,s){i?i[0].appendChild(this.placeholder[0]):e.item[0].parentNode.insertBefore(this.placeholder[0],"down"===this.direction?e.item[0]:e.item[0].nextSibling),this.counter=this.counter?++this.counter:1;var n=this.counter;
+this._delay(function(){n===this.counter&&this.refreshPositions(!s)})},_clear:function(t,e){function i(t,e,i){return function(s){i._trigger(t,s,e._uiHash(e))}}this.reverting=!1;var s,n=[];if(!this._noFinalSort&&this.currentItem.parent().length&&this.placeholder.before(this.currentItem),this._noFinalSort=null,this.helper[0]===this.currentItem[0]){for(s in this._storedCSS)("auto"===this._storedCSS[s]||"static"===this._storedCSS[s])&&(this._storedCSS[s]="");this.currentItem.css(this._storedCSS),this._removeClass(this.currentItem,"ui-sortable-helper")}else this.currentItem.show();for(this.fromOutside&&!e&&n.push(function(t){this._trigger("receive",t,this._uiHash(this.fromOutside))}),!this.fromOutside&&this.domPosition.prev===this.currentItem.prev().not(".ui-sortable-helper")[0]&&this.domPosition.parent===this.currentItem.parent()[0]||e||n.push(function(t){this._trigger("update",t,this._uiHash())}),this!==this.currentContainer&&(e||(n.push(function(t){this._trigger("remove",t,this._uiHash())}),n.push(function(t){return function(e){t._trigger("receive",e,this._uiHash(this))}}.call(this,this.currentContainer)),n.push(function(t){return function(e){t._trigger("update",e,this._uiHash(this))}}.call(this,this.currentContainer)))),s=this.containers.length-1;s>=0;s--)e||n.push(i("deactivate",this,this.containers[s])),this.containers[s].containerCache.over&&(n.push(i("out",this,this.containers[s])),this.containers[s].containerCache.over=0);if(this.storedCursor&&(this.document.find("body").css("cursor",this.storedCursor),this.storedStylesheet.remove()),this._storedOpacity&&this.helper.css("opacity",this._storedOpacity),this._storedZIndex&&this.helper.css("zIndex","auto"===this._storedZIndex?"":this._storedZIndex),this.dragging=!1,e||this._trigger("beforeStop",t,this._uiHash()),this.placeholder[0].parentNode.removeChild(this.placeholder[0]),this.cancelHelperRemoval||(this.helper[0]!==this.currentItem[0]&&this.helper.remove(),this.helper=null),!e){for(s=0;n.length>s;s++)n[s].call(this,t);this._trigger("stop",t,this._uiHash())}return this.fromOutside=!1,!this.cancelHelperRemoval},_trigger:function(){t.Widget.prototype._trigger.apply(this,arguments)===!1&&this.cancel()},_uiHash:function(e){var i=e||this;return{helper:i.helper,placeholder:i.placeholder||t([]),position:i.position,originalPosition:i.originalPosition,offset:i.positionAbs,item:i.currentItem,sender:e?e.element:null}}}),t.widget("ui.spinner",{version:"1.12.1",defaultElement:"<input>",widgetEventPrefix:"spin",options:{classes:{"ui-spinner":"ui-corner-all","ui-spinner-down":"ui-corner-br","ui-spinner-up":"ui-corner-tr"},culture:null,icons:{down:"ui-icon-triangle-1-s",up:"ui-icon-triangle-1-n"},incremental:!0,max:null,min:null,numberFormat:null,page:10,step:1,change:null,spin:null,start:null,stop:null},_create:function(){this._setOption("max",this.options.max),this._setOption("min",this.options.min),this._setOption("step",this.options.step),""!==this.value()&&this._value(this.element.val(),!0),this._draw(),this._on(this._events),this._refresh(),this._on(this.window,{beforeunload:function(){this.element.removeAttr("autocomplete")}})},_getCreateOptions:function(){var e=this._super(),i=this.element;return t.each(["min","max","step"],function(t,s){var n=i.attr(s);null!=n&&n.length&&(e[s]=n)}),e},_events:{keydown:function(t){this._start(t)&&this._keydown(t)&&t.preventDefault()},keyup:"_stop",focus:function(){this.previous=this.element.val()},blur:function(t){return this.cancelBlur?(delete this.cancelBlur,void 0):(this._stop(),this._refresh(),this.previous!==this.element.val()&&this._trigger("change",t),void 0)},mousewheel:function(t,e){if(e){if(!this.spinning&&!this._start(t))return!1;this._spin((e>0?1:-1)*this.options.step,t),clearTimeout(this.mousewheelTimer),this.mousewheelTimer=this._delay(function(){this.spinning&&this._stop(t)},100),t.preventDefault()}},"mousedown .ui-spinner-button":function(e){function i(){var e=this.element[0]===t.ui.safeActiveElement(this.document[0]);e||(this.element.trigger("focus"),this.previous=s,this._delay(function(){this.previous=s}))}var s;s=this.element[0]===t.ui.safeActiveElement(this.document[0])?this.previous:this.element.val(),e.preventDefault(),i.call(this),this.cancelBlur=!0,this._delay(function(){delete this.cancelBlur,i.call(this)}),this._start(e)!==!1&&this._repeat(null,t(e.currentTarget).hasClass("ui-spinner-up")?1:-1,e)},"mouseup .ui-spinner-button":"_stop","mouseenter .ui-spinner-button":function(e){return t(e.currentTarget).hasClass("ui-state-active")?this._start(e)===!1?!1:(this._repeat(null,t(e.currentTarget).hasClass("ui-spinner-up")?1:-1,e),void 0):void 0},"mouseleave .ui-spinner-button":"_stop"},_enhance:function(){this.uiSpinner=this.element.attr("autocomplete","off").wrap("<span>").parent().append("<a></a><a></a>")},_draw:function(){this._enhance(),this._addClass(this.uiSpinner,"ui-spinner","ui-widget ui-widget-content"),this._addClass("ui-spinner-input"),this.element.attr("role","spinbutton"),this.buttons=this.uiSpinner.children("a").attr("tabIndex",-1).attr("aria-hidden",!0).button({classes:{"ui-button":""}}),this._removeClass(this.buttons,"ui-corner-all"),this._addClass(this.buttons.first(),"ui-spinner-button ui-spinner-up"),this._addClass(this.buttons.last(),"ui-spinner-button ui-spinner-down"),this.buttons.first().button({icon:this.options.icons.up,showLabel:!1}),this.buttons.last().button({icon:this.options.icons.down,showLabel:!1}),this.buttons.height()>Math.ceil(.5*this.uiSpinner.height())&&this.uiSpinner.height()>0&&this.uiSpinner.height(this.uiSpinner.height())},_keydown:function(e){var i=this.options,s=t.ui.keyCode;switch(e.keyCode){case s.UP:return this._repeat(null,1,e),!0;case s.DOWN:return this._repeat(null,-1,e),!0;case s.PAGE_UP:return this._repeat(null,i.page,e),!0;case s.PAGE_DOWN:return this._repeat(null,-i.page,e),!0}return!1},_start:function(t){return this.spinning||this._trigger("start",t)!==!1?(this.counter||(this.counter=1),this.spinning=!0,!0):!1},_repeat:function(t,e,i){t=t||500,clearTimeout(this.timer),this.timer=this._delay(function(){this._repeat(40,e,i)},t),this._spin(e*this.options.step,i)},_spin:function(t,e){var i=this.value()||0;this.counter||(this.counter=1),i=this._adjustValue(i+t*this._increment(this.counter)),this.spinning&&this._trigger("spin",e,{value:i})===!1||(this._value(i),this.counter++)},_increment:function(e){var i=this.options.incremental;return i?t.isFunction(i)?i(e):Math.floor(e*e*e/5e4-e*e/500+17*e/200+1):1},_precision:function(){var t=this._precisionOf(this.options.step);return null!==this.options.min&&(t=Math.max(t,this._precisionOf(this.options.min))),t},_precisionOf:function(t){var e=""+t,i=e.indexOf(".");return-1===i?0:e.length-i-1},_adjustValue:function(t){var e,i,s=this.options;return e=null!==s.min?s.min:0,i=t-e,i=Math.round(i/s.step)*s.step,t=e+i,t=parseFloat(t.toFixed(this._precision())),null!==s.max&&t>s.max?s.max:null!==s.min&&s.min>t?s.min:t},_stop:function(t){this.spinning&&(clearTimeout(this.timer),clearTimeout(this.mousewheelTimer),this.counter=0,this.spinning=!1,this._trigger("stop",t))},_setOption:function(t,e){var i,s,n;return"culture"===t||"numberFormat"===t?(i=this._parse(this.element.val()),this.options[t]=e,this.element.val(this._format(i)),void 0):(("max"===t||"min"===t||"step"===t)&&"string"==typeof e&&(e=this._parse(e)),"icons"===t&&(s=this.buttons.first().find(".ui-icon"),this._removeClass(s,null,this.options.icons.up),this._addClass(s,null,e.up),n=this.buttons.last().find(".ui-icon"),this._removeClass(n,null,this.options.icons.down),this._addClass(n,null,e.down)),this._super(t,e),void 0)},_setOptionDisabled:function(t){this._super(t),this._toggleClass(this.uiSpinner,null,"ui-state-disabled",!!t),this.element.prop("disabled",!!t),this.buttons.button(t?"disable":"enable")},_setOptions:r(function(t){this._super(t)}),_parse:function(t){return"string"==typeof t&&""!==t&&(t=window.Globalize&&this.options.numberFormat?Globalize.parseFloat(t,10,this.options.culture):+t),""===t||isNaN(t)?null:t},_format:function(t){return""===t?"":window.Globalize&&this.options.numberFormat?Globalize.format(t,this.options.numberFormat,this.options.culture):t},_refresh:function(){this.element.attr({"aria-valuemin":this.options.min,"aria-valuemax":this.options.max,"aria-valuenow":this._parse(this.element.val())})},isValid:function(){var t=this.value();return null===t?!1:t===this._adjustValue(t)},_value:function(t,e){var i;""!==t&&(i=this._parse(t),null!==i&&(e||(i=this._adjustValue(i)),t=this._format(i))),this.element.val(t),this._refresh()},_destroy:function(){this.element.prop("disabled",!1).removeAttr("autocomplete role aria-valuemin aria-valuemax aria-valuenow"),this.uiSpinner.replaceWith(this.element)},stepUp:r(function(t){this._stepUp(t)}),_stepUp:function(t){this._start()&&(this._spin((t||1)*this.options.step),this._stop())},stepDown:r(function(t){this._stepDown(t)}),_stepDown:function(t){this._start()&&(this._spin((t||1)*-this.options.step),this._stop())},pageUp:r(function(t){this._stepUp((t||1)*this.options.page)}),pageDown:r(function(t){this._stepDown((t||1)*this.options.page)}),value:function(t){return arguments.length?(r(this._value).call(this,t),void 0):this._parse(this.element.val())},widget:function(){return this.uiSpinner}}),t.uiBackCompat!==!1&&t.widget("ui.spinner",t.ui.spinner,{_enhance:function(){this.uiSpinner=this.element.attr("autocomplete","off").wrap(this._uiSpinnerHtml()).parent().append(this._buttonHtml())},_uiSpinnerHtml:function(){return"<span>"},_buttonHtml:function(){return"<a></a><a></a>"}}),t.ui.spinner,t.widget("ui.tabs",{version:"1.12.1",delay:300,options:{active:null,classes:{"ui-tabs":"ui-corner-all","ui-tabs-nav":"ui-corner-all","ui-tabs-panel":"ui-corner-bottom","ui-tabs-tab":"ui-corner-top"},collapsible:!1,event:"click",heightStyle:"content",hide:null,show:null,activate:null,beforeActivate:null,beforeLoad:null,load:null},_isLocal:function(){var t=/#.*$/;return function(e){var i,s;i=e.href.replace(t,""),s=location.href.replace(t,"");try{i=decodeURIComponent(i)}catch(n){}try{s=decodeURIComponent(s)}catch(n){}return e.hash.length>1&&i===s}}(),_create:function(){var e=this,i=this.options;this.running=!1,this._addClass("ui-tabs","ui-widget 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+
+    <!-- Dagre layout -->
+    <!-- <script src="js/dagre-0.8.5.min.js"></script> -->
+    <!-- <script src="js/cytoscape-dagre-2.3.2.js"></script> -->
+
+    <!-- Data -->
+    <script >network = {
+  "elements": {
+    "nodes": [
+      {
+        "data": {
+          "id": "CMPD_0000000013",
+          "type": "chemical",
+          "smiles": "OO",
+          "inchi": "InChI=1S/H2O2/c1-2/h1-2H",
+          "inchikey": "MHAJPDPJQMAIIY-UHFFFAOYSA-N",
+          "sink_chemical": true,
+          "target_chemical": false,
+          "label": "H2O2",
+          "all_labels": [
+            "H2O2"
+          ],
+          "svg": "data:image/svg+xml;charset=utf-8,%3C%3Fxml%20version%3D%271.0%27%20encoding%3D%27iso-8859-1%27%3F%3E%0A%3Csvg%20version%3D%271.1%27%20baseProfile%3D%27full%27%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20xmlns%3D%27http%3A//www.w3.org/2000/svg%27%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20xmlns%3Ardkit%3D%27http%3A//www.rdkit.org/xml%27%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20xmlns%3Axlink%3D%27http%3A//www.w3.org/1999/xlink%27%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20xml%3Aspace%3D%27preserve%27%0Awidth%3D%27200px%27%20height%3D%27200px%27%20viewBox%3D%270%200%20200%20200%27%3E%0A%3C%21--%20END%20OF%20HEADER%20--%3E%0A%3Crect%20style%3D%27opacity%3A1.0%3Bfill%3A%23FFFFFF%3Bstroke%3Anone%27%20width%3D%27200.0%27%20height%3D%27200.0%27%20x%3D%270.0%27%20y%3D%270.0%27%3E%20%3C/rect%3E%0A%3Cpath%20class%3D%27bond-0%20atom-0%20atom-1%27%20d%3D%27M%2058.7%2C100.0%20L%20140.5%2C100.0%27%20style%3D%27fill%3Anone%3Bfill-rule%3Aevenodd%3Bstroke%3A%23FF0000%3Bstroke-width%3A2.0px%3Bstroke-linecap%3Abutt%3Bstroke-linejoin%3Amiter%3Bstroke-opacity%3A1%27%20/%3E%0A%3Cpath%20%20class%3D%27atom-0%27%20d%3D%27M%205.7%2086.0%0AL%209.5%2086.0%0AL%209.5%2098.0%0AL%2024.0%2098.0%0AL%2024.0%2086.0%0AL%2027.8%2086.0%0AL%2027.8%20114.3%0AL%2024.0%20114.3%0AL%2024.0%20101.2%0AL%209.5%20101.2%0AL%209.5%20114.3%0AL%205.7%20114.3%0AL%205.7%2086.0%0A%27%20fill%3D%27%23FF0000%27/%3E%0A%3Cpath%20%20class%3D%27atom-0%27%20d%3D%27M%2029.8%20100.1%0AQ%2029.8%2093.3%2C%2033.2%2089.5%0AQ%2036.6%2085.7%2C%2042.8%2085.7%0AQ%2049.1%2085.7%2C%2052.5%2089.5%0AQ%2055.8%2093.3%2C%2055.8%20100.1%0AQ%2055.8%20107.0%2C%2052.4%20110.9%0AQ%2049.0%20114.8%2C%2042.8%20114.8%0AQ%2036.6%20114.8%2C%2033.2%20110.9%0AQ%2029.8%20107.0%2C%2029.8%20100.1%0AM%2042.8%20111.6%0AQ%2047.2%20111.6%2C%2049.5%20108.7%0AQ%2051.8%20105.8%2C%2051.8%20100.1%0AQ%2051.8%2094.5%2C%2049.5%2091.7%0AQ%2047.2%2088.9%2C%2042.8%2088.9%0AQ%2038.5%2088.9%2C%2036.2%2091.7%0AQ%2033.8%2094.5%2C%2033.8%20100.1%0AQ%2033.8%20105.8%2C%2036.2%20108.7%0AQ%2038.5%20111.6%2C%2042.8%20111.6%0A%27%20fill%3D%27%23FF0000%27/%3E%0A%3Cpath%20%20class%3D%27atom-1%27%20d%3D%27M%20142.9%20100.1%0AQ%20142.9%2093.3%2C%20146.2%2089.5%0AQ%20149.6%2085.7%2C%20155.9%2085.7%0AQ%20162.2%2085.7%2C%20165.5%2089.5%0AQ%20168.9%2093.3%2C%20168.9%20100.1%0AQ%20168.9%20107.0%2C%20165.5%20110.9%0AQ%20162.1%20114.8%2C%20155.9%20114.8%0AQ%20149.6%20114.8%2C%20146.2%20110.9%0AQ%20142.9%20107.0%2C%20142.9%20100.1%0AM%20155.9%20111.6%0AQ%20160.2%20111.6%2C%20162.5%20108.7%0AQ%20164.9%20105.8%2C%20164.9%20100.1%0AQ%20164.9%2094.5%2C%20162.5%2091.7%0AQ%20160.2%2088.9%2C%20155.9%2088.9%0AQ%20151.6%2088.9%2C%20149.2%2091.7%0AQ%20146.9%2094.5%2C%20146.9%20100.1%0AQ%20146.9%20105.8%2C%20149.2%20108.7%0AQ%20151.6%20111.6%2C%20155.9%20111.6%0A%27%20fill%3D%27%23FF0000%27/%3E%0A%3Cpath%20%20class%3D%27atom-1%27%20d%3D%27M%20172.3%2086.0%0AL%20176.1%2086.0%0AL%20176.1%2098.0%0AL%20190.6%2098.0%0AL%20190.6%2086.0%0AL%20194.4%2086.0%0AL%20194.4%20114.3%0AL%20190.6%20114.3%0AL%20190.6%20101.2%0AL%20176.1%20101.2%0AL%20176.1%20114.3%0AL%20172.3%20114.3%0AL%20172.3%2086.0%0A%27%20fill%3D%27%23FF0000%27/%3E%0A%3C/svg%3E%0A",
+          "value": "CMPD_0000000013",
+          "name": "H2O2"
+        }
+      },
+      {
+        "data": {
+          "id": "TARGET_0000000001",
+          "type": "chemical",
+          "smiles": "CC(O)C(=O)O",
+          "inchi": "InChI=1S/C3H6O3/c1-2(4)3(5)6/h2,4H,1H3,(H,5,6)",
+          "inchikey": "JVTAAEKCZFNVCJ-UHFFFAOYSA-N",
+          "sink_chemical": false,
+          "target_chemical": true,
+          "label": "TARGET_0000000001",
+          "all_labels": [
+            "TARGET_0000000001"
+          ],
+          "svg": 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+          "value": "TARGET_0000000001",
+          "name": "TARGET_0000000001"
+        }
+      },
+      {
+        "data": {
+          "id": "TRS_0_0_16_MNXR133653_9998",
+          "type": "reaction",
+          "rsmiles": "CC(O)C(=O)O.O=O>>CC(=O)C(=O)O.OO",
+          "diameter": "12",
+          "rule_ids": [
+            "RR-02-0f2f669fd09feecb-12-F"
+          ],
+          "rule_score": "1.9912260756924949",
+          "ec_numbers": [
+            "1.1.3.15"
+          ],
+          "iteration": "0",
+          "rxn_template_ids": [
+            "MNXR133653"
+          ],
+          "label": "1.1.3.15",
+          "all_labels": [
+            "1.1.3.15"
+          ],
+          "value": "TRS_0_0_16_MNXR133653_9998",
+          "name": "1.1.3.15"
+        }
+      }
+    ],
+    "edges": [
+      {
+        "data": {
+          "coeff": 1,
+          "id": "TARGET_0000000001_=>_TRS_0_0_16_MNXR133653_9998",
+          "source": "TARGET_0000000001",
+          "target": "TRS_0_0_16_MNXR133653_9998"
+        }
+      },
+      {
+        "data": {
+          "coeff": 1,
+          "id": "TRS_0_0_16_MNXR133653_9998_=>_CMPD_0000000013",
+          "source": "TRS_0_0_16_MNXR133653_9998",
+          "target": "CMPD_0000000013"
+        }
+      }
+    ]
+  }
+}</script>
+
+    <!-- Viewer -->
+    <script >/*jshint esversion: 6 */
+/*
+__author__ = 'Thomas Duigou'
+__license__ = 'MIT'
+*/
+
+// Utils ///////////////////////////
+
+/**
+ * Put chemical info into the information panel
+ */
+function panel_chemical_info(node, show=false){
+    if (show){
+        // Collect
+        let node_id = node.data('id');
+        let label = node.data('label');
+        let svg = node.data('svg');
+        let smiles = node.data('smiles');
+        let inchi = node.data('inchi');
+        let inchikey = node.data('inchikey');
+        if (node.data('cofactor') == 1){
+            var cofactor = 'Yes';
+        } else {
+            var cofactor = 'No';
+        }
+        if (node.data('sink_chemical')){
+            var insink = 'Yes';
+        } else {
+            var insink = 'No';
+        }
+        // Inject
+        $("span.chem_info_label").html(label);
+        if (inchikey == "" || inchikey == null){
+            $("span.chem_info_inchikey").html("NA");
+            $("span.chem_info_inchikey_search").html("");
+        } else {
+            $("span.chem_info_inchikey").html(inchikey);
+            $("span.chem_info_inchikey_search").html('<a target="_blank" href="http://www.google.com/search?q=' + encodeURI(inchikey) + '">Look for identical structure using Google</a>');
+        }
+        if (inchi == ""|| inchi == null){
+            $("span.chem_info_inchi").html("NA");
+            $("span.chem_info_inchi_search").html("");
+        } else {
+            $("span.chem_info_inchi").html(inchi);
+            $("span.chem_info_inchi_search").html('<a target="_blank" href="https://pubchem.ncbi.nlm.nih.gov/search/#collection=compounds&query_type=structure&query_subtype=identity&query=' + encodeURI(inchi) + '">Look for identical structure using PubChem</a>');
+        }
+        if (smiles == ""|| smiles == null){
+            $("span.chem_info_smiles").html("NA");
+            $("span.chem_info_smiles_search").html("");
+        } else {
+            $("span.chem_info_smiles").html(smiles);
+            $("span.chem_info_smiles_search").html('<a target="_blank" href="https://pubchem.ncbi.nlm.nih.gov/search/#collection=compounds&query_type=structure&query_subtype=identity&query=' + encodeURI(smiles) + '">Look for identical structure using PubChem</a>');
+        }
+        $("span.chem_info_iscofactor").html(cofactor);
+        $("span.chem_info_isprecursor").html(insink);
+        
+        // Inject SVG depiction as a background image (if any)
+        if (svg !== null && svg !== ""){
+            $('div.img-box').show();
+            $('div.chem_info_svg').css('background-image', "url('" + svg + "')");
+        } else {
+            $('div.img-box').hide();
+        }
+        // Show
+        $("#panel_chemical_info").show();
+    } else {
+        $("#panel_chemical_info").hide();
+    }
+}
+
+/**
+ * Append crosslink for EC numbers
+ * @param {string} ec_number
+ */
+function append_ec_number_crosslink(ec_number){
+    let url = '<a href="https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=' 
+            + ec_number + '">' + ec_number + '</a>';
+    return url;
+}
+
+function append_template_reaction_crosslink(template_id){
+    let url = '<a href="https://www.metanetx.org/equa_info/'
+            + template_id + '">' + template_id + '</a>';
+    return url;
+}
+
+/**
+ * Put intro info into the information panel
+ * @param {boolean} show True to show the startup legend
+ */
+function panel_startup_legend(show=true){
+    if (show){
+        $("#panel_startup_legend").show();
+    } else {
+        $("#panel_startup_legend").hide();
+    }
+}
+
+/**
+ * Put reaction info into the information panel
+ */
+function panel_reaction_info(node, show=true){
+    if (show){
+        // Collect
+        let node_id = node.data('id');
+        let label = node.data('label')
+        let rsmiles = node.data('rsmiles');
+        let rule_ids = node.data('rule_ids');
+        let rxn_template_ids = node.data('rxn_template_ids');
+        let ec_numbers = node.data('ec_numbers');
+        let thermo_value = node.data('thermo_dg_m_gibbs');
+        let rule_score = node.data('rule_score');
+        let uniprot_ids = node.data('uniprot_ids');
+        // Inject 
+        $("span.reaction_info_rsmiles").html(rsmiles);
+        // Reaction name
+        $("span.reaction_info_name").html(label);
+        // Rule IDs
+        $("div.reaction_info_ruleids").html('');  // Reset div content
+        for (let i = 0; i < rule_ids.length; i++){
+            $("div.reaction_info_ruleids").append(rule_ids[i] + '<br/>');
+        }
+        // Reaction template IDs
+        $("div.reaction_info_reaction_template_ids").html('');  // Reset div content
+        console.log(rxn_template_ids);
+        for (let i = 0; i < rxn_template_ids.length; i++){
+            let url = append_template_reaction_crosslink(rxn_template_ids[i]);
+            console.log(url);
+            $("div.reaction_info_reaction_template_ids").append(url + '<br/>');
+        }
+        // EC numbers
+        $("div.reaction_info_ecnumbers").html('');  // Reset div content
+        if (ec_numbers == null || ec_numbers.length == 0){
+            $("div.reaction_info_ecnumbers").append('None<br/>');
+        } else {
+            for (let i = 0; i < ec_numbers.length; i++){
+                let url = append_ec_number_crosslink(ec_numbers[i]);
+                $("div.reaction_info_ecnumbers").append(url + '<br/>');
+            }
+        }
+
+
+        https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=1.3.99.31
+
+        // // Inject crosslinks
+        // $("div.reaction_info_xlinks").html('');  // Reset div content
+        // if (xlinks != null && xlinks.length > 0){
+        //     for (let i = 0; i < xlinks.length; i++){
+        //         $("div.reaction_info_xlinks").append('<a target="_blank" href="' + xlinks[i]['url'] + '">' + xlinks[i]['db_name'] + ':' + xlinks[i]['entity_id'] + '</a>');
+        //         $("div.reaction_info_xlinks").append('<br/>');
+        //     }
+        // } else {
+        //     $("div.reaction_info_xlinks").append('None<br/>');
+        // }
+        // Thermodynamic value
+        if (isNaN(thermo_value)){
+            thermo_value = "NaN";
+        } else {
+            thermo_value = parseFloat(thermo_value).toFixed(3);
+        }
+        $("span.reaction_info_thermo").html(thermo_value);
+        // Rule score
+        if (isNaN(rule_score)){
+            rule_score = "NaN";
+        } else {
+            rule_score = parseFloat(rule_score).toFixed(3);
+        }
+        $("span.reaction_info_rule_score").html(rule_score);
+        // Inject UniProt IDs
+        $("div.reaction_info_uniprot_crosslinks").html('');  // Reset div content
+        let nb_ids = 0;
+        for (let uid in uniprot_ids) {
+            ++nb_ids;
+            let selenzy_score = parseFloat(uniprot_ids[uid]['score']).toFixed(1)
+            $("div.reaction_info_uniprot_crosslinks").append(
+                    '<a href="' + get_uniprot_xlink(uid) + '">' + uid + '</a> (' + selenzy_score + ')'
+                );
+            $("div.reaction_info_uniprot_crosslinks").append(
+                '<br/>'
+                );
+        }
+        if (nb_ids == 0){
+            $("div.reaction_info_uniprot_crosslinks").append('None<br/>');
+        }
+        // Selenzyme crosslink
+        $("span.reaction_info_selenzyme_crosslink").html('<a target="_blank" href="http://selenzyme.synbiochem.co.uk/results?smarts=' + encodeURIComponent( rsmiles ) + '">Crosslink to Selenzyme</a>');
+        // Show
+        $("#panel_reaction_info").show();
+    } else {
+        $("#panel_reaction_info").hide();
+    }
+}
+
+
+/**
+ * Generate links to UniProt web site
+ * @param {uid} UniProt ID to be used 
+ */
+function get_uniprot_xlink(uid){
+    return 'https://www.uniprot.org/uniprot/' + uid
+}
+
+
+/**
+ * Make labels for chemicals
+ *
+ * @param {Integer} max_length: string size cutoff before label truncation
+ */
+function make_chemical_labels(max_length=6){
+    let nodes = cy.nodes().filter('[type = "chemical"]');
+    for (let i = 0; i < nodes.size(); i++){
+        let node = nodes[i];
+        let label = node.data('label');
+        if ((typeof label != 'undefined') && (label != 'None') && (label != '')){
+            if (label.length > max_length){
+                short_label = label.substr(0, max_length-2)+'..';
+            } else {
+                short_label = label;
+            }
+        } else {
+            short_label = '';
+        }
+        node.data('short_label', short_label);
+    }
+}
+
+/**
+ * Make labels for reactions
+ *
+ * @param {Integer} max_length: string size cutoff before label truncation
+ */
+function make_reaction_labels(max_length=10){
+    let nodes = cy.nodes().filter('[type = "reaction"]');
+    for (let i = 0; i < nodes.size(); i++){
+        let node = nodes[i];
+        let label = node.data('label');
+        if ((typeof label != 'undefined') && (label != 'None') && (label != '')){
+            if (label.length > max_length){
+                short_label = label.substr(0, max_length-2)+'..';
+            } else {
+                short_label = label;
+            }
+        } else {
+            short_label = '';
+        }
+        node.data('short_label', short_label);
+    }
+}
+
+// Live ///////////////////////////
+
+
+$(function(){
+
+    // Cytoscape object to play with all along
+    var cy = window.cy = cytoscape({
+        container: document.getElementById('cy'),
+        motionBlur: true
+    });
+
+    // Basic stuff to do only once
+    panel_startup_legend(true)
+    panel_chemical_info(null, false);
+    panel_reaction_info(null, false);
+    init_network(true);
+    refresh_layout();
+    show_cofactors(false);
+
+    /**
+     * Initialise the network, but hide everything
+     *
+     * @param show_graph (bool): show the loaded network
+     */
+    function init_network(show_graph=true){
+        // Reset the graph
+        cy.json({elements: {}});
+        cy.minZoom(1e-50);
+        
+        // Load the full network
+        cy.json({elements: network['elements']});
+        
+        // Create node labels
+        make_chemical_labels(20);
+        make_reaction_labels(9);
+        
+        // Hide them 'by default'
+        if (! show_graph){
+            show_pathways(selected_paths='__NONE__');
+        } else {
+            $('input[name=path_checkbox]').prop('checked', true);  // Check all
+        }
+        
+        // Once the layout is done:
+        // * set the min zoom level
+        // * put default info
+        cy.on('layoutstop', function(e){
+            cy.minZoom(cy.zoom());
+        });
+        
+        cy.style(
+            cytoscape.stylesheet()
+                .selector("node[type='reaction']")
+                    .css({
+                        'height': 60,
+                        'width': 120,
+                        'background-color': 'white',
+                        'border-width': 5,
+                        'border-color': 'darkgray',
+                        'border-style': 'solid',
+                        'content': 'data(short_label)',
+                        'text-valign': 'center',
+                        'text-halign': 'center',
+                        'text-opacity': 1,
+                        'color': '#575757',
+                        'font-size': '20px',
+                    })
+                .selector("node[type='chemical']")
+                    .css({
+                        'background-color': '#52be80',
+                        'background-fit':'contain',
+                        'shape': 'roundrectangle',
+                        'width': 80,
+                        'height': 80,
+                        'label': 'data(short_label)',
+                        'font-size': '20px',
+                        // 'font-weight': 'bold',
+                        'text-valign': 'top',
+                        'text-halign': 'center',
+                        'text-margin-y': 8,
+                        'text-opacity': 1,
+                        'text-background-color': 'White',
+                        'text-background-opacity': 0.85,
+                        'text-background-shape': 'roundrectangle',
+                    })
+                .selector("node[type='chemical'][?target_chemical]")
+                    .css({
+                        'background-color': '#B22222',
+                        'border-color': '#B22222',
+                    })
+                .selector("node[type='chemical'][?sink_chemical]")
+                    .css({
+                        'background-color': '#68956D',
+                        'border-color': '#68956D'
+                    })
+                .selector("node[type='chemical'][!target_chemical][!sink_chemical]")  // ie: intermediates
+                    .css({
+                        'background-color': '#235789',
+                        'border-color': '#235789',
+                    })
+                .selector("node[type='chemical'][?svg]")  // The beauty of it: "?" will match only non null values
+                    .css({
+                        'background-image': 'data(svg)',
+                        'background-fit': 'contain',
+                        'border-width': 8,
+                    })
+                .selector('edge')
+                    .css({
+                        'curve-style': 'bezier',
+                        'line-color': 'darkgray',
+                        'width': '5px',
+                        'target-arrow-shape': 'triangle',
+                        'target-arrow-color': 'darkgray',
+                        'arrow-scale' : 2
+                    })                    
+                .selector('.faded')
+                    .css({
+                        'opacity': 0.15,
+                        'text-opacity': 0.25
+                    })
+                .selector('.highlighted')
+                    .css({
+                        'width': '9px'
+                    })
+                .selector('node:selected')
+                    .css({
+                        'border-width': 5,
+                        'border-color': 'black'
+                    })
+        );
+        
+        cy.on('tap', 'node', function(evt){
+            let node = evt.target;
+            // Print info
+            if (node.is('[type = "chemical"]')){
+                panel_reaction_info(null, false);
+                panel_chemical_info(node, true);
+            } else if (node.is('[type = "reaction"]')){
+                panel_chemical_info(null, false);
+                panel_reaction_info(node, true);
+            }
+        });
+
+        cy.on('tap', 'edge', function(evt){
+            let edge = evt.target;
+        });
+        
+    }
+    
+    /**
+     * Trigger a layout rendering
+     * 
+     * @param {cytoscape collection} element_collection: a collection of elements.
+     */
+    function render_layout(element_collection){
+        // Playing with zoom to get the best fit
+        cy.minZoom(1e-50);
+        cy.on('layoutstop', function(e){
+            cy.minZoom(cy.zoom()*0.9);  // 0.9 to enable the user dezoom a little
+        });
+        // Layout breadthfirst
+        let layout = element_collection.layout({
+            name: 'breadthfirst',
+            circle: false,
+            roots: cy.elements("node[?target_chemical]"),
+            transform: function (node, position ){  // Target at the bottom
+                return {
+                    x: -1 * position.x,
+                    y: -1 * position.y
+                };
+            }
+        })
+        // Layout concentric
+        // let layout = element_collection.layout({
+        //     name: 'concentric',
+        //     directed: true,
+        //     circle: true,
+        //     padding: 30,
+        //     minNodeSpacing: 20,
+        //     concentric: function(node){return node.data('concentric') * -1;},
+        //     levelWidth: function(){return 1;},
+        //     animate: false,
+        //     roots: cy.elements("node[?target_chemical]")
+        // });
+        // Layout cose
+        // let layout = element_collection.layout({
+        //     name: 'cose',
+        //     directed: true,
+        //     animate: false,
+        //     padding: 30,
+        //     componentSpacing: 40,
+        //     roots: cy.elements("node[?target_chemical]")
+        // });
+        // Layout cola
+        // let layout = element_collection.layout({
+        //     name: 'cose-bilkent',
+        //     quality: 'proof',
+        //     padding: 10,
+        //     nodeRepulsion: 9000,
+        //     idealEdgeLength: 100,
+        // })
+        layout.run();
+    }
+        
+
+    /** Handle cofactor display
+     *
+     * Hide of show all nodes annotated as cofactor
+     *
+     * @param show (bool): will show cofactors if true
+     */
+    function show_cofactors(show=true){
+        if (show){
+            cy.elements().style("display", "element");
+        } else {
+            cy.elements('node[?cofactor][?hiddable_cofactor]').style("display", "none");
+            cy.elements('node[?cofactor]').style("display", "none");
+        }
+        refresh_layout();
+    }
+
+    
+    /**
+     * Refresh layout according to visible nodes
+     */
+    function refresh_layout(){
+        render_layout(cy.elements().not(':hidden'));
+    }
+
+        
+    // Cofactors handling
+    $('#show_cofactors_button').on('click', function(event){
+        show_cofactors(true);
+    });
+    $('#remove_cofactors_button').on('click', function(event){
+        show_cofactors(false);
+    });
+    
+});
+</script>
+
+    <!-- CSS stuff -->
+    <style type="text/css">/*
+__author__ = 'Thomas Duigou'
+__license__ = 'MIT'
+*/
+
+/* Basic layout ***************************************************************/
+
+body {
+    margin: 0px;
+}
+
+#base {
+    width: 100%;
+    margin-left: auto;
+    margin-right: auto;
+}
+
+#viewer {
+    height: 80%;
+    box-shadow: 0 0 5px 0px black;
+}
+
+/* Left panel: pathway level interaction **************************************/
+#interaction {
+    position: absolute;
+    z-index: 11;
+    background-color: #E8E9E8;
+    padding: 0 1% 0 1%;
+    border-top-left-radius: 0px;
+    border-bottom-left-radius: 0px;
+    border-top-right-radius: 0px;
+    border-bottom-right-radius: 10px;
+    width: 20%;
+    height: 1000px;
+}
+
+#interaction div.info-title {
+    font-weight: bold;
+    font-size: 1.8em;
+    font-family: sans-serif;
+    font-variant: small-caps;
+    text-align: left;
+    padding-top: 5%;
+    padding-right: 5%;
+}
+
+#interaction div.info-name {
+    font-family: sans-serif;
+    text-align: left;
+    padding-right: 5%;
+}
+
+#interaction {
+    overflow-y: auto;
+}
+
+#pathway_selection > div#table_choice {
+    max-height: 40em;
+    overflow-x: hidden;
+    overflow-y: auto;
+}
+
+/* Central panel: the graph ***************************************************/
+#cy {
+    float: left;
+    width: 60%;
+    height: 1000px;
+    margin-left: 22%;  /* +2 to compensate left pannel padding */
+}
+
+/* Right side panel: info *****************************************************/
+#info {
+    float: right;
+    border-radius: 5px;
+    background-color: #E8E9E8;
+    width: 18%;  /* -2 to compensate left panel padding */
+    height: 1000px;
+    position: relative;
+    overflow-x: hidden;
+    overflow-y: auto;
+}
+
+#panel_startup_legend {
+    display: block;
+}
+
+#panel_startup_legend > .help-content > p {
+    text-align: left;
+    display: block;
+    padding-top: 0.1em;
+    padding-bottom: 0.1em;
+    margin-left: 1em;
+    margin-right: 1em;
+}
+
+#panel_startup_legend span.pathway_info_icon {
+    margin: auto;
+    content: "";
+    background-image: url('data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 20 20"><path fill-rule="evenodd" d="M13.646 13.354a.5.5 0 010-.708L16.293 10l-2.647-2.646a.5.5 0 01.708-.708l3 3a.5.5 0 010 .708l-3 3a.5.5 0 01-.708 0z" clip-rule="evenodd"></path><path fill-rule="evenodd" d="M6.5 10a.5.5 0 01.5-.5h9a.5.5 0 010 1H7a.5.5 0 01-.5-.5z" clip-rule="evenodd"></path><path fill-rule="evenodd" d="M4 15.5A1.5 1.5 0 012.5 14V6A1.5 1.5 0 014 4.5h7A1.5 1.5 0 0112.5 6v1.5a.5.5 0 01-1 0V6a.5.5 0 00-.5-.5H4a.5.5 0 00-.5.5v8a.5.5 0 00.5.5h7a.5.5 0 00.5-.5v-1.5a.5.5 0 011 0V14a1.5 1.5 0 01-1.5 1.5H4z" clip-rule="evenodd"></path></svg>');
+    background-repeat: no-repeat;
+    display: inline-block;
+    width: 1.5em;
+    height: 1.5em;
+    vertical-align: bottom;
+}
+
+#panel_startup_legend > .help-tip {
+    text-align: left;
+    font-family: serif;
+    font-style: italic;
+    padding-top: 1em;
+    margin-left: 1em;
+    margin-right: 1em;
+}
+
+#panel_startup_legend > .help-content .symbol-compound {
+    font-size: 1.5em;
+    font-weight: bold;
+}
+
+#panel_startup_legend > .help-content .symbol-transformation {
+    font-size: 1.5em;
+    font-weight: bold;
+}
+
+#panel_startup_legend > .help-content .symbol-target-color {
+    color: #B22222;
+}
+
+#panel_startup_legend > .help-content .symbol-inter-color {
+    color: #235789;
+}
+
+#panel_startup_legend > .help-content .symbol-precursor-color {
+    color: #68956D;
+}
+
+#panel_chemical_info, #panel_reaction_info {
+    display: none;
+}
+
+#panel_chemical_info .chem_info_pathids {
+    max-height: 20em;
+    overflow-y: auto;
+}
+
+#panel_reaction_info .reaction_info_pathids {
+    max-height: 20em;
+    overflow-y: auto;
+}
+
+#info div.info-title {
+    font-weight: bold;
+    font-size: 1.8em;
+    font-family: sans-serif;
+    font-variant: small-caps;
+    text-align: right;
+    padding-top: 5%;
+    padding-right: 5%;
+}
+
+#info div.info-name {
+    font-family: sans-serif;
+    text-align: right;
+    padding-right: 5%;
+}
+
+#info div.spacer {
+    width: 80%;
+    margin: 5%;
+}
+
+/* Based on http://www.mademyday.de/css-height-equals-width-with-pure-css.html */
+#info div.img-box {
+    /* v1 */
+    box-shadow: 0 0 10px 0px black;
+    position: relative;
+    width: 50%;
+    margin-left: auto;
+    margin-right: auto;
+    margin-top: 5%;
+
+    /* v2
+    position: relative;
+    width: 100%;
+    margin-left: auto;
+    margin-right: auto;
+    margin-top: 20px;
+    background-color: White;
+    border-left: 4px solid #4CAF50;
+    */
+}
+
+#info div.img-box::before {
+    /* v1 */
+    content: "";
+    display: block;
+    padding-top: 100%;
+
+    /* v2
+    content: "";
+    display: block;
+    padding-top: 50%;
+    */
+}
+
+#info div.img-box div.chem_info_svg {
+    /* v1 */
+    position: absolute;
+    top: 0;
+    left: 0;
+    bottom: 0;
+    right: 0;
+    background-size: cover;
+
+    /* v2
+    position: absolute;
+    top: 0;
+    left: 25%;
+    bottom: 0;
+    right: 25%;
+    background-size: contain;
+    */
+}
+
+#info div.info-subtitle {
+    font-family: sans-serif;
+    padding-left: 2%;
+    padding-top: 5%;
+}
+
+#info div.raw-text {
+    line-height: 1.4;
+    width: auto;
+    background-color: #fff;
+    padding: 8px 12px;
+    margin-right: -1%;
+    border-left: 4px solid #4CAF50;
+    font-family: Consolas,"courier new", "monospace";
+    font-size: 1em;
+}
+
+#info .raw-text {
+    /* overflow-x: scroll; */
+    /* white-space: nowrap; */
+    white-space: normal;
+    word-wrap: break-word;
+    margin-left: 2%;
+}
+
+#info .link {
+    text-align: right;
+}
+
+#info .link span {
+    font-size: 0.9em;
+    font-family: sans-serif;
+}
+
+#info .raw-text a,
+#info .raw-text a:visited
+{
+    color: #575757;
+}
+
+/* Nodes and edges CSS ********************************************************/
+/* Should be set directly at the cytoscape.js level  **************************/
+
+
+/* Table to select pathways ***************************************************/
+#table_choice table {
+    border: solid 1px #DDEEEE;
+    border-collapse: collapse;
+    border-spacing: 0;
+    /* font: normal 13px Arial, sans-serif; */
+}
+#table_choice table thead th {
+    background-color: #DDEFEF;
+    border: solid 1px #DDEEEE;
+    color: #336B6B;
+    text-align: center;
+    text-shadow: 1px 1px 1px #fff;
+}
+#table_choice table tbody td {
+    border: solid 1px #DDEEEE;
+    color: #333;
+    padding: 0 10px 0 10px;
+    text-shadow: 1px 1px 1px #fff;
+}
+#table_choice table tbody td.checkbox {
+    text-align: center;
+}
+#table_choice table tbody td.path_id:hover {
+    border: solid 1px #DDEEEE;
+    background-color: #FF7E4F44;
+    padding: 0 10px 0 10px;
+    text-shadow: 1px 1px 1px #fff;
+    border-radius: 5px;
+    cursor: pointer;
+}
+#table_choice table tbody td.path_colour input {
+    border: 0px;
+    width: 5em;
+    /* height: 5px; */
+}
+#table_choice table tbody td.pinned {
+    border: solid 1px #DDEEEE;
+    background-color: #FF7E4F44 ;
+    padding: 0 10px 0 10px;
+    text-shadow: 1px 1px 1px #fff;
+    border-radius: 5px;
+}
+#table_choice table tbody td.path_info {
+    /* display: inline-block; */
+    /* height: 1em; */
+    margin: auto;
+    content: "";
+    background-image: url('data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 20 20"><path fill-rule="evenodd" d="M13.646 13.354a.5.5 0 010-.708L16.293 10l-2.647-2.646a.5.5 0 01.708-.708l3 3a.5.5 0 010 .708l-3 3a.5.5 0 01-.708 0z" clip-rule="evenodd"></path><path fill-rule="evenodd" d="M6.5 10a.5.5 0 01.5-.5h9a.5.5 0 010 1H7a.5.5 0 01-.5-.5z" clip-rule="evenodd"></path><path fill-rule="evenodd" d="M4 15.5A1.5 1.5 0 012.5 14V6A1.5 1.5 0 014 4.5h7A1.5 1.5 0 0112.5 6v1.5a.5.5 0 01-1 0V6a.5.5 0 00-.5-.5H4a.5.5 0 00-.5.5v8a.5.5 0 00.5.5h7a.5.5 0 00.5-.5v-1.5a.5.5 0 011 0V14a1.5 1.5 0 01-1.5 1.5H4z" clip-rule="evenodd"></path></svg>');
+    background-repeat: no-repeat;
+}
+#table_choice table tbody td.path_info:hover {
+    cursor: pointer;
+}</style>
+
+    <!-- cose-bilkent layout -->
+    <!-- <script src="https://unpkg.com/layout-base/layout-base.js"></script> -->
+    <!-- <script src="https://unpkg.com/cose-base/cose-base.js"></script> -->
+    <!-- <script src="js/cytoscape-cose-bilkent.js"></script> -->
+
+</head>
+<body>
+
+    <div id="base">
+
+        <div id="viewer">
+            <div id="interaction" class="interact">
+                <!-- <div id="cofacor_handling">
+                    <div class="info-title">Cofactor options</div>
+                    <div class="spacer"></div>
+                    <input id="show_cofactors_button" type="button" value="Show cofactors"/>
+                    <input id="remove_cofactors_button" type="button" value="Hide cofactors"/>
+                </div> -->
+                <!-- Statup legend -->
+                <div id="panel_startup_legend">
+                    <div class="info-title">How to</div>
+                    <div class="help-tip">
+                        <p>Click on a node to view information on it.</p>
+                        <p>Clicking on a chemical node will show structural
+                            information (SMILES, InChI) as well as related
+                            entries in the PubChem database.</p>
+                        <p>Clicking on a reaction node will show related
+                            EC number(s), reaction template IDs (ie the reaction
+                            used to build the rule), and crosslinks to related
+                            entries in other database as well as in Selenzyme.</p>
+                    </div>
+                    <div class="info-subtitle">Node shape</div>
+                    <div class="help-content">
+                        <p><span class="symbol-compound">&#9634;</span>&nbsp;Chemical</p>
+                        <p><span class="symbol-transformation">&#9711;</span>&nbsp;Transformation (in/outgoing arrows show direction)</p>
+                    </div>
+                    <div class="info-subtitle">Compound color</div>
+                    <div class="help-content">
+                        <p><span class="symbol-compound symbol-target-color">▢</span>&nbsp;Target</p>
+                        <p><span class="symbol-compound symbol-inter-color">▢</span>&nbsp;Intermediate chemicals</p>
+                        <p><span class="symbol-compound symbol-precursor-color">▢</span>&nbsp;Precursors</p>
+                    </div>
+                </div>
+            </div>
+            <div id="cy"></div>
+            <div id="info">
+                <div id="molecule"></div>
+                <div class="info" id="information">
+                    <!-- Information on a selected chemical -->
+                    <div id="panel_chemical_info">
+                        <div class="info-title">Chemical</div>
+                        <div class="info-name"><span class="chem_info_label"></span></div>
+                        <div class="spacer"></div>
+                        <!-- SVG depiction -->
+                        <div>
+                            <div class="img-box">
+                                <div class="chem_info_svg"></div>
+                            </div>
+                        </div>
+                        <!-- SMILES -->
+                        <div>
+                            <div class="info-subtitle">SMILES</div>
+                            <div class="raw-text"><span class="chem_info_smiles"></span></div>
+                            <div class="link raw-text"><span class="chem_info_smiles_search"></span></div>
+                        </div>
+                        <!-- Inchi -->
+                        <div>
+                            <div class="info-subtitle">InChI</div>
+                            <div class="raw-text"><span class="chem_info_inchi"></span></div>
+                            <div class="link raw-text"><span class="chem_info_inchi_search"></span></div>
+                        </div>
+                        <!-- Inchikey -->
+                        <div>
+                            <div class="info-subtitle">InChIKey</div>
+                            <div class="raw-text"><span class="chem_info_inchikey"></span></div>
+                            <div class="link raw-text"><span class="chem_info_inchikey_search"></span></div>
+                        </div>
+                        <!-- Cofactor -->
+                        <div>
+                            <div class="info-subtitle">Cofactor?</div>
+                            <div class="raw-text"><span class="chem_info_iscofactor"></span></div>
+                        </div>
+                        <!-- Precursor -->
+                        <div>
+                            <div class="info-subtitle">Sink?</div>
+                            <div class="raw-text"><span class="chem_info_isprecursor"></span></div>
+                        </div>
+                    </div>
+                    <!-- Information on a selected reaction -->
+                    <div id="panel_reaction_info">
+                        <div class="info-title">Reaction</div>
+                        <div class="info-name"><span class="reaction_info_name"></span></div>
+                        <div class="spacer"></div>
+                        <!-- EC numbers -->
+                        <div>
+                            <div class="info-subtitle">EC number(s)</div>
+                            <div class="raw-text reaction_info_ecnumbers"></div>
+                        </div>
+                        <!-- Reaction template IDs -->
+                        <div>
+                            <div class="info-subtitle">Reaction template ID(s)</div>
+                            <div class="raw-text reaction_info_reaction_template_ids"></div>
+                        </div>
+                        <!-- Crosslink to Selenzyme -->
+                        <div>
+                            <div class="info-subtitle">Enzyme selection using Selenzyme</div>
+                            <div class="raw-text"><span class="reaction_info_selenzyme_crosslink"></span></div>
+                        </div>
+                        <!-- Rule score -->
+                        <div>
+                            <div class="info-subtitle">Rule score</div>
+                            <div class="raw-text"><span class="reaction_info_rule_score"></span></div>
+                        </div>
+                        <!-- Reaction SMILES -->
+                        <div>
+                            <div class="info-subtitle">Reaction SMILES</div>
+                            <div class="raw-text"><span class="reaction_info_rsmiles"></span></div>
+                        </div>
+                        <!-- Reaction rule IDs -->
+                        <div>
+                            <div class="info-subtitle">Rule ID(s)</div>
+                            <div class="raw-text reaction_info_ruleids"></div>
+                        </div>
+                    </div>
+                </div>
+
+            </div>
+        </div>
+
+    </div>
+
+</body>
+</html>

From e41ed8b7182c2d15982d8285cf4bdf34c0626e5b Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Mon, 12 Jun 2023 14:47:23 +0200
Subject: [PATCH 22/61] feat(workflows): add `straindesign` (#132)

---
 .../straindesign_workflow-tests.yml           |  20 +
 .../straindesign_workflow.ga                  | 491 ++++++++++++++++++
 2 files changed, 511 insertions(+)
 create mode 100644 workflows/straindesign_workflow/straindesign_workflow-tests.yml
 create mode 100644 workflows/straindesign_workflow/straindesign_workflow.ga

diff --git a/workflows/straindesign_workflow/straindesign_workflow-tests.yml b/workflows/straindesign_workflow/straindesign_workflow-tests.yml
new file mode 100644
index 00000000..0329a0a5
--- /dev/null
+++ b/workflows/straindesign_workflow/straindesign_workflow-tests.yml
@@ -0,0 +1,20 @@
+- doc: StrainDesign
+  job:
+    Medium file:
+      class: File
+      location: https://raw.github.com/brsynth/straindesign/main/tests/straindesign/dataset/medium/butanol.tsv
+    Model chassis:
+      class: File
+      location: https://raw.github.com/brsynth/straindesign/main/tests/straindesign/dataset/model/iAF1260.xml
+    Heterologous pathway:
+      class: File
+      location: https://raw.github.com/brsynth/straindesign/main/tests/straindesign/dataset/pathway/butanol.xml
+    Biomass Reaction ID: BIOMASS_Ec_iAF1260_core_59p81M
+    Target Reaction ID: EX_1btol_e
+    Substrate Reaction ID: EX_glc__D_e
+  outputs:
+    straindesign:
+      asserts:
+        has_size:
+          value: "30000"
+          delta: "10000"
diff --git a/workflows/straindesign_workflow/straindesign_workflow.ga b/workflows/straindesign_workflow/straindesign_workflow.ga
new file mode 100644
index 00000000..525e50e8
--- /dev/null
+++ b/workflows/straindesign_workflow/straindesign_workflow.ga
@@ -0,0 +1,491 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Perform deletion of genes to produce a compound",
+    "creator": [
+        {
+            "class": "Organization",
+            "name": "BioRetroSynth",
+            "url": "https://github.com/brsynth"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "name": "StrainDesign",
+    "steps": {
+        "0": {
+            "annotation": "SBML type expected",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "SBML type expected",
+                    "name": "Model chassis"
+                }
+            ],
+            "label": "Model chassis",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 210.5,
+                "height": 63,
+                "left": 345,
+                "right": 545,
+                "top": 147.5,
+                "width": 200,
+                "x": 345,
+                "y": 147.5
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "97aabce5-3fc3-4144-a371-575bb52f1659",
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "Tabular type expected",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Tabular type expected",
+                    "name": "Medium file"
+                }
+            ],
+            "label": "Medium file",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 311.5,
+                "height": 63,
+                "left": 345,
+                "right": 545,
+                "top": 248.5,
+                "width": 200,
+                "x": 345,
+                "y": 248.5
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": true}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "0503bba7-3d65-47b6-9063-0a363b3a567f",
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "Reaction ID",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Reaction ID",
+                    "name": "Biomass Reaction ID"
+                }
+            ],
+            "label": "Biomass Reaction ID",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 433.5,
+                "height": 84,
+                "left": 345,
+                "right": 545,
+                "top": 349.5,
+                "width": 200,
+                "x": 345,
+                "y": 349.5
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "ef1634ab-2bd3-419e-b92d-c451ffc4962a",
+            "workflow_outputs": []
+        },
+        "3": {
+            "annotation": "SBML type expected",
+            "content_id": null,
+            "errors": null,
+            "id": 3,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "SBML type expected",
+                    "name": "Heterologous pathway"
+                }
+            ],
+            "label": "Heterologous pathway",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 555.5,
+                "height": 84,
+                "left": 345,
+                "right": 545,
+                "top": 471.5,
+                "width": 200,
+                "x": 345,
+                "y": 471.5
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": true}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "5c9e7c6c-fc18-4afa-a463-0984eaffa600",
+            "workflow_outputs": []
+        },
+        "4": {
+            "annotation": "Reaction ID",
+            "content_id": null,
+            "errors": null,
+            "id": 4,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Reaction ID",
+                    "name": "Target Reaction ID"
+                }
+            ],
+            "label": "Target Reaction ID",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 676.5,
+                "height": 84,
+                "left": 346,
+                "right": 546,
+                "top": 592.5,
+                "width": 200,
+                "x": 346,
+                "y": 592.5
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "67937d19-0e0b-490e-acc6-a41227646799",
+            "workflow_outputs": []
+        },
+        "5": {
+            "annotation": "Reaction ID",
+            "content_id": null,
+            "errors": null,
+            "id": 5,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Reaction ID",
+                    "name": "Substrate Reaction ID"
+                }
+            ],
+            "label": "Substrate Reaction ID",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 819.5,
+                "height": 105,
+                "left": 345,
+                "right": 545,
+                "top": 714.5,
+                "width": 200,
+                "x": 345,
+                "y": 714.5
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "12550252-99f0-4c89-994a-fa117ce0a432",
+            "workflow_outputs": []
+        },
+        "6": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/straindesign_simulate_deletion/straindesign_simulate_deletion/3.1.0+galaxy1",
+            "errors": null,
+            "id": 6,
+            "input_connections": {
+                "biomass_rxn_id": {
+                    "id": 2,
+                    "output_name": "output"
+                },
+                "input_strategy|substrate_rxn_id": {
+                    "id": 5,
+                    "output_name": "output"
+                },
+                "medium": {
+                    "id": 1,
+                    "output_name": "output"
+                },
+                "model": {
+                    "id": 0,
+                    "output_name": "output"
+                },
+                "pathway": {
+                    "id": 3,
+                    "output_name": "output"
+                },
+                "target_rxn_id": {
+                    "id": 4,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "StrainDesign simulate-deletion",
+            "outputs": [
+                {
+                    "name": "output_tsv",
+                    "type": "tabular"
+                }
+            ],
+            "position": {
+                "bottom": 250.5,
+                "height": 292,
+                "left": 673,
+                "right": 873,
+                "top": -41.5,
+                "width": 200,
+                "x": 673,
+                "y": -41.5
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/straindesign_simulate_deletion/straindesign_simulate_deletion/3.1.0+galaxy1",
+            "tool_shed_repository": {
+                "changeset_revision": "33c6ffbd098f",
+                "name": "straindesign_simulate_deletion",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"biomass_rxn_id\": {\"__class__\": \"ConnectedValue\"}, \"input_strategy\": {\"strategy\": \"ko\", \"__current_case__\": 0, \"substrate_rxn_id\": {\"__class__\": \"ConnectedValue\"}, \"annotate\": \"false\"}, \"max_knockouts\": \"3\", \"max_time_cond\": {\"max_time_param\": \"no\", \"__current_case__\": 1}, \"medium\": {\"__class__\": \"ConnectedValue\"}, \"model\": {\"__class__\": \"ConnectedValue\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"target_rxn_id\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "3.1.0+galaxy1",
+            "type": "tool",
+            "uuid": "166ac096-162b-4bbd-bc78-fc756eefc5d7",
+            "workflow_outputs": [
+                {
+                    "label": "StrainDesign simulate-deletion(ko)",
+                    "output_name": "output_tsv",
+                    "uuid": "4fab08c4-e4bc-4376-9364-560712ccb870"
+                }
+            ]
+        },
+        "7": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/straindesign_analyzing_model/straindesign_analyzing_model/3.1.0+galaxy1",
+            "errors": null,
+            "id": 7,
+            "input_connections": {
+                "biomass_rxn_id": {
+                    "id": 2,
+                    "output_name": "output"
+                },
+                "medium": {
+                    "id": 1,
+                    "output_name": "output"
+                },
+                "model": {
+                    "id": 0,
+                    "output_name": "output"
+                },
+                "pathway": {
+                    "id": 3,
+                    "output_name": "output"
+                },
+                "substrate_cond|substrate_rxn_id": {
+                    "id": 5,
+                    "output_name": "output"
+                },
+                "target_rxn_id": {
+                    "id": 4,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "StrainDesign analyzing-model",
+            "outputs": [
+                {
+                    "name": "output_png",
+                    "type": "png"
+                }
+            ],
+            "position": {
+                "bottom": 592.5,
+                "height": 292,
+                "left": 673,
+                "right": 873,
+                "top": 300.5,
+                "width": 200,
+                "x": 673,
+                "y": 300.5
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/straindesign_analyzing_model/straindesign_analyzing_model/3.1.0+galaxy1",
+            "tool_shed_repository": {
+                "changeset_revision": "490a37e24bed",
+                "name": "straindesign_analyzing_model",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"biomass_rxn_id\": {\"__class__\": \"ConnectedValue\"}, \"medium\": {\"__class__\": \"ConnectedValue\"}, \"model\": {\"__class__\": \"ConnectedValue\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"substrate_cond\": {\"substrate_param\": \"yes\", \"__current_case__\": 0, \"substrate_rxn_id\": {\"__class__\": \"ConnectedValue\"}}, \"target_rxn_id\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "3.1.0+galaxy1",
+            "type": "tool",
+            "uuid": "2602ede6-0d47-44da-bd85-c1c07376a6a7",
+            "workflow_outputs": [
+                {
+                    "label": "StrainDesign analyzing-model",
+                    "output_name": "output_png",
+                    "uuid": "c476faa7-7b68-4fcc-ab5c-591262ecc6b6"
+                }
+            ]
+        },
+        "8": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/straindesign_reduce_model/straindesign_reduce_model/3.1.0+galaxy1",
+            "errors": null,
+            "id": 8,
+            "input_connections": {
+                "model": {
+                    "id": 0,
+                    "output_name": "output"
+                },
+                "sd_strategy|sd_tsv": {
+                    "id": 6,
+                    "output_name": "output_tsv"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "StrainDesign reduce-model",
+            "outputs": [
+                {
+                    "name": "output_sbml",
+                    "type": "sbml"
+                }
+            ],
+            "position": {
+                "bottom": 261.5,
+                "height": 189,
+                "left": 951,
+                "right": 1151,
+                "top": 72.5,
+                "width": 200,
+                "x": 951,
+                "y": 72.5
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/straindesign_reduce_model/straindesign_reduce_model/3.1.0+galaxy1",
+            "tool_shed_repository": {
+                "changeset_revision": "78b7443af284",
+                "name": "straindesign_reduce_model",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"input_gene_str\": \"\", \"model\": {\"__class__\": \"ConnectedValue\"}, \"sd_strategy\": {\"sd_cond\": \"yes\", \"__current_case__\": 0, \"sd_tsv\": {\"__class__\": \"ConnectedValue\"}, \"sd_strategy_str\": \"yield-max\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "3.1.0+galaxy1",
+            "type": "tool",
+            "uuid": "e5af6044-76fd-4d01-93d3-dced5ecca572",
+            "workflow_outputs": [
+                {
+                    "label": "StrainDesign reduce-model",
+                    "output_name": "output_sbml",
+                    "uuid": "eb4069a8-fdf3-466c-9d7a-fda83227b0d7"
+                }
+            ]
+        },
+        "9": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/straindesign_analyzing_model/straindesign_analyzing_model/3.1.0+galaxy1",
+            "errors": null,
+            "id": 9,
+            "input_connections": {
+                "biomass_rxn_id": {
+                    "id": 2,
+                    "output_name": "output"
+                },
+                "medium": {
+                    "id": 1,
+                    "output_name": "output"
+                },
+                "model": {
+                    "id": 8,
+                    "output_name": "output_sbml"
+                },
+                "pathway": {
+                    "id": 3,
+                    "output_name": "output"
+                },
+                "substrate_cond|substrate_rxn_id": {
+                    "id": 5,
+                    "output_name": "output"
+                },
+                "target_rxn_id": {
+                    "id": 4,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool StrainDesign analyzing-model",
+                    "name": "medium"
+                },
+                {
+                    "description": "runtime parameter for tool StrainDesign analyzing-model",
+                    "name": "model"
+                },
+                {
+                    "description": "runtime parameter for tool StrainDesign analyzing-model",
+                    "name": "pathway"
+                }
+            ],
+            "label": null,
+            "name": "StrainDesign analyzing-model",
+            "outputs": [
+                {
+                    "name": "output_png",
+                    "type": "png"
+                }
+            ],
+            "position": {
+                "bottom": 747.5,
+                "height": 271,
+                "left": 1239,
+                "right": 1439,
+                "top": 476.5,
+                "width": 200,
+                "x": 1239,
+                "y": 476.5
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/straindesign_analyzing_model/straindesign_analyzing_model/3.1.0+galaxy1",
+            "tool_shed_repository": {
+                "changeset_revision": "490a37e24bed",
+                "name": "straindesign_analyzing_model",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"biomass_rxn_id\": {\"__class__\": \"ConnectedValue\"}, \"medium\": {\"__class__\": \"RuntimeValue\"}, \"model\": {\"__class__\": \"RuntimeValue\"}, \"pathway\": {\"__class__\": \"RuntimeValue\"}, \"substrate_cond\": {\"substrate_param\": \"yes\", \"__current_case__\": 0, \"substrate_rxn_id\": {\"__class__\": \"ConnectedValue\"}}, \"target_rxn_id\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "3.1.0+galaxy1",
+            "type": "tool",
+            "uuid": "95b2e9ce-d31d-42d0-829d-f85736bbe804",
+            "workflow_outputs": [
+                {
+                    "label": "straindesign",
+                    "output_name": "output_png",
+                    "uuid": "e0b3c37d-260d-4033-b015-bad7822bd7b8"
+                }
+            ]
+        }
+    },
+    "tags": [
+        "brs",
+        "straindesign"
+    ],
+    "uuid": "5ef85967-2620-4ef3-8514-a72267a0c87b",
+    "version": 13
+}
\ No newline at end of file

From 4dcb0f3b3ea3aebe146f3f0bbecea1c8eb8753e2 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Mon, 12 Jun 2023 14:51:38 +0200
Subject: [PATCH 23/61] feat(workflows): add `genetic assembly` (#133)

---
 .../genetic_assembly_workflow.ga              | 454 ++++++++++++++++++
 1 file changed, 454 insertions(+)
 create mode 100644 workflows/genetic_assembly_workflow/genetic_assembly_workflow.ga

diff --git a/workflows/genetic_assembly_workflow/genetic_assembly_workflow.ga b/workflows/genetic_assembly_workflow/genetic_assembly_workflow.ga
new file mode 100644
index 00000000..8b26d2b9
--- /dev/null
+++ b/workflows/genetic_assembly_workflow/genetic_assembly_workflow.ga
@@ -0,0 +1,454 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "",
+    "creator": [
+        {
+            "class": "Organization",
+            "name": "BioRetroSynth",
+            "url": "https://github.com/brsynth"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "name": "Genetic Design (Gibson, Golden Gate, LCR)",
+    "steps": {
+        "0": {
+            "annotation": "SBML files",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "SBML files",
+                    "name": "Heterologous pathway"
+                }
+            ],
+            "label": "Heterologous pathway",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 481,
+                "height": 84,
+                "left": -473.5,
+                "right": -273.5,
+                "top": 397,
+                "width": 200,
+                "x": -473.5,
+                "y": 397
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "6ae37b45-f137-46a4-bf60-8a6e973613e4",
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "Taxon ID",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Taxon ID",
+                    "name": "Host taxon ID"
+                }
+            ],
+            "label": "Host taxon ID",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 564,
+                "height": 63,
+                "left": -477.5,
+                "right": -277.5,
+                "top": 501,
+                "width": 200,
+                "x": -477.5,
+                "y": 501
+            },
+            "tool_id": null,
+            "tool_state": "{\"default\": 83333, \"parameter_type\": \"integer\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "e56bd850-e18f-45d0-922b-a74617e1c371",
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "Comma separated",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Comma separated",
+                    "name": "Taxon IDs of output enzyme sequences"
+                }
+            ],
+            "label": "Taxon IDs of output enzyme sequences",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 691,
+                "height": 105,
+                "left": -475.5,
+                "right": -275.5,
+                "top": 586,
+                "width": 200,
+                "x": -475.5,
+                "y": 586
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "4b6f3f52-3722-4f43-b44b-955c615ba2b7",
+            "workflow_outputs": []
+        },
+        "3": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "adv|enzyme_taxIDs": {
+                    "id": 2,
+                    "output_name": "output"
+                },
+                "adv|host_taxID": {
+                    "id": 1,
+                    "output_name": "output"
+                },
+                "pathway": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Selenzyme",
+            "outputs": [
+                {
+                    "name": "uniprot_ids",
+                    "type": "xml"
+                },
+                {
+                    "name": "uniprot_ids_csv",
+                    "type": "csv"
+                }
+            ],
+            "position": {
+                "bottom": 649,
+                "height": 230,
+                "left": -176.5,
+                "right": 23.5,
+                "top": 419,
+                "width": 200,
+                "x": -176.5,
+                "y": 419
+            },
+            "post_job_actions": {
+                "HideDatasetActionuniprot_ids": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "uniprot_ids"
+                },
+                "HideDatasetActionuniprot_ids_csv": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "uniprot_ids_csv"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0",
+            "tool_shed_repository": {
+                "changeset_revision": "34a9d136a5bf",
+                "name": "selenzy",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"host_taxID\": {\"__class__\": \"ConnectedValue\"}, \"enzyme_taxIDs\": {\"__class__\": \"ConnectedValue\"}, \"nb_ids\": \"-1\", \"nb_targets\": \"500\", \"direction\": \"0.0\", \"NoMSA\": \"true\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.2.0",
+            "type": "tool",
+            "uuid": "4cb691c9-c1d5-4e74-9a92-8e9334bd2292",
+            "workflow_outputs": []
+        },
+        "4": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/sbml2sbol/sbml2sbol/0.1.13",
+            "errors": null,
+            "id": 4,
+            "input_connections": {
+                "sbml_single_input": {
+                    "id": 3,
+                    "output_name": "uniprot_ids"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "SbmlToSbol",
+            "outputs": [
+                {
+                    "name": "sbol_outfile",
+                    "type": "xml"
+                }
+            ],
+            "position": {
+                "bottom": 429,
+                "height": 116,
+                "left": 82.5,
+                "right": 282.5,
+                "top": 313,
+                "width": 200,
+                "x": 82.5,
+                "y": 313
+            },
+            "post_job_actions": {
+                "HideDatasetActionsbol_outfile": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "sbol_outfile"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/sbml2sbol/sbml2sbol/0.1.13",
+            "tool_shed_repository": {
+                "changeset_revision": "83108f3c65aa",
+                "name": "sbml2sbol",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"rbs\": \"true\", \"max_prot_per_react\": \"3\", \"tirs\": \"\", \"pathway_id\": \"rp_pathway\", \"uniprotID_key\": \"selenzy\"}, \"sbml_single_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.1.13",
+            "type": "tool",
+            "uuid": "66f1558b-8b6d-4b86-9279-e6a4cfab827c",
+            "workflow_outputs": []
+        },
+        "5": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/partsgenie/PartsGenie/1.0.1",
+            "errors": null,
+            "id": 5,
+            "input_connections": {
+                "enzymes_file": {
+                    "id": 4,
+                    "output_name": "sbol_outfile"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "PartsGenie",
+            "outputs": [
+                {
+                    "name": "parts",
+                    "type": "xml"
+                }
+            ],
+            "position": {
+                "bottom": 459,
+                "height": 95,
+                "left": 330.5,
+                "right": 530.5,
+                "top": 364,
+                "width": 200,
+                "x": 330.5,
+                "y": 364
+            },
+            "post_job_actions": {
+                "HideDatasetActionparts": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "parts"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/partsgenie/PartsGenie/1.0.1",
+            "tool_shed_repository": {
+                "changeset_revision": "295a21fc55d0",
+                "name": "partsgenie",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"url\": \"https://partsgenie.micalis.inrae.fr\"}, \"enzymes_file\": {\"__class__\": \"ConnectedValue\"}, \"taxonomy_id\": \"83333\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.0.1",
+            "type": "tool",
+            "uuid": "6de5ce99-5548-4473-bb4f-eade579882bb",
+            "workflow_outputs": []
+        },
+        "6": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/optdoe/optdoe/2.0.2",
+            "errors": null,
+            "id": 6,
+            "input_connections": {
+                "adv|genes_sbol_file": {
+                    "id": 5,
+                    "output_name": "parts"
+                },
+                "genes_file": {
+                    "id": 3,
+                    "output_name": "uniprot_ids_csv"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Design of Experiment",
+                    "name": "adv"
+                }
+            ],
+            "label": null,
+            "name": "Design of Experiment",
+            "outputs": [
+                {
+                    "name": "constructs",
+                    "type": "xml"
+                }
+            ],
+            "position": {
+                "bottom": 541.5,
+                "height": 199,
+                "left": 645.5,
+                "right": 845.5,
+                "top": 342.5,
+                "width": 200,
+                "x": 645.5,
+                "y": 342.5
+            },
+            "post_job_actions": {
+                "HideDatasetActionconstructs": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "constructs"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/optdoe/optdoe/2.0.2",
+            "tool_shed_repository": {
+                "changeset_revision": "c3f32929a4b7",
+                "name": "optdoe",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"genes_sbol_file\": {\"__class__\": \"ConnectedValue\"}, \"ref_parts_file\": {\"__class__\": \"RuntimeValue\"}, \"libsize\": \"32\", \"get_sequences\": \"true\", \"backtranslate\": \"true\", \"codon_table\": \"Eecoli.cut\"}, \"genes_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.0.2",
+            "type": "tool",
+            "uuid": "3210cb4e-5c8f-43bd-bae7-a732b57b9504",
+            "workflow_outputs": []
+        },
+        "7": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnaweaver/dnaweaver/1.0.2",
+            "errors": null,
+            "id": 7,
+            "input_connections": {
+                "input": {
+                    "id": 6,
+                    "output_name": "constructs"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool DNA Weaver",
+                    "name": "input"
+                }
+            ],
+            "label": null,
+            "name": "DNA Weaver",
+            "outputs": [
+                {
+                    "name": "output",
+                    "type": "xlsx"
+                }
+            ],
+            "position": {
+                "bottom": 490,
+                "height": 116,
+                "left": 978.5,
+                "right": 1178.5,
+                "top": 374,
+                "width": 200,
+                "x": 978.5,
+                "y": 374
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnaweaver/dnaweaver/1.0.2",
+            "tool_shed_repository": {
+                "changeset_revision": "c519517e3ade",
+                "name": "dnaweaver",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"adv\": {\"max_constructs\": \"-1\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"method\": \"golden_gate\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.0.2",
+            "type": "tool",
+            "uuid": "970ae428-0737-4d4c-8388-2f8332cdf7c4",
+            "workflow_outputs": [
+                {
+                    "label": "DNA Weaver - Assembly Plan",
+                    "output_name": "output",
+                    "uuid": "d34b220e-4c49-4158-ad02-b86a945637fb"
+                }
+            ]
+        },
+        "8": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/lcrgenie/LCRGenie/1.0.2",
+            "errors": null,
+            "id": 8,
+            "input_connections": {
+                "LCR_input": {
+                    "id": 6,
+                    "output_name": "constructs"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool LCR Genie",
+                    "name": "LCR_input"
+                }
+            ],
+            "label": null,
+            "name": "LCR Genie",
+            "outputs": [
+                {
+                    "name": "LCR_output",
+                    "type": "xlsx"
+                }
+            ],
+            "position": {
+                "bottom": 639,
+                "height": 116,
+                "left": 981.5,
+                "right": 1181.5,
+                "top": 523,
+                "width": 200,
+                "x": 981.5,
+                "y": 523
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/lcrgenie/LCRGenie/1.0.2",
+            "tool_shed_repository": {
+                "changeset_revision": "afbbecdcc0e3",
+                "name": "lcrgenie",
+                "owner": "tduigou",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"LCR_input\": {\"__class__\": \"RuntimeValue\"}, \"adv\": {\"melting_temp\": \"60.0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.0.2",
+            "type": "tool",
+            "uuid": "708d8372-93fe-4c40-aa56-6ff28054cc8a",
+            "workflow_outputs": [
+                {
+                    "label": "LCR Genie: Assembly Plan",
+                    "output_name": "LCR_output",
+                    "uuid": "40a04511-dc63-449c-b937-7805aec37daf"
+                }
+            ]
+        }
+    },
+    "tags": [
+        "brs",
+        "assembly"
+    ],
+    "uuid": "2dcc920c-2c3e-425f-9726-2d32d441d8d2",
+    "version": 4
+}
\ No newline at end of file

From 246067538ba27ec1c312efaeca0acfa3be8089b9 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 13 Jun 2023 10:35:30 +0200
Subject: [PATCH 24/61] chore(github): fix syntax

---
 .github/workflows/release_schedule.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/release_schedule.yml b/.github/workflows/release_schedule.yml
index 2750de15..59cfef71 100644
--- a/.github/workflows/release_schedule.yml
+++ b/.github/workflows/release_schedule.yml
@@ -18,10 +18,8 @@ jobs:
           ref: 'stable'
       - name: "Check diff"
         id: set-diff
-        continue-on-error: true
         run: |
-          git diff --quiet stable..origin/main
-          nb=$?
+          nb=$(git diff --shortstat stable..origin/main | cut -f2 -d ' ')
           echo "Find diff: ${nb}"
           echo "nb=${nb}" >> "${GITHUB_OUTPUT}"
 

From 6f759e31905a8f6bb619c87ef726bf5f13694d23 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Mon, 19 Jun 2023 10:28:57 +0200
Subject: [PATCH 25/61] chore(github): update workflows to skip

---
 .github/workflows/test_workflows_skip.txt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test_workflows_skip.txt b/.github/workflows/test_workflows_skip.txt
index 59da3239..5e07a6ef 100644
--- a/.github/workflows/test_workflows_skip.txt
+++ b/.github/workflows/test_workflows_skip.txt
@@ -1 +1,3 @@
 retrosynthesis_workflow
+genetic_assembly_workflow
+straindesign_workflow

From c5acde8be8b4f7f9f3176e270d8c97571fbc2e51 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Mon, 19 Jun 2023 11:37:36 +0200
Subject: [PATCH 26/61] chore(github): fix artefacts log

---
 .github/workflows/testtools.yml | 7 ++++---
 scripts/aggregate_test.py       | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/testtools.yml b/.github/workflows/testtools.yml
index afd4ea07..718fe0a1 100644
--- a/.github/workflows/testtools.yml
+++ b/.github/workflows/testtools.yml
@@ -63,12 +63,14 @@ jobs:
         run: |
           planemo shed_lint --urls --xsd --ensure_metadata "tools/${{ matrix.repo }}"
           ./scripts/shed_lint.py -i "tools/${{ matrix.repo }}"
+      - name: 'Prepare'
+        run: |
+          mkdir -p "log/${{ matrix.repo }}"
       - name: 'Test tool'
         if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
         timeout-minutes: 120
         continue-on-error: true
         run: |
-          mkdir -p "log/${{ matrix.repo }}"
           planemo test \
             --biocontainers \
             --no_dependency_resolution \
@@ -80,8 +82,7 @@ jobs:
             "tools/${{ matrix.repo }}"
       - name: 'Prepare artefact'
         run: |
-          mkdir -p "log/${{ matrix.repo }}"
-          zip -r -9 log.zip "log/${{ matrix.repo }}"
+          zip -r -9 log.zip log
       - name: 'Upload Artifact Version'
         uses: actions/upload-artifact@v3
         with:
diff --git a/scripts/aggregate_test.py b/scripts/aggregate_test.py
index 895ea0c0..727abde4 100755
--- a/scripts/aggregate_test.py
+++ b/scripts/aggregate_test.py
@@ -41,5 +41,5 @@ def parse_artifacts(finputs: List[str]) -> int:
         )
     if len(finputs) < 1:
         parser.error("No file provided")
-
+    print("Found: ", ",".join(finputs))
     parse_artifacts(finputs)

From 0039ba858e95b91a07a018b2eece0e0737e6a20a Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Mon, 19 Jun 2023 13:21:35 +0200
Subject: [PATCH 27/61] Tools: `selenzy_wrapper` (#134)

* fix(tools): selenzy_wrapper, update test section
---
 .github/workflows/testtools.yml           |  2 +-
 tools/selenzy_wrapper/selenzy_wrapper.xml | 48 +++++++++--------------
 2 files changed, 19 insertions(+), 31 deletions(-)

diff --git a/.github/workflows/testtools.yml b/.github/workflows/testtools.yml
index 718fe0a1..f9d20cdc 100644
--- a/.github/workflows/testtools.yml
+++ b/.github/workflows/testtools.yml
@@ -78,8 +78,8 @@ jobs:
             --galaxy_source https://github.com/galaxyproject/galaxy \
             --galaxy_branch release_22.05 \
             --galaxy_python_version 3.7 \
-            --job_output_files "log/${{ matrix.repo }}" \
             "tools/${{ matrix.repo }}"
+          mv tool_test_output.json "log/${{ matrix.repo }}"
       - name: 'Prepare artefact'
         run: |
           zip -r -9 log.zip log
diff --git a/tools/selenzy_wrapper/selenzy_wrapper.xml b/tools/selenzy_wrapper/selenzy_wrapper.xml
index 43fa1e04..14cf7a3a 100644
--- a/tools/selenzy_wrapper/selenzy_wrapper.xml
+++ b/tools/selenzy_wrapper/selenzy_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+<tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
     <description>Performs enzyme selection from a reaction query</description>
     <macros>
         <token name="@VERSION_SUFFIX@">0</token>
@@ -54,7 +54,12 @@
         <test>
         <!-- test 1: check if identical outputs are produced with default parameters  -->
             <param name="pathway" value="pathway.xml" />
-            <output name="uniprot_ids" file="uniprod_ids_out.xml" compare="diff" sort="true"/>
+            <output name="uniprot_ids">
+                <assert_contents>
+                    <is_valid_xml />
+                    <has_n_lines n="7968" />
+                </assert_contents>
+            </output>
             <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
         </test>
         <test>
@@ -64,13 +69,18 @@
                 <param name="host_taxID_type" value="tsv" />
             </conditional>
             <param name="host_taxID_file" value="taxID.tsv" />
-            <output name="uniprot_ids" file="uniprod_ids_out.xml" compare="diff" sort="true"/>
+            <output name="uniprot_ids">
+                <assert_contents>
+                    <is_valid_xml />
+                    <has_n_lines n="7968" />
+                </assert_contents>
+            </output>
             <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
         </test>
     </tests>
     <help><![CDATA[
 Selenzyme
-================
+=========
 
 Selenzyme searches for enzymes corresponding to each reaction of the pathway. It performs a reaction similarity search in the reference reaction database `MetaNetX <https://www.metanetx.org/>`_ and outputs an updated SBML file annotated with the enzyme UniProt IDs, as well as in CSV format.
 
@@ -90,33 +100,11 @@ Output
 
 * **Uniprot IDs (SBML)**\ : Annotated SBML pathway.
 * **Uniprot IDs (CSV)**\ : Annotated CSV pathway.
-
-Project Links
-------------------
-
-* `GitHub <https://github.com/brsynth/selenzy-wrapper>`_
-
-Version
-----------
-
-0.3.0
-
-Authors
--------
-* **Joan Hérisson**
-
-License
--------
-
-* `MIT <https://github.com/brsynth/selenzy-wrapper/blob/master/LICENSE>`_
-
-Acknowledgments
----------------
-
-* Thomas Duigou
-
     ]]></help>
+    <creator>
+        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
+    </creator>
     <citations>
         <citation type="doi">10.1093/bioinformatics/bty065</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>

From 358bd271ad2735d690bd65782235c5a07224e231 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 20 Jun 2023 10:58:58 +0200
Subject: [PATCH 28/61] chore(github): workflows, fix workflow call

---
 .github/workflows/release.yml          |  2 ++
 .github/workflows/release_schedule.yml | 10 ++--------
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 660dcdf8..9aa4ed40 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -2,6 +2,8 @@ name: Release
 
 on:
   workflow_call:
+    secrets:
+
 
 jobs:
 
diff --git a/.github/workflows/release_schedule.yml b/.github/workflows/release_schedule.yml
index 59cfef71..77cc962a 100644
--- a/.github/workflows/release_schedule.yml
+++ b/.github/workflows/release_schedule.yml
@@ -24,13 +24,7 @@ jobs:
           echo "nb=${nb}" >> "${GITHUB_OUTPUT}"
 
   Call:
-    runs-on: ubuntu-latest
     needs: [Diff]
     if: ${{ needs.Diff.outputs.nb > 0 }}
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          persist-credentials: false
-          fetch-depth: 0
-      - name: 'Dispatch'
-        uses: ./.github/workflows/release.yml
+    uses: ./.github/workflows/release.yml
+    secrets: inherit

From 4818f94adea0f7c9e2754284f9611ba6f0447c7e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 27 Jun 2023 08:38:15 +0200
Subject: [PATCH 29/61] chore(deps): bump tj-actions/changed-files from 36 to
 37 (#135)

Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 36 to 37.
- [Release notes](https://github.com/tj-actions/changed-files/releases)
- [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md)
- [Commits](https://github.com/tj-actions/changed-files/compare/v36...v37)

---
updated-dependencies:
- dependency-name: tj-actions/changed-files
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/pr.yml          | 2 +-
 .github/workflows/prworkflows.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index e83fac63..b4d13ff5 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -24,7 +24,7 @@ jobs:
       - name: 'Select modified files'
         id: files
         #uses: Ana06/get-changed-files@v2.2.0
-        uses: tj-actions/changed-files@v36
+        uses: tj-actions/changed-files@v37
         with:
           files: tools/**
           separator: ","
diff --git a/.github/workflows/prworkflows.yml b/.github/workflows/prworkflows.yml
index e3ab3686..5462b6e9 100644
--- a/.github/workflows/prworkflows.yml
+++ b/.github/workflows/prworkflows.yml
@@ -24,7 +24,7 @@ jobs:
       - name: 'Select modified files'
         id: files
         #uses: Ana06/get-changed-files@v2.2.0
-        uses: tj-actions/changed-files@v36
+        uses: tj-actions/changed-files@v37
         with:
           files: workflows/**
           separator: ","

From 7dd996b8ce696060c27eb52b63ee1aa749a88aeb Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 27 Jun 2023 08:47:56 +0200
Subject: [PATCH 30/61] chore(github): merge release workflows

---
 .github/workflows/release.yml          | 35 +++++++++++++++++++++-----
 .github/workflows/release_schedule.yml | 30 ----------------------
 2 files changed, 29 insertions(+), 36 deletions(-)
 delete mode 100644 .github/workflows/release_schedule.yml

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 9aa4ed40..7d35fc58 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -1,13 +1,31 @@
 name: Release
 
 on:
-  workflow_call:
-    secrets:
-
+  schedule:
+    - cron: '0 0 * * 2'
 
 jobs:
 
+  Diff:
+    runs-on: ubuntu-latest
+    outputs:
+      nb: ${{ steps.set-diff.outputs.nb }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+          ref: 'stable'
+      - name: "Check diff"
+        id: set-diff
+        run: |
+          nb=$(git diff --shortstat stable..origin/main | cut -f2 -d ' ')
+          echo "Find diff: ${nb}"
+          echo "nb=${nb}" >> "${GITHUB_OUTPUT}"
+
   TagRaw:
+    needs: Diff
+    if: ${{ needs.Diff.outputs.nb > 0 }}
     runs-on: ubuntu-latest
     outputs:
       tag: ${{ steps.tag_label.outputs.tag }}
@@ -34,6 +52,8 @@ jobs:
           echo "tag=$TAG" >> "$GITHUB_OUTPUT"
 
   Changelog:
+    needs: Diff
+    if: ${{ needs.Diff.outputs.nb > 0 }}
     runs-on: ubuntu-latest
     needs: [TagRaw]
     steps:
@@ -65,7 +85,8 @@ jobs:
           retention-days: 1
 
   Commit:
-    needs: [Changelog]
+    needs: [Changelog, Diff]
+    if: ${{ needs.Diff.outputs.nb > 0 }}
     runs-on: ubuntu-latest
     steps:
       # Get Data
@@ -100,7 +121,8 @@ jobs:
           branch: main
 
   Tag:
-    needs: [Commit, TagRaw]
+    needs: [Commit, Diff, TagRaw]
+    if: ${{ needs.Diff.outputs.nb > 0 }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
@@ -117,7 +139,8 @@ jobs:
           tag_prefix:
 
   Release:
-    needs: [TagRaw, Tag]
+    needs: [Diff, TagRaw, Tag]
+    if: ${{ needs.Diff.outputs.nb > 0 }}
     runs-on: ubuntu-latest
     steps:
       - name: 'Create Release'
diff --git a/.github/workflows/release_schedule.yml b/.github/workflows/release_schedule.yml
deleted file mode 100644
index 77cc962a..00000000
--- a/.github/workflows/release_schedule.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-name: ReleaseSchedule
-
-on:
-  schedule:
-    - cron: '0 0 * * 2'
-
-jobs:
-
-  Diff:
-    runs-on: ubuntu-latest
-    outputs:
-      nb: ${{ steps.set-diff.outputs.nb }}
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          persist-credentials: false
-          fetch-depth: 0
-          ref: 'stable'
-      - name: "Check diff"
-        id: set-diff
-        run: |
-          nb=$(git diff --shortstat stable..origin/main | cut -f2 -d ' ')
-          echo "Find diff: ${nb}"
-          echo "nb=${nb}" >> "${GITHUB_OUTPUT}"
-
-  Call:
-    needs: [Diff]
-    if: ${{ needs.Diff.outputs.nb > 0 }}
-    uses: ./.github/workflows/release.yml
-    secrets: inherit

From 3f3ef2caac4af0bdec9ab4c9e7ee8a977bbdc581 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 27 Jun 2023 08:49:14 +0200
Subject: [PATCH 31/61] chore(github): fix syntax

---
 .github/workflows/release.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 7d35fc58..9b46ae6b 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -52,10 +52,9 @@ jobs:
           echo "tag=$TAG" >> "$GITHUB_OUTPUT"
 
   Changelog:
-    needs: Diff
+    needs: [Diff, TagRaw]
     if: ${{ needs.Diff.outputs.nb > 0 }}
     runs-on: ubuntu-latest
-    needs: [TagRaw]
     steps:
       - uses: actions/checkout@v3
         with:

From b29963ef22900ba666d9be11f1dc09e4e3febf8b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Thu, 29 Jun 2023 22:11:32 +0200
Subject: [PATCH 32/61] doc(sampler): update

---
 tools/doe_synbio/sampler.xml | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/tools/doe_synbio/sampler.xml b/tools/doe_synbio/sampler.xml
index 8a7c4d77..d444a9e9 100644
--- a/tools/doe_synbio/sampler.xml
+++ b/tools/doe_synbio/sampler.xml
@@ -87,7 +87,27 @@ To avoid this, we have set some filters to select the appropriate sampling metho
 
 Input
 -----
-* **CFPS Parameters File**: The first column is the parameter (or factor) names. The second column is the maxValue of the parameter that will be used in the sampling. The third column is the concnetration of the stock. The fourth column is the deadVolume of the parameter. This is used to calculate the volume of the parameter that will not be pipetted by the robot (because of viscosity). The fifth column is the specific ratios we want to have for this parameter. If nothing defined, then take ratios given in program options. If one single number is given, then take this number as a const value.
+
+Below is an example of an input file:
+
+| Parameter | maxValue | Ratios              |
+|-----------|----------|---------------------|
+| CP        | 125      | 0.0 0.1 0.3 0.5 1.0 |
+| CPK       | 125      | 1                   |
+| tRNA      | 125      |                     |
+| AA        | 125      |                     |
+| ribosomes | 125      |                     |
+| mRNA      | 125      |                     |
+| Mg        | 125      |                     |
+| K         | 125      |                     |
+
+The first column is the parameter (or factor) names.
+
+The second column is the maxValue of the parameter that will be used in the sampling.
+
+The third column is the specific ratios we want to have for this parameter. If nothing defined, then take ratios given in program options.
+If one single number is given, then take this number as a const value.
+If no value is given, then take the default ratios (`nb_samples` linear ratios from 0 to 1).
 
 Advanced options:
 -----------------

From f20f60fd4e265f3f710b711d1c72cd25c06938e4 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Mon, 3 Jul 2023 12:37:17 +0200
Subject: [PATCH 33/61] fix(tools): sampler, table syntax (#136)

---
 tools/doe_synbio/sampler.xml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/tools/doe_synbio/sampler.xml b/tools/doe_synbio/sampler.xml
index d444a9e9..f48d868a 100644
--- a/tools/doe_synbio/sampler.xml
+++ b/tools/doe_synbio/sampler.xml
@@ -90,16 +90,25 @@ Input
 
 Below is an example of an input file:
 
++-----------+----------+---------------------+
 | Parameter | maxValue | Ratios              |
-|-----------|----------|---------------------|
++===========+==========+=====================+
 | CP        | 125      | 0.0 0.1 0.3 0.5 1.0 |
++-----------+----------+---------------------+
 | CPK       | 125      | 1                   |
++-----------+----------+---------------------+
 | tRNA      | 125      |                     |
++-----------+----------+---------------------+
 | AA        | 125      |                     |
++-----------+----------+---------------------+
 | ribosomes | 125      |                     |
++-----------+----------+---------------------+
 | mRNA      | 125      |                     |
++-----------+----------+---------------------+
 | Mg        | 125      |                     |
++-----------+----------+---------------------+
 | K         | 125      |                     |
++-----------+----------+---------------------+
 
 The first column is the parameter (or factor) names.
 

From f48e512f2ed910da01a86a2088dfb1ba866ad47b Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 4 Jul 2023 01:17:11 +0000
Subject: [PATCH 34/61] doc(changelog): update

---
 CHANGELOG.md | 121 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 121 insertions(+)
 create mode 100644 CHANGELOG.md

diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 00000000..3d6112d7
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,121 @@
+# Changelog
+
+## [0.1.0](https://github.com/brsynth/galaxytools/tree/0.1.0) (2023-05-17)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/55db1c4095f1833e0122c5e1e8cf1df82fab81b6...0.1.0)
+
+**Merged pull requests:**
+
+- fix: XDG\_CACHE\_HOME [\#113](https://github.com/brsynth/galaxytools/pull/113) ([breakthewall](https://github.com/breakthewall))
+- Fix rptools - rpthermo: locate cache dir [\#112](https://github.com/brsynth/galaxytools/pull/112) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Fix straindesign: testtoolshed [\#111](https://github.com/brsynth/galaxytools/pull/111) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Updating sbol3\_diff from version 1.0a16 to 1.0a17 [\#110](https://github.com/brsynth/galaxytools/pull/110) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Updating sbol\_converter from version 1.0a16 to 1.0a17 [\#109](https://github.com/brsynth/galaxytools/pull/109) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- sbol\_converter: add citation tag [\#108](https://github.com/brsynth/galaxytools/pull/108) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Feat\(get sbml model\) [\#107](https://github.com/brsynth/galaxytools/pull/107) ([breakthewall](https://github.com/breakthewall))
+- chore\(deps\): bump github/super-linter from 4 to 5 [\#106](https://github.com/brsynth/galaxytools/pull/106) ([dependabot[bot]](https://github.com/apps/dependabot))
+- feat\(get\_sbml\_model\) [\#105](https://github.com/brsynth/galaxytools/pull/105) ([breakthewall](https://github.com/breakthewall))
+- Shed lint [\#104](https://github.com/brsynth/galaxytools/pull/104) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Updating rpbasicdesign from version 1.1.0 to 1.2.2 [\#103](https://github.com/brsynth/galaxytools/pull/103) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- retropath2\_wrapper - Id retropath2 ambiguous [\#102](https://github.com/brsynth/galaxytools/pull/102) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Updating retropath2\_wrapper from version 3.0.0 to 3.0.1 [\#101](https://github.com/brsynth/galaxytools/pull/101) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- fix\(github\): workflow syntax [\#97](https://github.com/brsynth/galaxytools/pull/97) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- chore\(github\): enable autoupdate [\#96](https://github.com/brsynth/galaxytools/pull/96) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Refactor repository [\#95](https://github.com/brsynth/galaxytools/pull/95) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- feat\(retropath2\_wrapper\): update to 3.0.0 [\#94](https://github.com/brsynth/galaxytools/pull/94) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- feat\(rrpser\): update [\#93](https://github.com/brsynth/galaxytools/pull/93) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- fix\(get\_sbml\_model\): output fmt [\#92](https://github.com/brsynth/galaxytools/pull/92) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- feat\(rp2paths\): output format [\#91](https://github.com/brsynth/galaxytools/pull/91) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Doe synbio [\#90](https://github.com/brsynth/galaxytools/pull/90) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- rptools [\#89](https://github.com/brsynth/galaxytools/pull/89) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Icfree [\#88](https://github.com/brsynth/galaxytools/pull/88) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Sbol3 diff [\#87](https://github.com/brsynth/galaxytools/pull/87) ([kenza12](https://github.com/kenza12))
+- style\(rpranker\): add single quotes and element\_identifier [\#86](https://github.com/brsynth/galaxytools/pull/86) ([kenza12](https://github.com/kenza12))
+- feat\(rptools\): add one common macro file and test only content in rpt… [\#85](https://github.com/brsynth/galaxytools/pull/85) ([kenza12](https://github.com/kenza12))
+- Iuc rptools [\#84](https://github.com/brsynth/galaxytools/pull/84) ([kenza12](https://github.com/kenza12))
+- Iuc rp2biosensor [\#83](https://github.com/brsynth/galaxytools/pull/83) ([kenza12](https://github.com/kenza12))
+- Iuc lcrgenie [\#82](https://github.com/brsynth/galaxytools/pull/82) ([kenza12](https://github.com/kenza12))
+- Iuc dnaweaver [\#81](https://github.com/brsynth/galaxytools/pull/81) ([kenza12](https://github.com/kenza12))
+- Update rptools suite to 6.0.1 [\#80](https://github.com/brsynth/galaxytools/pull/80) ([kenza12](https://github.com/kenza12))
+- doc\(rpExtractSink\): add creator names and update rptools [\#79](https://github.com/brsynth/galaxytools/pull/79) ([kenza12](https://github.com/kenza12))
+- Iuc rpfba [\#78](https://github.com/brsynth/galaxytools/pull/78) ([kenza12](https://github.com/kenza12))
+- Iuc rpreport [\#77](https://github.com/brsynth/galaxytools/pull/77) ([kenza12](https://github.com/kenza12))
+- Iuc rpviz [\#76](https://github.com/brsynth/galaxytools/pull/76) ([kenza12](https://github.com/kenza12))
+- doc\(optdoe\): optimize name and def tool [\#75](https://github.com/brsynth/galaxytools/pull/75) ([kenza12](https://github.com/kenza12))
+- fix\(OptDoE\): remove duplicates from codon tables [\#74](https://github.com/brsynth/galaxytools/pull/74) ([kenza12](https://github.com/kenza12))
+- Iuc rpranker [\#73](https://github.com/brsynth/galaxytools/pull/73) ([kenza12](https://github.com/kenza12))
+- Iuc optdoe [\#72](https://github.com/brsynth/galaxytools/pull/72) ([kenza12](https://github.com/kenza12))
+- Iuc rpranker [\#71](https://github.com/brsynth/galaxytools/pull/71) ([kenza12](https://github.com/kenza12))
+- Test sbml2sbol \(IUC requests\) [\#70](https://github.com/brsynth/galaxytools/pull/70) ([kenza12](https://github.com/kenza12))
+- Add straindesign wrapper [\#69](https://github.com/brsynth/galaxytools/pull/69) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Iuc sbml2sbol [\#68](https://github.com/brsynth/galaxytools/pull/68) ([kenza12](https://github.com/kenza12))
+- Iuc rp2paths [\#67](https://github.com/brsynth/galaxytools/pull/67) ([kenza12](https://github.com/kenza12))
+- fix\(Retropath2\_wrapper\): fix writing in tool dir with kinstall option [\#66](https://github.com/brsynth/galaxytools/pull/66) ([kenza12](https://github.com/kenza12))
+- IUC rp2paths [\#65](https://github.com/brsynth/galaxytools/pull/65) ([kenza12](https://github.com/kenza12))
+- Iuc rpcompletion [\#64](https://github.com/brsynth/galaxytools/pull/64) ([kenza12](https://github.com/kenza12))
+- test\(sbol-converter\): add few tests and README [\#63](https://github.com/brsynth/galaxytools/pull/63) ([kenza12](https://github.com/kenza12))
+- feat\(sbol\_converter\): add sbol converter \(splitted wrappers\) [\#62](https://github.com/brsynth/galaxytools/pull/62) ([kenza12](https://github.com/kenza12))
+- feat\(sbol-converter\): add first release of sbol-converter wrapper [\#61](https://github.com/brsynth/galaxytools/pull/61) ([kenza12](https://github.com/kenza12))
+- Iuc retropath2 [\#60](https://github.com/brsynth/galaxytools/pull/60) ([kenza12](https://github.com/kenza12))
+- Iuc retropath2 [\#59](https://github.com/brsynth/galaxytools/pull/59) ([kenza12](https://github.com/kenza12))
+- feat\(rrparser\): update rrparser and add rules-dir option [\#58](https://github.com/brsynth/galaxytools/pull/58) ([kenza12](https://github.com/kenza12))
+- Iuc selenzy [\#57](https://github.com/brsynth/galaxytools/pull/57) ([kenza12](https://github.com/kenza12))
+- Iuc rpextractsink [\#56](https://github.com/brsynth/galaxytools/pull/56) ([kenza12](https://github.com/kenza12))
+- Iuc rrparser [\#55](https://github.com/brsynth/galaxytools/pull/55) ([kenza12](https://github.com/kenza12))
+- feat\(rpbasicdesign\): add missing max\_gene\_per\_construct parameter and… [\#54](https://github.com/brsynth/galaxytools/pull/54) ([kenza12](https://github.com/kenza12))
+- Update rpfba [\#53](https://github.com/brsynth/galaxytools/pull/53) ([kenza12](https://github.com/kenza12))
+- Iuc rp2paths [\#52](https://github.com/brsynth/galaxytools/pull/52) ([kenza12](https://github.com/kenza12))
+- Iuc dnabot [\#51](https://github.com/brsynth/galaxytools/pull/51) ([kenza12](https://github.com/kenza12))
+- Test dnabot [\#49](https://github.com/brsynth/galaxytools/pull/49) ([kenza12](https://github.com/kenza12))
+- Iuc rpbasicdesign [\#48](https://github.com/brsynth/galaxytools/pull/48) ([kenza12](https://github.com/kenza12))
+- Test rpbasicdesign [\#47](https://github.com/brsynth/galaxytools/pull/47) ([kenza12](https://github.com/kenza12))
+- test\(rp2biosensor\): add sink test file and update to 3.1.0 [\#46](https://github.com/brsynth/galaxytools/pull/46) ([kenza12](https://github.com/kenza12))
+- Test rpbasicdesign [\#45](https://github.com/brsynth/galaxytools/pull/45) ([kenza12](https://github.com/kenza12))
+- feat\(rp2biosensor\): add input sink file and upgrade to 3.0.0 [\#44](https://github.com/brsynth/galaxytools/pull/44) ([kenza12](https://github.com/kenza12))
+- Test rp2biosensor [\#43](https://github.com/brsynth/galaxytools/pull/43) ([kenza12](https://github.com/kenza12))
+- Test dnabot [\#42](https://github.com/brsynth/galaxytools/pull/42) ([kenza12](https://github.com/kenza12))
+- feat: add rp\_fba\_analysis [\#41](https://github.com/brsynth/galaxytools/pull/41) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Test rpreport [\#40](https://github.com/brsynth/galaxytools/pull/40) ([kenza12](https://github.com/kenza12))
+- Test rpranker [\#39](https://github.com/brsynth/galaxytools/pull/39) ([kenza12](https://github.com/kenza12))
+- Test rpscore [\#38](https://github.com/brsynth/galaxytools/pull/38) ([kenza12](https://github.com/kenza12))
+- Test rpcompletion [\#37](https://github.com/brsynth/galaxytools/pull/37) ([kenza12](https://github.com/kenza12))
+- Test sbml2sbol [\#36](https://github.com/brsynth/galaxytools/pull/36) ([kenza12](https://github.com/kenza12))
+- Test rpextractsink [\#35](https://github.com/brsynth/galaxytools/pull/35) ([kenza12](https://github.com/kenza12))
+- Test rpthermo [\#34](https://github.com/brsynth/galaxytools/pull/34) ([kenza12](https://github.com/kenza12))
+- Test selenzy [\#33](https://github.com/brsynth/galaxytools/pull/33) ([kenza12](https://github.com/kenza12))
+- test\(retropath2\): update test section with small inputs [\#32](https://github.com/brsynth/galaxytools/pull/32) ([kenza12](https://github.com/kenza12))
+- Test retropath2 [\#31](https://github.com/brsynth/galaxytools/pull/31) ([kenza12](https://github.com/kenza12))
+- Test dnaweaver [\#30](https://github.com/brsynth/galaxytools/pull/30) ([kenza12](https://github.com/kenza12))
+- Feat inchi to sink [\#29](https://github.com/brsynth/galaxytools/pull/29) ([kenza12](https://github.com/kenza12))
+- test\(LCRGenie\): update test section [\#28](https://github.com/brsynth/galaxytools/pull/28) ([kenza12](https://github.com/kenza12))
+- Test optdoe [\#27](https://github.com/brsynth/galaxytools/pull/27) ([kenza12](https://github.com/kenza12))
+- Test rrparser [\#26](https://github.com/brsynth/galaxytools/pull/26) ([kenza12](https://github.com/kenza12))
+- fix\(rpFBA\): fix objective\_rxn\_id parameter name [\#25](https://github.com/brsynth/galaxytools/pull/25) ([kenza12](https://github.com/kenza12))
+- Feat inchi to sink [\#24](https://github.com/brsynth/galaxytools/pull/24) ([kenza12](https://github.com/kenza12))
+- Test rpfba [\#23](https://github.com/brsynth/galaxytools/pull/23) ([kenza12](https://github.com/kenza12))
+- Feat rpfba [\#22](https://github.com/brsynth/galaxytools/pull/22) ([kenza12](https://github.com/kenza12))
+- Test rpfba [\#21](https://github.com/brsynth/galaxytools/pull/21) ([kenza12](https://github.com/kenza12))
+- Test get sbml model [\#20](https://github.com/brsynth/galaxytools/pull/20) ([kenza12](https://github.com/kenza12))
+- Test rpextractsink [\#19](https://github.com/brsynth/galaxytools/pull/19) ([kenza12](https://github.com/kenza12))
+- Feat rp2biosensor [\#18](https://github.com/brsynth/galaxytools/pull/18) ([kenza12](https://github.com/kenza12))
+- Test rpextractsink [\#17](https://github.com/brsynth/galaxytools/pull/17) ([kenza12](https://github.com/kenza12))
+- Test rpextractsink [\#16](https://github.com/brsynth/galaxytools/pull/16) ([kenza12](https://github.com/kenza12))
+- Test partsgenie [\#15](https://github.com/brsynth/galaxytools/pull/15) ([kenza12](https://github.com/kenza12))
+- Test lcr genie [\#14](https://github.com/brsynth/galaxytools/pull/14) ([kenza12](https://github.com/kenza12))
+- Test dnaweaver [\#13](https://github.com/brsynth/galaxytools/pull/13) ([kenza12](https://github.com/kenza12))
+- Test optdoe [\#12](https://github.com/brsynth/galaxytools/pull/12) ([kenza12](https://github.com/kenza12))
+- Test selenzy wrapper [\#11](https://github.com/brsynth/galaxytools/pull/11) ([kenza12](https://github.com/kenza12))
+- Test rprank [\#10](https://github.com/brsynth/galaxytools/pull/10) ([kenza12](https://github.com/kenza12))
+- Feat rpviz [\#9](https://github.com/brsynth/galaxytools/pull/9) ([kenza12](https://github.com/kenza12))
+- feat\(dnabot\): output a tar file and update data tests [\#8](https://github.com/brsynth/galaxytools/pull/8) ([kenza12](https://github.com/kenza12))
+- Test sbml2sbol [\#7](https://github.com/brsynth/galaxytools/pull/7) ([kenza12](https://github.com/kenza12))
+- test\(rpscore\): add test section and data tests [\#6](https://github.com/brsynth/galaxytools/pull/6) ([kenza12](https://github.com/kenza12))
+- Feat dnabot [\#5](https://github.com/brsynth/galaxytools/pull/5) ([kenza12](https://github.com/kenza12))
+- test\(rp2paths\): update data tests and test section [\#4](https://github.com/brsynth/galaxytools/pull/4) ([kenza12](https://github.com/kenza12))
+- Test rpthermo [\#3](https://github.com/brsynth/galaxytools/pull/3) ([kenza12](https://github.com/kenza12))
+- Test rpfba [\#2](https://github.com/brsynth/galaxytools/pull/2) ([kenza12](https://github.com/kenza12))
+- Test rpcompletion [\#1](https://github.com/brsynth/galaxytools/pull/1) ([kenza12](https://github.com/kenza12))
+
+
+
+\* *This Changelog was automatically generated by [github_changelog_generator](https://github.com/github-changelog-generator/github-changelog-generator)*

From cb8252ee0280a420233b52f6a7166c3da074ea8a Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 11 Jul 2023 01:10:00 +0000
Subject: [PATCH 35/61] doc(changelog): update

---
 CHANGELOG.md | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3d6112d7..5dd1a69d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,40 @@
 # Changelog
 
+## [0.2.0](https://github.com/brsynth/galaxytools/tree/0.2.0) (2023-07-03)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.1.0...0.2.0)
+
+**Implemented enhancements:**
+
+- Add workflow `strain design` [\#127](https://github.com/brsynth/galaxytools/issues/127)
+- Add workflow `genetic design` [\#125](https://github.com/brsynth/galaxytools/issues/125)
+- Add workflow `biosensor` [\#124](https://github.com/brsynth/galaxytools/issues/124)
+- Add workflow `retrosynthesis` [\#123](https://github.com/brsynth/galaxytools/issues/123)
+
+**Fixed bugs:**
+
+- workflow `pathway analysis` [\#126](https://github.com/brsynth/galaxytools/issues/126)
+- rp2biosensor: syntax [\#130](https://github.com/brsynth/galaxytools/pull/130) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+
+**Merged pull requests:**
+
+- Tools sample, table syntax [\#136](https://github.com/brsynth/galaxytools/pull/136) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- chore\(deps\): bump tj-actions/changed-files from 36 to 37 [\#135](https://github.com/brsynth/galaxytools/pull/135) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Tools: `selenzy_wrapper` [\#134](https://github.com/brsynth/galaxytools/pull/134) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Workflows: add `genetic assembly` [\#133](https://github.com/brsynth/galaxytools/pull/133) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Workflows: `straindesign` [\#132](https://github.com/brsynth/galaxytools/pull/132) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Workflows: add `biosensor` [\#131](https://github.com/brsynth/galaxytools/pull/131) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- workflows `retrosynthesis` [\#129](https://github.com/brsynth/galaxytools/pull/129) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- Add `pathway_analysis` workflow [\#128](https://github.com/brsynth/galaxytools/pull/128) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- fix `sbol_converter` [\#122](https://github.com/brsynth/galaxytools/pull/122) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- chore\(deps\): bump tj-actions/changed-files from 35 to 36 [\#120](https://github.com/brsynth/galaxytools/pull/120) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Workflows `basic_assembly_workflow` [\#119](https://github.com/brsynth/galaxytools/pull/119) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- chore: rm config folders [\#118](https://github.com/brsynth/galaxytools/pull/118) ([breakthewall](https://github.com/breakthewall))
+- Taxonid [\#117](https://github.com/brsynth/galaxytools/pull/117) ([breakthewall](https://github.com/breakthewall))
+- Taxonid [\#116](https://github.com/brsynth/galaxytools/pull/116) ([breakthewall](https://github.com/breakthewall))
+- chore\(selenzy\_wrapper\): rm comment [\#115](https://github.com/brsynth/galaxytools/pull/115) ([breakthewall](https://github.com/breakthewall))
+- taxonid [\#114](https://github.com/brsynth/galaxytools/pull/114) ([breakthewall](https://github.com/breakthewall))
+
 ## [0.1.0](https://github.com/brsynth/galaxytools/tree/0.1.0) (2023-05-17)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/55db1c4095f1833e0122c5e1e8cf1df82fab81b6...0.1.0)

From df9aa45c5d429775e15f43afac73244d0744934b Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 18 Jul 2023 01:38:54 +0000
Subject: [PATCH 36/61] doc(changelog): update

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5dd1a69d..c3e3864f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.1](https://github.com/brsynth/galaxytools/tree/0.2.1) (2023-07-04)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.0...0.2.1)
+
 ## [0.2.0](https://github.com/brsynth/galaxytools/tree/0.2.0) (2023-07-03)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.1.0...0.2.0)

From e4b75b1cea6d63df440c36bc3698d37af9f9b13d Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 25 Jul 2023 01:10:51 +0000
Subject: [PATCH 37/61] doc(changelog): update

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c3e3864f..0d554afc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.2](https://github.com/brsynth/galaxytools/tree/0.2.2) (2023-07-11)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.1...0.2.2)
+
 ## [0.2.1](https://github.com/brsynth/galaxytools/tree/0.2.1) (2023-07-04)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.0...0.2.1)

From a09f2db2f8b2c815f3d4fc0326c9dd1cb82c5fae Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 1 Aug 2023 01:07:29 +0000
Subject: [PATCH 38/61] doc(changelog): update

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0d554afc..60cbeba6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.3](https://github.com/brsynth/galaxytools/tree/0.2.3) (2023-07-18)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.2...0.2.3)
+
 ## [0.2.2](https://github.com/brsynth/galaxytools/tree/0.2.2) (2023-07-11)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.1...0.2.2)

From 6be8925922529e6c0c3f5f611a922176a6783f98 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 8 Aug 2023 01:00:01 +0000
Subject: [PATCH 39/61] doc(changelog): update

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 60cbeba6..f21779d6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.4](https://github.com/brsynth/galaxytools/tree/0.2.4) (2023-07-25)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.3...0.2.4)
+
 ## [0.2.3](https://github.com/brsynth/galaxytools/tree/0.2.3) (2023-07-18)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.2...0.2.3)

From c9c9c7b8247716d4b56ce789f3b6fca29bcd3dce Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 15 Aug 2023 00:51:02 +0000
Subject: [PATCH 40/61] doc(changelog): update

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f21779d6..889ad86f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.5](https://github.com/brsynth/galaxytools/tree/0.2.5) (2023-08-01)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.4...0.2.5)
+
 ## [0.2.4](https://github.com/brsynth/galaxytools/tree/0.2.4) (2023-07-25)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.3...0.2.4)

From 77c42c23ff1d728b531b5e2fa6fd933aaa2d42f1 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 22 Aug 2023 00:51:35 +0000
Subject: [PATCH 41/61] doc(changelog): update

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 889ad86f..ed5efd08 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.6](https://github.com/brsynth/galaxytools/tree/0.2.6) (2023-08-08)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.5...0.2.6)
+
 ## [0.2.5](https://github.com/brsynth/galaxytools/tree/0.2.5) (2023-08-01)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.4...0.2.5)

From 87a863d4074543870caef1116b8e9be58005dcdd Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Mon, 28 Aug 2023 16:23:27 +0200
Subject: [PATCH 42/61] get_sbml_model, enable to load file from history (#137)

* feat(tools): get_sbml_model, enable to load file from history
---
 .github/workflows/testtools.yml               |    1 +
 tools/get_sbml_model/get_sbml_model.xml       |  158 +-
 .../get_sbml_model/test-data/e_coli_core.xml  | 9898 +++++++++++++++++
 3 files changed, 9993 insertions(+), 64 deletions(-)
 create mode 100644 tools/get_sbml_model/test-data/e_coli_core.xml

diff --git a/.github/workflows/testtools.yml b/.github/workflows/testtools.yml
index f9d20cdc..8bb288cf 100644
--- a/.github/workflows/testtools.yml
+++ b/.github/workflows/testtools.yml
@@ -78,6 +78,7 @@ jobs:
             --galaxy_source https://github.com/galaxyproject/galaxy \
             --galaxy_branch release_22.05 \
             --galaxy_python_version 3.7 \
+            --docker_extra_volume ./ \
             "tools/${{ matrix.repo }}"
           mv tool_test_output.json "log/${{ matrix.repo }}"
       - name: 'Prepare artefact'
diff --git a/tools/get_sbml_model/get_sbml_model.xml b/tools/get_sbml_model/get_sbml_model.xml
index c19e620a..decdd783 100644
--- a/tools/get_sbml_model/get_sbml_model.xml
+++ b/tools/get_sbml_model/get_sbml_model.xml
@@ -1,4 +1,4 @@
-<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT">
+<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.4" profile="21.09" license="MIT">
     <description>Get an SBML model (BiGG)</description>
     <requirements>
         <requirement type="package" version="7.81.0">curl</requirement>
@@ -7,87 +7,117 @@
         <requirement type="package" version="2.29">requests</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
-        | gunzip > '$model';
+        #if str($cond_src.from_src) == 'from_bigg'
+            curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' &&
+        #else
+            cp '${cond_src.input_file}' '$model' &&
+        #end if
         python '$__tool_directory__/'get_infos.py
         '$model'
-        --hostid '$input'
+        --hostid '${cond_src.hostid}'
         --comp '$compartments'
         --biomass '$biomass'
         --taxid '$taxid'
     ]]></command>
     <inputs>
-        <param name="input" type="select" label="Strain">
-            <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option>
-            <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>
-            <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option>
-            <option value="iCN900">Clostridioides difficile 630 (iCN900)</option>
-            <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option>
-            <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option>
-            <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option>
-            <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option>
-            <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option>
-            <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option>
-            <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option>
-            <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option>
-            <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option>
-            <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option>
-            <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option>
-            <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option>
-            <option value="Recon3D">Homo sapiens (Recon3D)</option>
-            <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option>
-            <option value="RECON1">Homo sapiens (RECON1)</option>
-            <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option>
-            <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option>
-            <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option>
-            <option value="iMM1415">Mus musculus (iMM1415)</option>
-            <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option>
-            <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option>
-            <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option>
-            <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option>
-            <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option>
-            <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option>
-            <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option>
-            <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option>
-            <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option>
-            <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option>
-            <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option>
-            <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option>
-            <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option>
-            <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option>
-            <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option>
-            <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option>
-            <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option>
-            <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option>
-            <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option>
-            <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option>
-            <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option>
-            <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option>
-            <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>
-            <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
-        </param>
+        <conditional name="cond_src">
+            <param name="from_src" type="select" label="Select source">
+                <option value="from_bigg" selected="True">Download model from BiGG</option>
+                <option value="from_history">Select file from the History</option>
+            </param>
+            <when value="from_history">
+                <param name="hostid" type="text" help="ID of the model">
+                    <validator type="empty_field" message="An ID is required"/>
+                </param>
+                <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
+            </when>
+            <when value="from_bigg">
+                 <param name="hostid" type="select" label="Strain">
+                    <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option>
+                    <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>
+                    <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option>
+                    <option value="iCN900">Clostridioides difficile 630 (iCN900)</option>
+                    <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option>
+                    <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option>
+                    <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option>
+                    <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option>
+                    <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option>
+                    <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option>
+                    <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option>
+                    <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option>
+                    <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option>
+                    <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option>
+                    <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option>
+                    <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option>
+                    <option value="Recon3D">Homo sapiens (Recon3D)</option>
+                    <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option>
+                    <option value="RECON1">Homo sapiens (RECON1)</option>
+                    <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option>
+                    <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option>
+                    <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option>
+                    <option value="iMM1415">Mus musculus (iMM1415)</option>
+                    <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option>
+                    <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option>
+                    <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option>
+                    <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option>
+                    <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option>
+                    <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option>
+                    <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option>
+                    <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option>
+                    <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option>
+                    <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option>
+                    <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option>
+                    <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option>
+                    <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option>
+                    <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option>
+                    <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option>
+                    <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option>
+                    <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option>
+                    <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option>
+                    <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option>
+                    <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option>
+                    <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option>
+                    <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option>
+                    <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>
+                    <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
+                </param>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
-        <data name="model" format="sbml" label="${input}" />
-        <data name="taxid" format="tsv" label="${input} (taxon id)" />
-        <data name="compartments" format="tsv" label="${input} (compartments)" />
-        <data name="biomass" format="tsv" label="${input} (biomass reactions)" />
+        <data name="model" format="sbml" label="${cond_src.hostid}" />
+        <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" />
+        <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" />
+        <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" />
     </outputs>
     <tests>
         <test>
-        <!-- test 1: check if identical outputs are produced with iML1515 model input  -->
-            <param name="input" value="iML1515" />
-            <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/>
-            <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e"/>
-            <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/>
-            <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/>
+            <conditional name="cond_src">
+                <param name="from_src" value="from_bigg" />
+                <param name="hostid" value="iML1515" />
+            </conditional>
+            <output name="model" md5="9bf81d20cab5476700697ded95b716d1" />
+            <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
+            <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />
+            <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" />
         </test>
+        <test>
+            <conditional name="cond_src">
+                <param name="from_src" value="from_history" />
+                <param name="hostid" value="e_coli_core" />
+                <param name="input_file" value="e_coli_core.xml" />
+            </conditional>
+            <output name="model" md5="4574760460afe9e1b3388dc15f354706" />
+            <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
+            <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
+            <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />
+            </test>
     </tests>
     <help><![CDATA[
 Pick SBML Model
 =================
 
-Download the selected SBML model fromg BiGG database.
+Download the selected SBML model fromg BiGG database or get statistics from local SBML model.
     ]]></help>
     <creator>
         <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
diff --git a/tools/get_sbml_model/test-data/e_coli_core.xml b/tools/get_sbml_model/test-data/e_coli_core.xml
new file mode 100644
index 00000000..b1ee5c62
--- /dev/null
+++ b/tools/get_sbml_model/test-data/e_coli_core.xml
@@ -0,0 +1,9898 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1" sboTerm="SBO:0000624" fbc:required="false">
+  <model fbc:strict="true" id="e_coli_core">
+    <listOfUnitDefinitions>
+      <unitDefinition id="mmol_per_gDW_per_hr">
+        <listOfUnits>
+          <unit kind="mole" scale="-3" multiplier="1" exponent="1"/>
+          <unit kind="gram" scale="0" multiplier="1" exponent="-1"/>
+          <unit kind="second" scale="0" multiplier="3600" exponent="-1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <fbc:listOfObjectives fbc:activeObjective="obj">
+      <fbc:objective fbc:id="obj" fbc:type="maximize">
+        <fbc:listOfFluxObjectives>
+          <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ecoli_core_w_GAM" fbc:coefficient="1"/>
+        </fbc:listOfFluxObjectives>
+      </fbc:objective>
+    </fbc:listOfObjectives>
+    <listOfParameters>
+      <parameter value="-1000" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
+      <parameter value="1000" id="cobra_default_ub" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
+      <parameter value="0" id="cobra_0_bound" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
+      <parameter id="R_ATPM_lower_bound" value="8.39" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>
+      <parameter id="R_EX_glc__D_e_lower_bound" value="-10" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>
+    </listOfParameters>
+    <listOfCompartments>
+      <compartment id="e" name="extracellular space" constant="true"/>
+      <compartment id="c" name="cytosol" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="M_glc__D_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="D-Glucose" metaid="M_glc__D_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="C6H12O6">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#M_glc__D_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/glc__D"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:Glucopyranose"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:12965"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:20999"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:4167"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:17634"/>
+                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00122"/>
+                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB06564"/>
+                  <rdf:li rdf:resource="http://identifiers.org/inchi_key/WQZGKKKJIJFFOK-GASJEMHNSA-N"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D00009"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM41"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1406"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1407"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd26821"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00027"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+      </species>
+      <species id="M_gln__L_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="L-Glutamine" metaid="M_gln__L_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="0" fbc:chemicalFormula="C5H10N2O3">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#M_gln__L_c">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/gln__L"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42943"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42899"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32679"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32678"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:58359"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:28300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42812"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13110"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18050"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32666"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:6227"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32665"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:21308"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42814"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:5432"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:24316"/>
+                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00641"/>
+                  <rdf:li rdf:resource="http://identifiers.org/inchi_key/ZDXPYRJPNDTMRX-VKHMYHEASA-N"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00064"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00303"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D00015"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM37"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.compound/113522"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.compound/212615"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.compound/29472"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2011"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/74"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00253"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00053"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+      </species>
+      <species id="M_gln__L_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="L-Glutamine" metaid="M_gln__L_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="C5H10N2O3">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#M_gln__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/gln__L"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42943"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42899"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32679"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32678"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:58359"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:28300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42812"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13110"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18050"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32666"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:6227"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32665"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:21308"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42814"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:5432"/>
+                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:24316"/>
+                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00641"/>
+                  <rdf:li rdf:resource="http://identifiers.org/inchi_key/ZDXPYRJPNDTMRX-VKHMYHEASA-N"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00064"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00303"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D00015"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM37"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.compound/113522"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.compound/212615"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.compound/29472"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2011"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/74"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00253"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00053"/>
+                </rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/refseq_synonym/ECK2930"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/refseq_synonym/tpi"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P0A858"/>
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+      </fbc:geneProduct>
+    </fbc:listOfGeneProducts>
+    <listOfReactions>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.11"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102507"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16111"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16109"/>
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+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15903"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15901"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15904"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01106"/>
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+          <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3612"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4395"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0755"/>
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+        </fbc:geneProductAssociation>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29941"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29940"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29942"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05312"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09811"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09723"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09120"/>
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+          <speciesReference species="M_pi_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3493"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25291"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25293"/>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0356"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1478"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1241"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08032"/>
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+        <listOfProducts>
+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_actp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3115"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2296"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1849"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23072"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3956"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACONITATEDEHYDR-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95386"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10228"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00974"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_acon_C_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0118"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1276"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_icit_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0118"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1276"/>
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+        </fbc:geneProductAssociation>
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+              <fbc:and>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2779"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SUCCt3" fast="false" reversible="false" name="Succinate transport out via proton antiport" metaid="R_SUCCt3" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_ETOHt2r" fast="false" reversible="true" name="Ethanol reversible transport via proton symport" metaid="R_ETOHt2r" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ETOHt2r">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97981"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10146"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08427"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_etoh_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_etoh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_SUCDi" fast="false" reversible="false" name="Succinate dehydrogenase (irreversible)" metaid="R_SUCDi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99641"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29190"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29189"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29187"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29188"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09272"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0721"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0722"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0723"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0724"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SUCOAS" fast="false" reversible="true" name="Succinyl-CoA synthetase (ADP-forming)" metaid="R_SUCOAS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SUCCCOASYN-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104635"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-372977"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-70997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-70997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-70997"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-70997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-70997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-70997"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-70997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-70997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17664"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17663"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17662"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17661"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/260"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00285"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0728"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0729"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TALA" fast="false" reversible="true" name="Transaldolase" metaid="R_TALA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_TALA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANSALDOL-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01827"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104715"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17056"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17055"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17054"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17053"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_s7p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2464"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0008"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_THD2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10125"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09295"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h_e" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1602"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1603"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_TKT1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TKT1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.2.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104868"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_s7p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2935"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2465"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2TRANSKETO-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104869"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27627"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27628"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27626"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27629"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2935"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2465"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00747"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05319"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_lac__D_e" fast="false" reversible="false" name="D-lactate exchange" metaid="R_EX_lac__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_lac__D_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_lac__D_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12471"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08351"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_lac__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_mal__L_e" fast="false" reversible="false" name="L-Malate exchange" metaid="R_EX_mal__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_mal__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mal__L_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-225"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-224"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101367"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13793"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10967"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08868"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mal__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_nh4_e" fast="false" reversible="true" name="Ammonia exchange" metaid="R_EX_nh4_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_nh4_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_nh4_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-206"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9615"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-544"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101950"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28749"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28748"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28750"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28747"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13364"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09835"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05466"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08986"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09736"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_nh4_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_o2_e" fast="false" reversible="true" name="O2 exchange" metaid="R_EX_o2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_o2_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_o2_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-474"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102090"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09641"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05468"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09032"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09734"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_pi_e" fast="false" reversible="true" name="Phosphate exchange" metaid="R_EX_pi_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_pi_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-470"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32824"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32826"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32825"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32823"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/10985"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10838"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09722"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09121"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13178"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pi_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_pyr_e" fast="false" reversible="false" name="Pyruvate exchange" metaid="R_EX_pyr_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_pyr_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pyr_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-506"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-570"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103384"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12168"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10929"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09218"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pyr_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_succ_e" fast="false" reversible="false" name="Succinate exchange" metaid="R_EX_succ_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_succ_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_succ_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-552"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104619"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10952"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09271"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_succ_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_FBA" fast="false" reversible="true" name="Fructose-bisphosphate aldolase" metaid="R_FBA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FBA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.13"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01068"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99459"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14729"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14732"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14731"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14730"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1338"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00786"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2097"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1773"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2925"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FBP" fast="false" reversible="false" name="Fructose-bisphosphatase" metaid="R_FBP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FBP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.11"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99465"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11067"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11065"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11066"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11064"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2084"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3925"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4232"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FORt2" fast="false" reversible="false" name="Formate transport in via proton symport" metaid="R_FORt2" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99621"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08524"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05559"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_for_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0904"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2492"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FORt" fast="false" reversible="true" name="Formate transport via diffusion" metaid="R_FORt" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_0_bound" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29681"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29680"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29679"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12483"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09754"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08525"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08526"/>
+                </rdf:Bag>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_for_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0904"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2492"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FRD7" fast="false" reversible="false" name="Fumarate reductase" metaid="R_FRD7" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FRD7">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+      <reaction id="R_O2t" fast="false" reversible="true" name="O2 transport  diffusion " metaid="R_O2t" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_O2t">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O2t"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-474"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102090"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09641"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05468"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09032"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09734"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PDH" fast="false" reversible="false" name="Pyruvate dehydrogenase" metaid="R_PDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PDH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PDH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRUVDEH-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.1.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.51"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.4.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.12"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00209"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102425"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373177"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28043"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28045"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28044"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28042"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/523"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00154"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0114"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0115"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0116"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>

From 3412c99a2358f50c047cf40b65427850c0557113 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 29 Aug 2023 00:52:22 +0000
Subject: [PATCH 43/61] doc(changelog): update

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ed5efd08..26907138 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.7](https://github.com/brsynth/galaxytools/tree/0.2.7) (2023-08-15)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.6...0.2.7)
+
 ## [0.2.6](https://github.com/brsynth/galaxytools/tree/0.2.6) (2023-08-08)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.5...0.2.6)

From 4cffff21ce7706ac1a54689fc6dd1b44da9bcb05 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Fri, 1 Sep 2023 16:57:40 +0200
Subject: [PATCH 44/61] fix load from file

---
 tools/get_sbml_model/get_infos.py       | 56 +++++++++++++++----------
 tools/get_sbml_model/get_sbml_model.xml | 38 ++++++++++-------
 2 files changed, 59 insertions(+), 35 deletions(-)

diff --git a/tools/get_sbml_model/get_infos.py b/tools/get_sbml_model/get_infos.py
index 5523aee5..0eb113a9 100644
--- a/tools/get_sbml_model/get_infos.py
+++ b/tools/get_sbml_model/get_infos.py
@@ -12,6 +12,12 @@ def entry_point():
         type=str,
         help='SBML input file (xml)'
     )
+    # argument to tag file from BiGG
+    parser.add_argument(
+        '--bigg',
+        action='store_true',
+        help='Tag file from BiGG'
+    )
     parser.add_argument(
         '--comp',
         type=str,
@@ -52,33 +58,41 @@ def entry_point():
                     f.write(f'{rxn.getId()}\n')
 
     if params.taxid:
-        # Extended Name
-        server = 'http://bigg.ucsd.edu/api/v2/models/'
-        ext = params.hostid
-        r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
-        if not r.ok:
-            print(f"Warning: unable to retrieve host name for id {params.hostid}")
-        else:
-            try:
-                hostname = r.json()["organism"]
-            except KeyError:
-                print(f"Warning: unable to retrieve host name for id {params.hostid}")
-                hostname = ''
-        if not hostname:
-            taxid = ''
-        else:
-            # TAXON ID
-            server = 'https://rest.ensembl.org'
-            ext = f'/taxonomy/id/{hostname}?'
+        hostname = ''
+
+        # Model from BiGG
+        if params.bigg:
+            # Extended Name
+            server = 'http://bigg.ucsd.edu/api/v2/models/'
+            ext = params.hostid
             r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
             if not r.ok:
-                print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
+                print(f"Warning: unable to retrieve host name for id {params.hostid}")
             else:
                 try:
-                    taxid = r.json()["id"]
+                    hostname = r.json()["organism"]
                 except KeyError:
+                    print(f"Warning: unable to retrieve host name for id {params.hostid}")
+            if not hostname:
+                taxid = ''
+            else:
+                # TAXON ID
+                server = 'https://rest.ensembl.org'
+                ext = f'/taxonomy/id/{hostname}?'
+                r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
+                if not r.ok:
                     print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
-                    taxid = ''
+                else:
+                    try:
+                        taxid = r.json()["id"]
+                    except KeyError:
+                        print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
+                        taxid = ''
+
+        # Model from user
+        else:
+            taxid = params.hostid
+
         with open(params.taxid, 'w') as f:
             f.write('#ID\n')
             f.write(f'{taxid}\n')
diff --git a/tools/get_sbml_model/get_sbml_model.xml b/tools/get_sbml_model/get_sbml_model.xml
index decdd783..62c93b42 100644
--- a/tools/get_sbml_model/get_sbml_model.xml
+++ b/tools/get_sbml_model/get_sbml_model.xml
@@ -5,19 +5,28 @@
         <requirement type="package" version="1.11">gzip</requirement>
         <requirement type="package" version="5.19.2">python-libsbml</requirement>
         <requirement type="package" version="2.29">requests</requirement>
+        <requirement type="package" version="0.1.0">taxonid</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if str($cond_src.from_src) == 'from_bigg'
             curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' &&
-        #else
-            cp '${cond_src.input_file}' '$model' &&
         #end if
         python '$__tool_directory__/'get_infos.py
-        '$model'
-        --hostid '${cond_src.hostid}'
-        --comp '$compartments'
-        --biomass '$biomass'
-        --taxid '$taxid'
+            #if str($cond_src.from_src) == 'from_bigg'
+                '$model'
+            #else
+                '${cond_src.input_file}'
+            #end if
+            --hostid '${cond_src.hostid}'
+            --comp '$compartments'
+            --biomass '$biomass'
+        #if str($cond_src.from_src) == 'from_bigg'
+            --taxid '$taxid'
+        #else
+            python -m taxonid '${cond_src.hostid}' --output-file tmpfile
+            echo "#ID" > '$taxid'
+            cat tmpfile >> '$taxid'
+        #end if
     ]]></command>
     <inputs>
         <conditional name="cond_src">
@@ -26,8 +35,8 @@
                 <option value="from_history">Select file from the History</option>
             </param>
             <when value="from_history">
-                <param name="hostid" type="text" help="ID of the model">
-                    <validator type="empty_field" message="An ID is required"/>
+                <param name="hostid" type="text" help="Fullname of the model">
+                    <validator type="empty_field" message="The fullname of the organism is required"/>
                 </param>
                 <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
             </when>
@@ -85,7 +94,9 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="model" format="sbml" label="${cond_src.hostid}" />
+        <when value="from_bigg">
+            <data name="model" format="sbml" label="${cond_src.hostid}" />
+        </when>
         <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" />
         <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" />
         <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" />
@@ -104,13 +115,12 @@
         <test>
             <conditional name="cond_src">
                 <param name="from_src" value="from_history" />
-                <param name="hostid" value="e_coli_core" />
+                <param name="hostid" value="Escherichia coli str. K-12 substr. MG1655" />
                 <param name="input_file" value="e_coli_core.xml" />
             </conditional>
-            <output name="model" md5="4574760460afe9e1b3388dc15f354706" />
             <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
-            <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
-            <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />
+            <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />
+            <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" />
             </test>
     </tests>
     <help><![CDATA[

From b23cdd4421f329e587780226fa00a064fbd11690 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 5 Sep 2023 00:51:36 +0000
Subject: [PATCH 45/61] doc(changelog): update

---
 CHANGELOG.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 26907138..045b1184 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # Changelog
 
+## [0.2.8](https://github.com/brsynth/galaxytools/tree/0.2.8) (2023-08-28)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.7...0.2.8)
+
+**Merged pull requests:**
+
+- get\_sbml\_model, enable to load file from history [\#137](https://github.com/brsynth/galaxytools/pull/137) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+
 ## [0.2.7](https://github.com/brsynth/galaxytools/tree/0.2.7) (2023-08-15)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.6...0.2.7)

From ad7e677e59e2935a4ac7fd6375d6ce641c65c21b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 5 Sep 2023 12:38:52 +0200
Subject: [PATCH 46/61] chore(deps): bump actions/checkout from 3 to 4 (#140)

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v3...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/lint.yml          |  2 +-
 .github/workflows/pr.yml            |  8 ++++----
 .github/workflows/prworkflows.yml   |  8 ++++----
 .github/workflows/release.yml       | 10 +++++-----
 .github/workflows/shed.yml          |  4 ++--
 .github/workflows/testtools.yml     |  6 +++---
 .github/workflows/testworkflows.yml |  6 +++---
 .github/workflows/update.yml        |  4 ++--
 8 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index b198a022..3ca3d80c 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Lint Code Base
diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index b4d13ff5..12f2e450 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -20,7 +20,7 @@ jobs:
       nb: ${{ steps.set-matrix.outputs.nb }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'Select modified files'
         id: files
         #uses: Ana06/get-changed-files@v2.2.0
@@ -46,7 +46,7 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'List repos'
         id: set-matrix
         run: |
@@ -64,7 +64,7 @@ jobs:
         repo: ${{ fromJson(needs.list.outputs.matrix) }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: "Setup python"
         uses: actions/setup-python@v4
         with:
@@ -121,7 +121,7 @@ jobs:
         repo: ${{ fromJson(needs.list.outputs.matrix) }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: "Setup python"
         uses: actions/setup-python@v4
         with:
diff --git a/.github/workflows/prworkflows.yml b/.github/workflows/prworkflows.yml
index 5462b6e9..521ba3f1 100644
--- a/.github/workflows/prworkflows.yml
+++ b/.github/workflows/prworkflows.yml
@@ -20,7 +20,7 @@ jobs:
       nb: ${{ steps.set-matrix.outputs.nb }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'Select modified files'
         id: files
         #uses: Ana06/get-changed-files@v2.2.0
@@ -46,7 +46,7 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'List repos'
         id: set-matrix
         run: |
@@ -64,7 +64,7 @@ jobs:
         repo: ${{ fromJson(needs.list.outputs.matrix) }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: "Setup python"
         uses: actions/setup-python@v4
         with:
@@ -101,7 +101,7 @@ jobs:
         repo: ${{ fromJson(needs.list.outputs.matrix) }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: "Setup python"
         uses: actions/setup-python@v4
         with:
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 9b46ae6b..e27aa9c4 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -11,7 +11,7 @@ jobs:
     outputs:
       nb: ${{ steps.set-diff.outputs.nb }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -31,7 +31,7 @@ jobs:
       tag: ${{ steps.tag_label.outputs.tag }}
       changelog: ${{ steps.tag_raw.outputs.changelog }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -56,7 +56,7 @@ jobs:
     if: ${{ needs.Diff.outputs.nb > 0 }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -90,7 +90,7 @@ jobs:
     steps:
       # Get Data
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -124,7 +124,7 @@ jobs:
     if: ${{ needs.Diff.outputs.nb > 0 }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
diff --git a/.github/workflows/shed.yml b/.github/workflows/shed.yml
index 6ae99990..6305b15c 100644
--- a/.github/workflows/shed.yml
+++ b/.github/workflows/shed.yml
@@ -12,7 +12,7 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'List repos'
         id: set-matrix
         run: echo "matrix=$(find tools -mindepth 1 -maxdepth 1 -type d | jq -R -s -c 'split("\n")[:-1] | map(split("/")[-1])')" >> "${GITHUB_OUTPUT}"
@@ -27,7 +27,7 @@ jobs:
         repo: ${{ fromJson(needs.list.outputs.matrix) }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: "Setup python"
         uses: actions/setup-python@v4
         with:
diff --git a/.github/workflows/testtools.yml b/.github/workflows/testtools.yml
index 8bb288cf..a2e3c763 100644
--- a/.github/workflows/testtools.yml
+++ b/.github/workflows/testtools.yml
@@ -12,7 +12,7 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'List repos'
         id: set-matrix
         run: echo "matrix=$(find tools -mindepth 1 -maxdepth 1 -type d | jq -R -s -c 'split("\n")[:-1] | map(split("/")[-1])')" >> "${GITHUB_OUTPUT}"
@@ -23,7 +23,7 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'List repos'
         id: set-matrix
         run: |
@@ -40,7 +40,7 @@ jobs:
         repo: ${{ fromJson(needs.list.outputs.matrix) }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: "Setup python"
diff --git a/.github/workflows/testworkflows.yml b/.github/workflows/testworkflows.yml
index acb1fd2e..fcb92af5 100644
--- a/.github/workflows/testworkflows.yml
+++ b/.github/workflows/testworkflows.yml
@@ -12,7 +12,7 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'List repos'
         id: set-matrix
         run: echo "matrix=$(find workflows -mindepth 1 -maxdepth 1 -type d | jq -R -s -c 'split("\n")[:-1] | map(split("/")[-1])')" >> "${GITHUB_OUTPUT}"
@@ -23,7 +23,7 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'List repos'
         id: set-matrix
         run: |
@@ -40,7 +40,7 @@ jobs:
         repo: ${{ fromJson(needs.list.outputs.matrix) }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: "Setup python"
diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml
index fbd69802..a9130721 100644
--- a/.github/workflows/update.yml
+++ b/.github/workflows/update.yml
@@ -15,7 +15,7 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'List repos'
         id: set-matrix
         run: echo "matrix=$(find tools -mindepth 1 -maxdepth 1 -type d | jq -R -s -c 'split("\n")[:-1] | map(split("/")[-1])')" >> "${GITHUB_OUTPUT}"
@@ -29,7 +29,7 @@ jobs:
          repo: ${{ fromJson(needs.list.outputs.matrix) }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           token: ${{ secrets.USER_TOKEN }}
           ref: main

From 37d7be976c6f8b15b6d9dddc5301e8b8d7dca619 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 12 Sep 2023 00:51:08 +0000
Subject: [PATCH 47/61] doc(changelog): update

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 045b1184..f2e9c588 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.9](https://github.com/brsynth/galaxytools/tree/0.2.9) (2023-09-01)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.8...0.2.9)
+
 ## [0.2.8](https://github.com/brsynth/galaxytools/tree/0.2.8) (2023-08-28)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.7...0.2.8)

From 6d13d6409bb0b103a7cf2887c3fcf1d0fc2e5b39 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 19 Sep 2023 00:53:16 +0000
Subject: [PATCH 48/61] doc(changelog): update

---
 CHANGELOG.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f2e9c588..48a79273 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # Changelog
 
+## [0.2.10](https://github.com/brsynth/galaxytools/tree/0.2.10) (2023-09-05)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.9...0.2.10)
+
+**Merged pull requests:**
+
+- chore\(deps\): bump actions/checkout from 3 to 4 [\#140](https://github.com/brsynth/galaxytools/pull/140) ([dependabot[bot]](https://github.com/apps/dependabot))
+
 ## [0.2.9](https://github.com/brsynth/galaxytools/tree/0.2.9) (2023-09-01)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.8...0.2.9)

From 6a7b408e749f955fe3db8d35bd0281a5acbaa67c Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 26 Sep 2023 00:53:24 +0000
Subject: [PATCH 49/61] doc(changelog): update

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 48a79273..bfd21c90 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.11](https://github.com/brsynth/galaxytools/tree/0.2.11) (2023-09-12)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.10...0.2.11)
+
 ## [0.2.10](https://github.com/brsynth/galaxytools/tree/0.2.10) (2023-09-05)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.9...0.2.10)

From 1a86e55d9e8c539de5fe8110ba85a2489473bde4 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Tue, 26 Sep 2023 14:58:06 +0200
Subject: [PATCH 50/61] feat(tools): get_sbml_model, load file from history
 (#139)

---
 tools/get_sbml_model/get_sbml_model.xml | 44 +++++++++++++------------
 1 file changed, 23 insertions(+), 21 deletions(-)

diff --git a/tools/get_sbml_model/get_sbml_model.xml b/tools/get_sbml_model/get_sbml_model.xml
index 62c93b42..63e22322 100644
--- a/tools/get_sbml_model/get_sbml_model.xml
+++ b/tools/get_sbml_model/get_sbml_model.xml
@@ -1,4 +1,4 @@
-<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.4" profile="21.09" license="MIT">
+<tool id="get_sbml_model" name="Pick SBML Model" version="0.1.0" profile="21.09" license="MIT">
     <description>Get an SBML model (BiGG)</description>
     <requirements>
         <requirement type="package" version="7.81.0">curl</requirement>
@@ -10,23 +10,23 @@
     <command detect_errors="exit_code"><![CDATA[
         #if str($cond_src.from_src) == 'from_bigg'
             curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' &&
+        #else
+            python -m taxonid '${cond_src.hostname}' --output-file tmpfile &&
+            echo "#ID" > '$taxid' &&
+            cat tmpfile >> '$taxid' &&
         #end if
+        echo "listdir:";
+        ls;
         python '$__tool_directory__/'get_infos.py
             #if str($cond_src.from_src) == 'from_bigg'
                 '$model'
+                --taxid '$taxid'
             #else
                 '${cond_src.input_file}'
             #end if
             --hostid '${cond_src.hostid}'
             --comp '$compartments'
             --biomass '$biomass'
-        #if str($cond_src.from_src) == 'from_bigg'
-            --taxid '$taxid'
-        #else
-            python -m taxonid '${cond_src.hostid}' --output-file tmpfile
-            echo "#ID" > '$taxid'
-            cat tmpfile >> '$taxid'
-        #end if
     ]]></command>
     <inputs>
         <conditional name="cond_src">
@@ -35,9 +35,12 @@
                 <option value="from_history">Select file from the History</option>
             </param>
             <when value="from_history">
-                <param name="hostid" type="text" help="Fullname of the model">
+                <param name="hostname" type="text" help="Fullname of the model">
                     <validator type="empty_field" message="The fullname of the organism is required"/>
                 </param>
+                <param name="hostid" type="text" help="ID of the model">
+                    <validator type="empty_field" message="ID of the organism is required"/>
+                </param>
                 <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
             </when>
             <when value="from_bigg">
@@ -94,33 +97,32 @@
         </conditional>
     </inputs>
     <outputs>
-        <when value="from_bigg">
-            <data name="model" format="sbml" label="${cond_src.hostid}" />
-        </when>
+        <data name="model" format="sbml" label="${cond_src.hostid}">
+            <filter>cond_src['from_src'] == 'from_bigg'</filter>
+        </data>
         <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" />
         <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" />
         <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" />
     </outputs>
     <tests>
         <test>
-            <conditional name="cond_src">
-                <param name="from_src" value="from_bigg" />
-                <param name="hostid" value="iML1515" />
-            </conditional>
+            <param name="from_src" value="from_bigg" />
+            <param name="hostid" value="iML1515" />
             <output name="model" md5="9bf81d20cab5476700697ded95b716d1" />
-            <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
+            <output name="taxid" md5="7c62bd818057838b3557c8d87cca47fc" />
             <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />
             <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" />
         </test>
         <test>
             <conditional name="cond_src">
                 <param name="from_src" value="from_history" />
-                <param name="hostid" value="Escherichia coli str. K-12 substr. MG1655" />
+                <param name="hostname" value="Escherichia coli str. K-12 substr. MG1655" />
+                <param name="hostid" value="e_coli_core" />
                 <param name="input_file" value="e_coli_core.xml" />
             </conditional>
-            <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
-            <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />
-            <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" />
+            <output name="taxid" md5="ee08b511771328e6254775a51779d421" />
+            <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
+            <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />
             </test>
     </tests>
     <help><![CDATA[

From 57acb54b6dd02149517aebc4aead758947f5bd74 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Tue, 26 Sep 2023 18:33:11 +0200
Subject: [PATCH 51/61] fix(get_sbml_model.xml): rm weird commands

---
 tools/get_sbml_model/get_sbml_model.xml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tools/get_sbml_model/get_sbml_model.xml b/tools/get_sbml_model/get_sbml_model.xml
index 63e22322..dbb361e5 100644
--- a/tools/get_sbml_model/get_sbml_model.xml
+++ b/tools/get_sbml_model/get_sbml_model.xml
@@ -15,8 +15,6 @@
             echo "#ID" > '$taxid' &&
             cat tmpfile >> '$taxid' &&
         #end if
-        echo "listdir:";
-        ls;
         python '$__tool_directory__/'get_infos.py
             #if str($cond_src.from_src) == 'from_bigg'
                 '$model'

From 8c6b733ffe81b3dc4f9e7d8267c629e38a346372 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Tue, 26 Sep 2023 18:37:00 +0200
Subject: [PATCH 52/61] fix(get_sbml_model.xml): add --bigg

---
 tools/get_sbml_model/get_sbml_model.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/get_sbml_model/get_sbml_model.xml b/tools/get_sbml_model/get_sbml_model.xml
index dbb361e5..005c836f 100644
--- a/tools/get_sbml_model/get_sbml_model.xml
+++ b/tools/get_sbml_model/get_sbml_model.xml
@@ -18,6 +18,7 @@
         python '$__tool_directory__/'get_infos.py
             #if str($cond_src.from_src) == 'from_bigg'
                 '$model'
+                --bigg
                 --taxid '$taxid'
             #else
                 '${cond_src.input_file}'

From d7b02764aba67f8aa870f8114775dbc011a9cba6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Tue, 26 Sep 2023 22:30:37 +0200
Subject: [PATCH 53/61] feat: add --biomass-id arg + refactor

---
 tools/get_sbml_model/get_infos.py |    164 +-
 tools/get_sbml_model/model.sbml   | 169810 +++++++++++++++++++++++++++
 2 files changed, 169931 insertions(+), 43 deletions(-)
 create mode 100644 tools/get_sbml_model/model.sbml

diff --git a/tools/get_sbml_model/get_infos.py b/tools/get_sbml_model/get_infos.py
index 0eb113a9..70e0938d 100644
--- a/tools/get_sbml_model/get_infos.py
+++ b/tools/get_sbml_model/get_infos.py
@@ -5,7 +5,86 @@
 from requests import get as r_get
 
 
-def entry_point():
+def get_biomass_rxn(sbml_doc):
+    '''
+    Returns the biomass reaction of the model
+    
+    Parameters
+    ----------
+    sbml_doc: libsbml.SBMLDocument
+        SBML model
+        
+    Returns
+    -------
+    biomass_rxn: libsbml.Reaction
+        Biomass reaction
+    '''
+    reactions = sbml_doc.getModel().getListOfReactions()
+    # Search for 'biomass' keyword in reaction name
+    for rxn in reactions:
+        if 'biomass' in rxn.getName().lower():
+            return rxn
+    # Search for 'biomass' keyword in products
+    # AND not in reactants
+    for rxn in reactions:
+        in_reactants = False
+        for reac in rxn.getListOfReactants():
+            if 'biomass' in reac.getSpecies().lower():
+                in_reactants = True
+                break
+        if not in_reactants:
+            for prod in rxn.getListOfProducts():
+                if 'biomass' in prod.getSpecies().lower():
+                    return rxn
+    return None
+
+
+def get_taxon_id(hostid):
+    '''
+    Returns the taxonomy ID of the host organism
+    
+    Parameters
+    ----------
+    hostid: str
+        Extended name of the host organism
+        
+    Returns
+    -------
+    taxid: str
+        Taxonomy ID of the host organism
+    '''
+    taxid = get_taxon_id(hostid)
+    hostname = ''
+    # Extended Name
+    server = 'http://bigg.ucsd.edu/api/v2/models/'
+    ext = hostid
+    r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
+    if not r.ok:
+        print(f"Warning: unable to retrieve host name for id {hostid}")
+    else:
+        try:
+            hostname = r.json()["organism"]
+        except KeyError:
+            print(f"Warning: unable to retrieve host name for id {hostid}")
+    if not hostname:
+        taxid = ''
+    else:
+        # TAXON ID
+        server = 'https://rest.ensembl.org'
+        ext = f'/taxonomy/id/{hostname}?'
+        r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
+        if not r.ok:
+            print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
+        else:
+            try:
+                taxid = r.json()["id"]
+            except KeyError:
+                print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
+                taxid = ''
+    return taxid
+
+
+def args():
     parser = ArgumentParser('Returns cell informations')
     parser.add_argument(
         'infile',
@@ -28,6 +107,11 @@ def entry_point():
         type=str,
         help='Path to store biomass reaction ID'
     )
+    parser.add_argument(
+        '--biomass-id',
+        type=str,
+        help='ID of biomass reaction'
+    )
     parser.add_argument(
         '--hostid',
         type=str,
@@ -39,63 +123,57 @@ def entry_point():
         help='Path to store host taxonomy ID'
     )
     params = parser.parse_args()
+    return params
+
+
+def entry_point():
+
+    params = args()
 
     sbml_doc = readSBMLFromFile(params.infile)
 
+    compartments = sbml_doc.getModel().getListOfCompartments()
+    comp_str = ''
+    for comp in compartments:
+        comp_str += f'{comp.getId()}\t{comp.getName()}\n'
     if params.comp:
-        compartments = sbml_doc.getModel().getListOfCompartments()
         with open(params.comp, 'w') as f:
             f.write('#ID\tNAME\n')
-            for comp in compartments:
-                f.write(f'{comp.getId()}\t{comp.getName()}\n')
+            f.write(comp_str)
+    else:
+        print('Compartments:')
+        for comp in compartments:
+            print(f'{comp.getId()}\t{comp.getName()}'.replace('\n', ' | '))
 
+    if params.biomass_id:
+        biomass_rxn = sbml_doc.getModel().getReaction(params.biomass_id)
+    else:
+        biomass_rxn = get_biomass_rxn(sbml_doc)
+    if not biomass_rxn:
+        print('Warning: unable to retrieve biomass reaction')
+        biomass_id = ''
+    else:
+        biomass_id = biomass_rxn.getId()
     if params.biomass:
-        reactions = sbml_doc.getModel().getListOfReactions()
         with open(params.biomass, 'w') as f:
             f.write('#ID\n')
-            for rxn in reactions:
-                if 'biomass' in rxn.getId().lower():
-                    f.write(f'{rxn.getId()}\n')
+            f.write(f'{biomass_id}\n')
+    else:
+        print(f'Biomass reaction ID: {biomass_id}')
 
-    if params.taxid:
-        hostname = ''
-
-        # Model from BiGG
-        if params.bigg:
-            # Extended Name
-            server = 'http://bigg.ucsd.edu/api/v2/models/'
-            ext = params.hostid
-            r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
-            if not r.ok:
-                print(f"Warning: unable to retrieve host name for id {params.hostid}")
-            else:
-                try:
-                    hostname = r.json()["organism"]
-                except KeyError:
-                    print(f"Warning: unable to retrieve host name for id {params.hostid}")
-            if not hostname:
-                taxid = ''
-            else:
-                # TAXON ID
-                server = 'https://rest.ensembl.org'
-                ext = f'/taxonomy/id/{hostname}?'
-                r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
-                if not r.ok:
-                    print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
-                else:
-                    try:
-                        taxid = r.json()["id"]
-                    except KeyError:
-                        print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
-                        taxid = ''
-
-        # Model from user
-        else:
-            taxid = params.hostid
+    # Model from BiGG
+    if params.bigg:
+        taxid = get_taxon_id(params.hostid)
+    # Model from user
+    else:
+        taxid = params.hostid
 
+    if params.taxid:
         with open(params.taxid, 'w') as f:
             f.write('#ID\n')
             f.write(f'{taxid}\n')
+    else:
+        print(f'Taxonomy ID: {taxid}')
 
 
 if __name__ == "__main__":
diff --git a/tools/get_sbml_model/model.sbml b/tools/get_sbml_model/model.sbml
new file mode 100644
index 00000000..75655c7c
--- /dev/null
+++ b/tools/get_sbml_model/model.sbml
@@ -0,0 +1,169810 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1" sboTerm="SBO:0000624" fbc:required="false">
+  <model fbc:strict="true" id="iML1515">
+    <listOfUnitDefinitions>
+      <unitDefinition id="mmol_per_gDW_per_hr">
+        <listOfUnits>
+          <unit kind="mole" scale="-3" multiplier="1" exponent="1"/>
+          <unit kind="gram" scale="0" multiplier="1" exponent="-1"/>
+          <unit kind="second" scale="0" multiplier="3600" exponent="-1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <fbc:listOfObjectives fbc:activeObjective="obj">
+      <fbc:objective fbc:id="obj" fbc:type="maximize">
+        <fbc:listOfFluxObjectives>
+          <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ec_iML1515_core_75p37M" fbc:coefficient="1"/>
+        </fbc:listOfFluxObjectives>
+      </fbc:objective>
+    </fbc:listOfObjectives>
+    <listOfParameters>
+      <parameter value="-1000" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
+      <parameter value="1000" id="cobra_default_ub" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
+      <parameter value="0" id="cobra_0_bound" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
+      <parameter id="R_EX_glc__D_e_lower_bound" value="-10" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>
+      <parameter id="R_ATPM_lower_bound" value="6.86" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>
+    </listOfParameters>
+    <listOfCompartments>
+      <compartment id="c" name="cytosol" constant="true"/>
+      <compartment id="e" name="extracellular space" constant="true"/>
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+    </fbc:listOfGeneProducts>
+    <listOfReactions>
+      <reaction id="R_CYTDK2" fast="false" reversible="false" name="Cytidine kinase (GTP)" metaid="R_CYTDK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CYTDK2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYTDK2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CYTIDINEKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.48"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00517"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97042"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28165"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28164"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28162"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28163"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00369"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cytd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2066"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_XPPT" fast="false" reversible="false" name="Xanthine phosphoribosyltransferase" metaid="R_XPPT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_XPPT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XPPT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:XANPRIBOSYLTRAN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.22"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02142"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105243"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10800"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10803"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10802"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10801"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/194"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01544"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xan_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xmp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0238"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HXPRT" fast="false" reversible="false" name="Hypoxanthine phosphoribosyltransferase (Hypoxanthine)" metaid="R_HXPRT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_HXPRT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HXPRT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:HYPOXANPRIBOSYLTRAN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01132"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100752"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17976"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17974"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17973"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17975"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/81"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00836"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_hxan_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_imp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0238"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0125"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NDPK5" fast="false" reversible="true" name="Nucleoside-diphosphate kinase (ATP:dGDP)" metaid="R_NDPK5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NDPK5">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NDPK5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DGDPKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01857"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96118"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27692"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27690"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27691"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27693"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/183"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01353"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dgdp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dgtp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0474"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2518"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SHK3Dr" fast="false" reversible="true" name="Shikimate dehydrogenase" metaid="R_SHK3Dr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_SHK3Dr">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SHK3Dr"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SHIKIMATE-5-DEHYDROGENASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.25"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.282"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02413"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104378"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MTU-964842"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17739"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17738"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17737"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17740"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2351"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01740"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3dhsk_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_skm_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3281"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1692"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NDPK6" fast="false" reversible="true" name="Nucleoside-diphosphate kinase (ATP:dUDP)" metaid="R_NDPK6" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NDPK6">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NDPK6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DUDPKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02331"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101938"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28584"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28583"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28582"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28585"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/421"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01678"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dudp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dutp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0474"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2518"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NDPK8">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NDPK8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DADPKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01137"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101940"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27675"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27674"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27677"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27676"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00839"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_datp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0474"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2518"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHORTS" fast="false" reversible="true" name="Dihydroorotase" metaid="R_DHORTS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DHORTS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHORTS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DIHYDROOROT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.2.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01993"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97428"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-73571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-73571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-73571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-73571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-73571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-73571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-73571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-73571"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-73571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-73571"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-73571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24298"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24299"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24297"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/399"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01465"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dhor__S_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cbasp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1062"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_OMPDC" fast="false" reversible="false" name="Orotidine-5'-phosphate decarboxylase" metaid="R_OMPDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_OMPDC">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OMPDC"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:OROTPDECARB-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.23"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00965"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102190"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-73564"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-419461"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-73564"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-73564"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-73564"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-73564"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-73564"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-73564"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-73564"/>
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+          <speciesReference species="M_orot5p_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1281"/>
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+          <speciesReference species="M_uri_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_r1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ura_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3831"/>
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glu5sa_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0243"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0720"/>
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+          <speciesReference species="M_pyam5p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2551"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_2dr1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ura_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4384"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1662"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3614"/>
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+          <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3614"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11064"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3925"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2930"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3697"/>
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+          <speciesReference species="M_pydx5p_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0870"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29199"/>
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+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4468"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4467"/>
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+        </fbc:geneProductAssociation>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3770"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4467"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0072"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3642"/>
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+          <speciesReference species="M_s7p_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_s17bp_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3916"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27696"/>
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+        <listOfProducts>
+          <speciesReference species="M_3mop_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3771"/>
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+          <speciesReference species="M_pyr_c" stoichiometry="2" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_alac__S_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0078"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3671"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trp__L_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1261"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_skm5p_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3psme_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0908"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28754"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28751"/>
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+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2242"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2241"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3426"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3885"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3697"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRUVFORMLY-RXN"/>
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+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3952"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2579"/>
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+          <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_anth_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1263"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1264"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FRD2" fast="false" reversible="false" name="Fumarate reductase" metaid="R_FRD2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29216"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29215"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29218"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29217"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08527"/>
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+            </rdf:Description>
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+          <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4152"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4151"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4153"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4154"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FRD3" fast="false" reversible="false" name="Fumarate reductase" metaid="R_FRD3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99639"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08528"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dmmq8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4152"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4151"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4153"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4154"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ANPRT" fast="false" reversible="false" name="Anthranilate phosphoribosyltransferase" metaid="R_ANPRT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ANPRT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ANPRT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PRTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.18"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01073"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95842"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11771"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11770"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11768"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11769"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00791"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anth_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pran_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1263"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_POX" fast="false" reversible="false" name="Pyruvate oxidase" metaid="R_POX" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_POX">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103067"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29168"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29170"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29167"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29169"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09167"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0871"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CHORM" fast="false" reversible="false" name="Chorismate mutase" metaid="R_CHORM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CHORM">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHORM"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CHORISMATEMUT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.99.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01715"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96708"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13897"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13899"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13898"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13900"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1827"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01256"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_chor_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pphn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2599"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2600"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PTAr" fast="false" reversible="true" name="Phosphotransacetylase" metaid="R_PTAr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PTAr">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PTAr"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PHOSACETYLTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00230"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103319"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19521"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19523"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19522"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19524"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/72"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00173"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_actp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2297"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2458"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CHORS" fast="false" reversible="false" name="Chorismate synthase" metaid="R_CHORS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CHORS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHORS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CHORISMATE-SYNTHASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.3.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01714"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96709"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21020"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21023"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21022"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21021"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1826"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01255"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3psme_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_chor_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2329"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_IGPS" fast="false" reversible="false" name="Indole-3-glycerol-phosphate synthase" metaid="R_IGPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_IGPS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:IGPSYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.48"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03508"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100814"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23476"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23479"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23477"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23478"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02507"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2cpr5p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3ig3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1262"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACKr" fast="false" reversible="true" name="Acetate kinase" metaid="R_ACKr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ACKr">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACKr"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACETATEKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.2.15"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.2.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00315"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95269"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11355"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11353"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11352"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/71"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00225"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_actp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2296"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1849"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3115"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_cellb_e" fast="false" reversible="false" name="Cellobiose exchange" metaid="R_EX_cellb_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96760"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cellb_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_crn_e" fast="false" reversible="false" name="L-Carnitine exchange" metaid="R_EX_crn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34960"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34959"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34961"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09773"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09858"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_arg__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_arg__L_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-448"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95951"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32145"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32143"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32144"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32146"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7983"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08155"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_arg__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_asp__L_e" fast="false" reversible="false" name="L-Aspartate exchange" metaid="R_EX_asp__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_asp__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_asp__L_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-554"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96107"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10906"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08170"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13232"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_asp__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_pyr_e" fast="false" reversible="false" name="Pyruvate exchange" metaid="R_EX_pyr_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_pyr_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pyr_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-506"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-570"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103384"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12168"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10929"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09218"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pyr_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_succ_e" fast="false" reversible="false" name="Succinate exchange" metaid="R_EX_succ_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_succ_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_succ_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-552"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104619"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10952"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09271"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_succ_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_thymd_e" fast="false" reversible="false" name="Thymidine exchange" metaid="R_EX_thymd_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_thymd_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_thymd_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104821"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10916"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09299"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_thymd_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_rib__D_e" fast="false" reversible="false" name="D-Ribose exchange" metaid="R_EX_rib__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_rib__D_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_rib__D_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104036"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09228"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_rib__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_tyr__L_e" fast="false" reversible="false" name="L-Tyrosine exchange" metaid="R_EX_tyr__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_tyr__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_tyr__L_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-446"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105002"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13471"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09339"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10974"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tyr__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_cytd_e" fast="false" reversible="false" name="Cytidine exchange" metaid="R_EX_cytd_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_cytd_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cytd_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97043"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13338"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08290"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10997"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cytd_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_dcyt_e" fast="false" reversible="false" name="Deoxycytidine exchange" metaid="R_EX_dcyt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_dcyt_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dcyt_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08317"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11014"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dcyt_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_MOAT" fast="false" reversible="false" name="3-deoxy-D-manno-octulosonic acid transferase" metaid="R_MOAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MOAT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MOAT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:KDOTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.99.12"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04658"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28067"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28068"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28066"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28069"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03182"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ckdo_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipidA_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_kdolipid4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3633"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_fum_e" fast="false" reversible="false" name="Fumarate exchange" metaid="R_EX_fum_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_fum_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fum_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-553"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99715"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08544"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11013"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fum_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_sbt__D_e" fast="false" reversible="false" name="D-Sorbitol exchange" metaid="R_EX_sbt__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_sbt__D_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_sbt__D_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104288"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09243"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09662"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_sbt__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_glu__L_e" fast="false" reversible="false" name="L-Glutamate exchange" metaid="R_EX_glu__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_glu__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glu__L_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-234"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-232"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100301"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-212658"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-210439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12283"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08633"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09750"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13304"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13120"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10917"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glu__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_UDCPDPS" fast="false" reversible="false" name="Undecaprenyl diphosphate synthase" metaid="R_UDCPDPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_UDCPDPS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDCPDPS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9138"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.M1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.31"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105043"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12133"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_frdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ipdp_c" stoichiometry="8" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ppi_c" stoichiometry="8" constant="true"/>
+          <speciesReference species="M_udcpdp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0174"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ptrc_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103339"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09216"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13393"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ptrc_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EDA" fast="false" reversible="false" name="2-dehydro-3-deoxy-phosphogluconate aldolase" metaid="R_EDA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EDA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EDA"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:KDPGALDOL-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.14"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.55"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05605"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97897"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17092"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17091"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17089"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17090"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03884"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2ddg6p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1850"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_spmd_e" fast="false" reversible="false" name="Spermidine exchange" metaid="R_EX_spmd_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_spmd_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_spmd_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104495"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35040"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35039"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35042"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35041"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13767"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09266"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_spmd_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_thym_e" fast="false" reversible="false" name="Thymine exchange" metaid="R_EX_thym_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_thym_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_thym_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-524"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104853"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09309"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_thym_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_xtsn_e" fast="false" reversible="false" name="Xanthosine exchange" metaid="R_EX_xtsn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_xtsn_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_xtsn_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105247"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09382"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_xtsn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_NTPP1" fast="false" reversible="false" name="Nucleoside triphosphate pyrophosphorylase (dgtp)" metaid="R_NTPP1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTPP1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTPP1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-385"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.19"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01855"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102049"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28364"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28363"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28362"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28365"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/302"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01351"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dgtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dgmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0099"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2781"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_URIK1" fast="false" reversible="false" name="Uridine kinase  ATPUridine " metaid="R_URIK1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_URIK1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URIK1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:URIDINEKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.48"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00964"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105162"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16828"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16826"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16825"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16827"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/85"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00709"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uri_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2066"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_URIK2" fast="false" reversible="false" name="Uridine kinase (GTP:Uridine)" metaid="R_URIK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_URIK2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URIK2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:URKI-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.48"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00968"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105163"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27650"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27651"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27652"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27653"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00713"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uri_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2066"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTPP2" fast="false" reversible="false" name="Nucleoside triphosphate pyrophosphorylase (gtp)" metaid="R_NTPP2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTPP2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTPP2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14140"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00426"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29391"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29392"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29393"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29394"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/301"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00301"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0099"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2781"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PGL" fast="false" reversible="false" name="6-phosphogluconolactonase" metaid="R_PGL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PGL">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGL"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:6PGLUCONOLACT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.31"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02035"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102539"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-71296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12559"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12556"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12557"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12558"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/109"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01476"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_6pgl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_6pgc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0767"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTPTP1" fast="false" reversible="false" name="Nucleoside triphosphate tripolyhydrolase" metaid="R_NTPTP1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTPTP1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTPTP1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DGTPTRIPHYDRO-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.5.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01856"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102057"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15196"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15195"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15193"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15194"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/232"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01352"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dgtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dgsn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0160"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30559"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30560"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_gsn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0160"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_cytd_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2066"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RIBULP3EPIM-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01116"/>
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+          <speciesReference species="M_ru5p__D_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3386"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03084"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97449"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21098"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02213"/>
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+          <speciesReference species="M_3dhq_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3dhsk_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1693"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.85"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04426"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100878"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10894"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10893"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10895"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10892"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03062"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_3c2hmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3c4mop_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0073"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1800"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95645"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13195"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13193"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05115"/>
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+          <speciesReference species="M_5aizc_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_5caiz_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0523"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17054"/>
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+          <speciesReference species="M_s7p_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0008"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2464"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfProducts>
+          <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_r1p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4384"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01859"/>
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+        <listOfProducts>
+          <speciesReference species="M_2dr1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4384"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PUNP3" fast="false" reversible="true" name="Purine-nucleoside phosphorylase (Guanosine)" metaid="R_PUNP3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13234"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13235"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gua_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_r1p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2407"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4384"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ADSL2r" fast="false" reversible="true" name="Adenylosuccinate lyase" metaid="R_ADSL2r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-73800"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23923"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23922"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23921"/>
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+          <speciesReference species="M_25aics_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_aicar_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1131"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TKT1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.2.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104868"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_s7p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2935"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2465"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28487"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28489"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08475"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13286"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10963"/>
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+          <speciesReference species="M_fe2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27648"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27646"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/125"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01358"/>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ins_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_hxan_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_r1p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2407"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4384"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.4"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27750"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27751"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27753"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27752"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01985"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_din_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dr1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hxan_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4384"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2407"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_xtsn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_r1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xan_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2407"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00552"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0678"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104060"/>
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+          <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2582"/>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2234"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2235"/>
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+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3781"/>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2234"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2235"/>
+              </fbc:and>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1478"/>
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+          <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/>
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+                <fbc:geneProductRef fbc:geneProduct="G_b2235"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2582"/>
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+                <fbc:geneProductRef fbc:geneProduct="G_b2234"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2235"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn06075"/>
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+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dudp_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/>
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+                <fbc:geneProductRef fbc:geneProduct="G_b2235"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2582"/>
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+        <listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3011"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3003"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0493"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4269"/>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_dtmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1238"/>
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+        <listOfProducts>
+          <speciesReference species="M_36dahx_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4146"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-196840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-196840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-196840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-196840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-196840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-196840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-196840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-196840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16793"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16796"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16794"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16795"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/3090"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02341"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_4ppcys_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pan4p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3639"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FTHFD" fast="false" reversible="false" name="Formyltetrahydrofolate deformylase" metaid="R_FTHFD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FTHFD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00944"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99669"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19833"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19835"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19834"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19836"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1259"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1232"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_glc__D_e" fast="false" reversible="true" name="D-Glucose exchange" metaid="R_EX_glc__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="R_EX_glc__D_e_lower_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_glc__D_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-574"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100188"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7002"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/601"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09679"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08617"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glc__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_DHAD1" fast="false" reversible="false" name="Dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylbutanoate)" metaid="R_DHAD1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DHAD1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHAD1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DIHYDROXYISOVALDEHYDRAT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04441"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97358"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24810"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24811"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24809"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24812"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_23dhmb_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3mob_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3771"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_IPPMIa" fast="false" reversible="true" name="3-isopropylmalate dehydratase" metaid="R_IPPMIa" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_IPPMIa">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/IPPMIa"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-8991"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.33"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04001"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100827"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10679"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10677"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10678"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10676"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/3736"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02811"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3c2hmp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2ippm_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0071"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0072"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_alltn_e" fast="false" reversible="false" name="Allantoin exchange" metaid="R_EX_alltn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_alltn_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_alltn_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-557"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95771"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08117"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09698"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_alltn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_G3PD7" fast="false" reversible="false" name="Glycerol-3-phosphate dehydrogenase (demethylmenaquinone-8)" metaid="R_G3PD7" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_G3PD7">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PD7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.99.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99882"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08558"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2dmmq8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2243"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2242"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2241"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EDD" fast="false" reversible="false" name="6-phosphogluconate dehydratase" metaid="R_EDD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EDD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EDD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PGLUCONDEHYDRAT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.12"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02036"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97898"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17280"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17278"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17277"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17279"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01477"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_6pgc_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2ddg6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1851"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_ura_e" fast="false" reversible="false" name="Uracil exchange" metaid="R_EX_ura_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_ura_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ura_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-560"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105147"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27320"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28622"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27319"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27318"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10993"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09366"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ura_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_NADH9" fast="false" reversible="false" name="NADH dehydrogenase (demethylmenaquinone-8 &amp; 0 protons)" metaid="R_NADH9" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NADH9">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADH9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101876"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30509"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30510"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30508"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30507"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08976"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2dmmq8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1109"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1004"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0046"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3713"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_val__L_e" fast="false" reversible="false" name="L-Valine exchange" metaid="R_EX_val__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_val__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_val__L_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-269"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105190"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29706"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29703"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29705"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29704"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13468"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05245"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09375"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_val__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_NADH10" fast="false" reversible="false" name="NADH dehydrogenase (menaquinone-8 &amp; 0 protons)" metaid="R_NADH10" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NADH10">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADH10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101863"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29243"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29246"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29244"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29245"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08971"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:NADPYROPHOSPHAT-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11802"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11800"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11801"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11803"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/684"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00076"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05823"/>
+                </rdf:Bag>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nmn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3996"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2411"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_arab__L_e" fast="false" reversible="false" name="L-Arabinose exchange" metaid="R_EX_arab__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95913"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_arab__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_fru_e" fast="false" reversible="false" name="D-Fructose exchange" metaid="R_EX_fru_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99663"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-189222"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12996"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08537"/>
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+          <speciesReference species="M_fru_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THREODEHYD-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.103"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01465"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103402"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6798667"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13161"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13164"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13163"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13162"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1641"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01068"/>
+                </rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thr__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2aobut_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3616"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3589"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HEX4" fast="false" reversible="false" name="Hexokinase (D-mannose:ATP)" metaid="R_HEX4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MANNKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.1"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95795"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11028"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11030"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11029"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/575"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00975"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_man_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_man6p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34917"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34916"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34915"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7001"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10911"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08585"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_gal_e" stoichiometry="1" constant="true"/>
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+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2.7.7.1-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00137"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95841"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-8939959"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-8939959"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-8939959"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-8939959"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-8939959"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-8939959"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-8939959"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-8939959"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21362"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21360"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21363"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/706"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00105"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nmn_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4390"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0639"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105270"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09650"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_xyl__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97523"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22070"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22069"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22071"/>
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+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_alac__S_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3774"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02484"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4ampm_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2103"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2418"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00013"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100303"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10138"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10139"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10137"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10136"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00010"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glx_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2h3oppan_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0507"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ICHORS_copy2" fast="false" reversible="true" name="Isochorismate synthase" metaid="R_ICHORS_copy2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ICHORS_copy2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ICHORS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ISOCHORSYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.4.2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01717"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100784"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18986"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18985"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18988"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1829"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01258"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_chor_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ichor_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2265"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SUCBZS" fast="false" reversible="false" name="O-succinylbenzoate-CoA synthase" metaid="R_SUCBZS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_SUCBZS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SUCBZS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:O-SUCCINYLBENZOATE-COA-SYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.113"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR108605"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10196"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10199"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10198"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10197"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/3766"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02832"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2shchc_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sucbz_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2261"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHBD" fast="false" reversible="true" name="2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase" metaid="R_DHBD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DHBD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHBD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DHBDEHYD-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.28"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01505"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97368"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23826"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23827"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23825"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23824"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01094"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_23ddhb_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_23dhb_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0596"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ICHORT" fast="false" reversible="false" name="Isochorismatase" metaid="R_ICHORT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ICHORT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ICHORT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ISOCHORMAT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.3.2.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03037"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100785"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11112"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11115"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11114"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11113"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2886"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02177"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ichor_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_23ddhb_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0595"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_ser__L_e" fast="false" reversible="false" name="L-Serine exchange" metaid="R_EX_ser__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_ser__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-8932980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35033"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35034"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35032"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13463"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13973"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09248"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10999"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13110"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ser__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_thm_e" fast="false" reversible="false" name="Thiamin exchange" metaid="R_EX_thm_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_thm_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_thm_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR131128"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12167"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11006"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09300"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_thm_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_trp__L_e" fast="false" reversible="false" name="L-Tryptophan exchange" metaid="R_EX_trp__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_trp__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_trp__L_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-449"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104949"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/14017"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13425"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09327"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05222"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_trp__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_GLUTRR" fast="false" reversible="false" name="Glutamyl-tRNA reductase" metaid="R_GLUTRR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLUTRR">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLUTRR"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.70"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04109"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100294"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/9145"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn06591"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glutrna_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glu1sa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trnaglu_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1210"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLCS1" fast="false" reversible="false" name="Glycogen synthase (ADPGlc)" metaid="R_GLCS1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLCS1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCS1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.21"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100223"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13643"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_adpglc_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glycogen_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3429"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLCP" fast="false" reversible="false" name="Glycogen phosphorylase" metaid="R_GLCP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLCP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCP"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100214"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13299"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glycogen_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3428"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3417"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_din_e" fast="false" reversible="false" name="Deoxyinosine exchange" metaid="R_EX_din_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_din_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_din_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97466"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08344"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_din_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5116"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.16"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103433"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22075"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22072"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22074"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22073"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01763"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rbl__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ru5p__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0063"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_RBP4E" fast="false" reversible="true" name="L-ribulose-phosphate 4-epimerase" metaid="R_RBP4E" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RIBULPEPIM-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05850"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103434"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22370"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22371"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22368"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22369"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/67"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04082"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ru5p__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0061"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4198"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3583"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TARTD" fast="false" reversible="false" name="L(+)-tartrate dehydratase" metaid="R_TARTD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_TARTD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TARTD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:LTARTDEHYDRA-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.32"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00339"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104718"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15413"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15414"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00245"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tartr__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3062"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3061"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD2" fast="false" reversible="false" name="5'-nucleotidase (UMP)" metaid="R_NTD2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_NTD2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14025"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00963"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102032"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29362"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29360"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29359"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/210"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00708"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uri_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2744"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4374"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0675"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLCRAL" fast="false" reversible="false" name="5-dehydro-4-deoxyglucarate aldolase" metaid="R_GLCRAL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLCRAL">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCRAL"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:KDGALDOL-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.20"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02754"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100219"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27727"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27726"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27728"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27729"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01990"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_5dh4dglc_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2h3oppan_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3126"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD4" fast="false" reversible="false" name="5'-nucleotidase (CMP)" metaid="R_NTD4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD4">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14026"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00511"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102034"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29370"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29368"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29369"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29367"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/211"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00363"/>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cytd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2744"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0675"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD5" fast="false" reversible="false" name="5'-nucleotidase (dTMP)" metaid="R_NTD5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD5">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THYMIDYLATE-5-PHOSPHATASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.35"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.89"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01569"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102035"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11081"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11083"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11082"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11080"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/479"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01145"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dtmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thymd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2744"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4374"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2291"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2361"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_fmn_e" fast="false" reversible="false" name="FMN exchange" metaid="R_EX_fmn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_fmn_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fmn_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-595"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR124060"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fmn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_gthox_e" fast="false" reversible="false" name="Oxidized glutathione exchange" metaid="R_EX_gthox_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_gthox_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gthox_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100443"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09677"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08674"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_gthox_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_KAS14" fast="false" reversible="false" name="Beta-ketoacyl-ACP synthase" metaid="R_KAS14" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3-OXOACYL-ACP-SYNTH-BASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.180"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.85"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.86"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.41"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04355"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100912"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05347"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_actACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2323"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1095"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HEMEOS" fast="false" reversible="false" name="Heme O synthase" metaid="R_HEMEOS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_HEMEOS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07411"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100596"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-2995330"/>
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+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23449"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23448"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23451"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23450"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_kdo_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ckdo_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0918"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ECOAH3" fast="false" reversible="true" name="3-hydroxyacyl-CoA dehydratase (3-hydroxyoctanoyl-CoA)" metaid="R_ECOAH3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ECOAH3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ECOAH3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.17"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.74"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04746"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97888"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-77333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31202"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31200"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31199"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/4402"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03247"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3hocoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oc2coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2341"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3846"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UGLT" fast="false" reversible="true" name="UDPglucose--hexose-1-phosphate uridylyltransferase" metaid="R_UGLT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_UGLT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UGLT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GALACTURIDYLYLTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.12"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00955"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143436"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-70361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13989"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13991"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13992"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13990"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/8526"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00701"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gal1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpgal_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0758"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EDTXS1" fast="false" reversible="false" name="Endotoxin Synthesis (lauroyl transferase)" metaid="R_EDTXS1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EDTXS1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EDTXS1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.241"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97899"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ddcaACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_kdo2lipid4_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_kdo2lipid4L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1054"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DXPS" fast="false" reversible="false" name="1-deoxy-D-xylulose 5-phosphate synthase" metaid="R_DXPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DXPS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DXPS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DXS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.2.1.7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05636"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97831"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12605"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12607"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12608"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03909"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dxyl5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0420"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_OAADC" fast="false" reversible="false" name="Oxaloacetate decarboxylase" metaid="R_OAADC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_OAADC">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OAADC"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:OXALODECARB-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.38"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.40"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00217"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102097"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15641"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15642"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15643"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15644"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/149"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00162"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1850"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MNNH" fast="false" reversible="false" name="D-mannonate hydrolyase" metaid="R_MNNH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MNNH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MNNH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MANNONDEHYDRAT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138624"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20098"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20097"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20100"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20099"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03885"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mana_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2ddglcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4322"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CDPMEK" fast="false" reversible="false" name="4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase" metaid="R_CDPMEK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CDPMEK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDPMEK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2.7.1.148-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.148"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05634"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96558"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18437"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18440"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18438"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03908"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_4c2me_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2p4c2me_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1208"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EDTXS2" fast="false" reversible="false" name="Endotoxin Synthesis (myristoyl transferase)" metaid="R_EDTXS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EDTXS2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EDTXS2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.243"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97901"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_kdo2lipid4L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1855"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALTRH" fast="false" reversible="false" name="Altronate hydrolase" metaid="R_ALTRH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ALTRH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALTRH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ALTRODEHYDRAT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01540"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138045"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15959"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15960"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15957"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15958"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1704"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01122"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_altrn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2ddglcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3091"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MECDPS" fast="false" reversible="false" name="2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase" metaid="R_MECDPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MECDPS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-302"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.6.1.12"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05637"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101424"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23864"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23866"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23865"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03910"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2p4c2me_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2mecdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2746"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GUI1" fast="false" reversible="true" name="Glucuronate isomerase (D-glucuronate)" metaid="R_GUI1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GUI1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.12"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01482"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100468"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13051"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13050"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13049"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01080"/>
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+          <speciesReference species="M_glcur_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fruur_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3092"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EDTXS3" fast="false" reversible="false" name="Endotoxin Synthesis (palmitoleoyl ACP)" metaid="R_EDTXS3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EDTXS3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EDTXS3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97903"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_kdo2lipid4_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_kdo2lipid4p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2378"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PGAMT" fast="false" reversible="true" name="Phosphoglucosamine mutase" metaid="R_PGAMT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PGAMT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGAMT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:5.4.2.10-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.2.10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02060"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102526"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23427"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23425"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23426"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23424"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2077"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01485"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gam1p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gam6p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3176"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DDGLK" fast="false" reversible="false" name="2-dehydro-3-deoxygluconokinase" metaid="R_DDGLK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DDGLK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DDGLK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DEOXYGLUCONOKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.45"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.178"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01541"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138209"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14799"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14797"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14798"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14800"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01123"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2ddglcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2ddg6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3526"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EDTXS4" fast="false" reversible="false" name="Endotoxin Synthesis (myristoyl transferase)" metaid="R_EDTXS4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EDTXS4">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97904"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_kdo2lipid4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_cold_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1855"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_XYLI2" fast="false" reversible="true" name="Xylose isomerase" metaid="R_XYLI2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_XYLI2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XYLI2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUCISOM-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00307"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105254"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28546"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28547"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28549"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28548"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/800"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00223"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fru_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3565"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PMANM" fast="false" reversible="true" name="Phosphomannomutase" metaid="R_PMANM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PMANM">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PHOSMANMUT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.2.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01818"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101729"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-446201"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-446201"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-446201"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-446201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11141"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11143"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11142"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11140"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/69"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01329"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_man1p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_man6p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2048"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ICL" fast="false" reversible="false" name="Isocitrate lyase" metaid="R_ICL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ICL">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.3.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00479"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100789"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13248"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13245"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13246"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13247"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/911"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00336"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_icit_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glx_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4015"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UAGDP" fast="false" reversible="false" name="UDP-N-acetylglucosamine diphosphorylase" metaid="R_UAGDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_UAGDP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105033"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-446204"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-446204"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-446204"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-446204"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-446204"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-446204"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-446204"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-446204"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/870"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00293"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acgam1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uacgam_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3730"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UAGCVT" fast="false" reversible="false" name="UDP-N-acetylglucosamine 1-carboxyvinyltransferase" metaid="R_UAGCVT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_UAGCVT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UAGCVT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UDPNACETYLGLUCOSAMENOLPYRTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00660"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105032"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18681"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18684"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00461"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uacgam_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uaccg_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3189"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLUR" fast="false" reversible="true" name="Glutamate racemase" metaid="R_GLUR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLUR">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLUR"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUTRACE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.1.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00260"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100288"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12813"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12814"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12815"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12816"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/765"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00193"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glu__D_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3967"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_tmao_e" fast="false" reversible="false" name="Trimethylamine N-oxide exchange" metaid="R_EX_tmao_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_tmao_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_tmao_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104882"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09317"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tmao_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_UAG2E" fast="false" reversible="true" name="UDP-N-acetylglucosamine 2-epimerase" metaid="R_UAG2E" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_UAG2E">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UAG2E"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UDPGLCNACEPIM-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.14"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00420"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR141025"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17214"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17215"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17216"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00297"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_uacgam_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_uacmam_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3786"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_acald_e" fast="false" reversible="false" name="Acetaldehyde exchange" metaid="R_EX_acald_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_acald_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_acald_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-449872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09700"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08033"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08032"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acald_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_GLYCL" fast="false" reversible="false" name="Glycine Cleavage System" metaid="R_GLYCL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLYCL">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYCL"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.4.2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.1.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.2.10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01221"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100330"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27760"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27759"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27761"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27758"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2904"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2903"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0116"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2905"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CMPN" fast="false" reversible="false" name="CMP nucleosidase" metaid="R_CMPN" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CMPN">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CMPN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96804"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_csn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_NNDPR" fast="false" reversible="false" name="Nicotinate-nucleotide diphosphorylase (carboxylating)" metaid="R_NNDPR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NNDPR">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NNDPR"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:QUINOPRIBOTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.19"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03348"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-197268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12735"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12733"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12734"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12736"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/3155"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02402"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_quln_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nicrnt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0109"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HCYSMT" fast="false" reversible="false" name="Homocysteine S-methyltransferase" metaid="R_HCYSMT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_HCYSMT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HCYSMT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:HOMOCYSTEINE-S-METHYLTRANSFERASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00650"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100577"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21820"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21823"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21821"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21822"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1035"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00452"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0261"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_melib_e" fast="false" reversible="false" name="Melibiose exchange" metaid="R_EX_melib_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_melib_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_melib_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138589"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_melib_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_MACPD" fast="false" reversible="false" name="Malonyl-ACP decarboxylase" metaid="R_MACPD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MACPD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MACPD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALONYL-ACPDECARBOX-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.87"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09482"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101327"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08861"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2323"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DMQMT" fast="false" reversible="false" name="3-Dimethylubiquinonol 3-methyltransferase" metaid="R_DMQMT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DMQMT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DMQMT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DHHB-METHYLTRANSFER-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.64"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28680"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28679"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28681"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08353"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2omhmbl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2232"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UDPG4E" fast="false" reversible="true" name="UDPglucose 4-epimerase" metaid="R_UDPG4E" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00291"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-70369"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-70369"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-70369"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22170"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22168"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22169"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22171"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/8974"/>
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+          <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_udpgal_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0759"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_LACZ" fast="false" reversible="false" name="B-galactosidase" metaid="R_LACZ" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.23"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.108"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01100"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101000"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10077"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10078"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10076"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10079"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11244"/>
+                </rdf:Bag>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lcts_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gal_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0344"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRE6PHYDRO-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.122"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06113"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00837"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104925"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23009"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23010"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23008"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23011"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1178"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00606"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tre6p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4239"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_XYLI1" fast="false" reversible="true" name="Xylose isomerase" metaid="R_XYLI1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_XYLI1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XYLI1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:XYLISOM-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01432"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105253"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22818"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22816"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22819"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22817"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01044"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_xyl__D_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_xylu__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3565"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PPC" fast="false" reversible="false" name="Phosphoenolpyruvate carboxylase" metaid="R_PPC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PPC">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.31"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23072"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23075"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23074"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/150"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00251"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3956"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ICHORS_copy1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ICHORS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ISOCHORSYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.4.2"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100784"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18985"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18988"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1829"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01258"/>
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+        <listOfReactants>
+          <speciesReference species="M_chor_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ichor_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0593"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09275"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+            </rdf:Description>
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+          <speciesReference species="M_btal_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_but_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0615"/>
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+          <speciesReference species="M_pydx5p_c" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.40"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104798"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22949"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22950"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22951"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22948"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1339"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00787"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tagdp__D_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3132"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3137"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2095"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2096"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MANAO" fast="false" reversible="true" name="Mannonate oxidoreductase" metaid="R_MANAO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MANNONOXIDOREDUCT-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02454"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15729"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15732"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15731"/>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fruur_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4323"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TAGURr" fast="false" reversible="true" name="Tagaturonate reductase" metaid="R_TAGURr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ALTRO-OXIDOREDUCT-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17814"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17813"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17815"/>
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+          <speciesReference species="M_altrn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tagur_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1521"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DMSOR1" fast="false" reversible="false" name="Dimethyl sulfoxide reductase (Menaquinol 8)" metaid="R_DMSOR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97529"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29206"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29203"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29204"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29205"/>
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+          <speciesReference species="M_dmso_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dms_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1589"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1590"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1588"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1587"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0895"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0896"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0894"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GPH-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14371"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14370"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14372"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyclt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3385"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_2DGULRx" fast="false" reversible="false" name="2-dehydro-L-gulonate reductase (NADH)" metaid="R_2DGULRx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94787"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07969"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_2dhguln_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_idon__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3553"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DKGLCNR2y" fast="false" reversible="false" name="2,5-diketo-D-gluconate reductase (NADPH)" metaid="R_DKGLCNR2y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:YIAE1-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27635"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27634"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27636"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08347"/>
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+          <speciesReference species="M_25dkglcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_5dglcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3553"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_G1PTT" fast="false" reversible="false" name="Glucose-1-phosphate thymidylyltransferase" metaid="R_G1PTT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.24"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02328"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15226"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15227"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15225"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15228"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2281"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01675"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_dttp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dtdpglu_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2039"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3789"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TDPGDH" fast="false" reversible="false" name="DTDPglucose 4,6-dehydratase" metaid="R_TDPGDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17221"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17224"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01997"/>
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+          <speciesReference species="M_dtdpglu_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dtdp4d6dg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3788"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2041"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95440"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11674"/>
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+          <speciesReference species="M_chor_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4adcho_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1812"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3360"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_4abz_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4039"/>
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_idon__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3553"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18382"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18381"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18384"/>
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+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1200"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1198"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1199"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_EX_lac__D_e" fast="false" reversible="false" name="D-lactate exchange" metaid="R_EX_lac__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24132"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24133"/>
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+          <speciesReference species="M_udpgal_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_udpgalfur_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2036"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfProducts>
+          <speciesReference species="M_dtdp4d6dm_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2038"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21799"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dtdprmn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2040"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0910"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0171"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rdmbzi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0638"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4477"/>
+        </fbc:geneProductAssociation>
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+        </sbml:annotation>
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+          <speciesReference species="M_duri_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dump_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1238"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29225"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29224"/>
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+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2242"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2241"/>
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+        </fbc:geneProductAssociation>
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+        <listOfProducts>
+          <speciesReference species="M_alltt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0512"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12250"/>
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uaccg_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uamr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3972"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13019"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13020"/>
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+          <speciesReference species="M_ura_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2498"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27716"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27717"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27714"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3399"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2361"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0675"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2361"/>
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+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2744"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2361"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3399"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0675"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_ugmda_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_uagmda_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0087"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_uagmda_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uaagmda_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0090"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_NDPK7" fast="false" reversible="true" name="Nucleoside-diphosphate kinase (ATP:dCDP)" metaid="R_NDPK7" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101939"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27681"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27679"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01673"/>
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+          <speciesReference species="M_dcdp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dctp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0474"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2518"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THREOSPON-RXN"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_aact_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_GLYAT" fast="false" reversible="true" name="Glycine C-acetyltransferase" metaid="R_GLYAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+          <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2aobut_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3617"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rib__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0030"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_gmhep17bp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_gmhep1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0200"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfProducts>
+          <speciesReference species="M_gmhep7p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0222"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_indole_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1261"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dha_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0825"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3946"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AGMHE" fast="false" reversible="false" name="ADP-D-glycero-D-manno-heptose epimerase" metaid="R_AGMHE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AGMHE">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:5.1.3.20-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.20"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05176"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95551"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17579"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17578"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17577"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17580"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03511"/>
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+          </rdf:RDF>
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+          <speciesReference species="M_adphep_DD_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adphep_LD_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3619"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CRNBTCT" fast="false" reversible="true" name="Gamma-butyrobetainyl-CoA: carnitine CoA transferase" metaid="R_CRNBTCT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10644"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96894"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28420"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28418"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28421"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28419"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_bbtcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_crncoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gbbtn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0038"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CRNCBCT" fast="false" reversible="true" name="Crotonobetainyl-CoA: carnitine CoA transferase" metaid="R_CRNCBCT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CRNCBCT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNCBCT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14936"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.8.3.21"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10643"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96899"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28527"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28529"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28528"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28526"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ctbtcoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_crncoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ctbt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0038"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD10" fast="false" reversible="false" name="5'-nucleotidase (XMP)" metaid="R_NTD10" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD10">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:XMPXAN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02719"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102029"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28532"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28530"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28531"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28533"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/129"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01961"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xmp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xtsn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2744"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CRNCDH" fast="false" reversible="true" name="Carnityl-CoA dehydratse" metaid="R_CRNCDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CRNCDH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNCDH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CARNDETRU-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.149"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10675"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96900"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28339"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28341"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28338"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_crncoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ctbtcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0036"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GMHEPAT" fast="false" reversible="false" name="D-glycero-D-manno-hepose 1-phosphate adenyltransferase" metaid="R_GMHEPAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GMHEPAT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GMHEPAT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-4342"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.70"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05644"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100378"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27468"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27466"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27467"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27465"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13940"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03916"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gmhep1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adphep_DD_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3052"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_h2s_e" fast="false" reversible="false" name="Hydrogen sulfide exchange" metaid="R_EX_h2s_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_h2s_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_h2s_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-310"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100494"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08690"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08689"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10541"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2s_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ADPT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADPT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ADENPRIBOSYLTRAN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00190"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95482"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-74213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16610"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16612"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16611"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16609"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/80"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00139"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0469"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_gthrd_e" fast="false" reversible="false" name="Reduced glutathione exchange" metaid="R_EX_gthrd_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_gthrd_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gthrd_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100449"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-1247915"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-1500817"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08677"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10829"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gthrd_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_IDOND" fast="false" reversible="true" name="L-idonate 5-dehydrogenase" metaid="R_IDOND" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/IDOND"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12107"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100801"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21175"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21173"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21174"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21172"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/5279"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03953"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_5dglcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_idon__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4267"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21179"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21177"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_idon__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4267"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.45"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30150"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30149"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30147"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30148"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08458"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3844"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_GTPDPK" fast="false" reversible="false" name="GTP diphosphokinase" metaid="R_GTPDPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GTPPYPHOSKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.6.5"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22091"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22089"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22088"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22090"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/236"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00303"/>
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+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gdptp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2784"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_NADN" fast="false" reversible="false" name="NAD nucleosidase" metaid="R_NADN" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:NADNUCLEOSID-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-13859"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.-"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-8870346"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-8938076"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16302"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn14307"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adprib_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ncam_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLYCLTDx">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18229"/>
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glyclt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3553"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1033"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ADK1" fast="false" reversible="true" name="Adenylate kinase" metaid="R_ADK1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ADK1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ADENYL-KIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00127"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95450"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-110145"/>
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+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0474"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00117"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0474"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2518"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NDPK3" fast="false" reversible="true" name="Nucleoside-diphosphate kinase (ATP:CDP)" metaid="R_NDPK3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_NDPK3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NDPK3"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25240"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25239"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25237"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25238"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00409"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cdp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2518"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0474"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HPYRRy" fast="false" reversible="false" name="Hydroxypyruvate reductase (NADPH)" metaid="R_HPYRRy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.81"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100336"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18660"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18659"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18657"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18658"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/427"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01013"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_hpyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc__R_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1033"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3553"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NDPK4" fast="false" reversible="true" name="Nucleoside-diphosphate kinase (ATP:dTDP)" metaid="R_NDPK4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DTDPKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02093"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101937"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27684"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27685"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/423"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01512"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dtdp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dttp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0474"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2518"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACODA" fast="false" reversible="false" name="Acetylornithine deacetylase" metaid="R_ACODA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACETYLORNDEACET-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.16"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.14"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95377"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15941"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15942"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15944"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15943"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1049"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00469"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_acorn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3957"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ADA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ADENODEAMIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01560"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-5693346"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24411"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24408"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/134"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01137"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ins_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1623"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ADDALT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02556"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97076"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28193"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28190"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28192"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28191"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/281"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01858"/>
+                </rdf:Bag>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dad_2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_din_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1623"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ADD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01244"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95443"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23690"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23689"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23688"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23691"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00926"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_hxan_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3665"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FCLT" fast="false" reversible="false" name="Ferrochelatase" metaid="R_FCLT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FCLT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PROTOHEMEFERROCHELAT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.99.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00310"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99471"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22585"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22586"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22584"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22587"/>
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+            </rdf:Description>
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+          <speciesReference species="M_fe2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppp9_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pheme_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0475"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2431"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1019"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HBZOPT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:4OHBENZOATE-OCTAPRENYLTRANSFER-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.39"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05615"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100566"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27785"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27782"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03893"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_4hbz_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_octdp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3ophb_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4040"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PNTK" fast="false" reversible="false" name="Pantothenate kinase" metaid="R_PNTK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PNTK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PANTOTHENATE-KIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.33"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03018"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103050"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-199203"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11374"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_asn__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0674"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20016"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20013"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b4245"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4245"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14053"/>
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+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1215"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1092"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0029"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sucarg_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1747"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11122"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11120"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11121"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08277"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cynt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_hco3_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0340"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DAPE" fast="false" reversible="true" name="Diaminopimelate epimerase" metaid="R_DAPE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAPE"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DIAMINOPIMEPIM-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.1.7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02735"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97143"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15396"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15395"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15393"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15394"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01974"/>
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+            </rdf:Description>
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+          <speciesReference species="M_26dap_LL_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_26dap__M_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3809"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHDPRy" fast="false" reversible="false" name="Dihydrodipicolinate reductase (NADPH)" metaid="R_DHDPRy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.1.26"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR134418"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02929"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_23dhdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thdp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0031"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_acnam_e" fast="false" reversible="false" name="N-Acetylneuraminate exchange" metaid="R_EX_acnam_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_acnam_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_acnam_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-15315"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95292"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28994"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28993"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28992"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28991"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08051"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_acnam_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_HSK" fast="false" reversible="false" name="Homoserine kinase" metaid="R_HSK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HSK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:HOMOSERKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.39"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01771"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100737"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13985"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13986"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13988"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1866"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01300"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hom__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_phom_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0003"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_SDPTA" fast="false" reversible="true" name="Succinyldiaminopimelate transaminase" metaid="R_SDPTA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_SDPTA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SUCCINYLDIAMINOPIMTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.17"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04475"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104301"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11960"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11961"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11963"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11962"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03087"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sl26da_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sl2a6o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3359"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1302"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1748"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2662"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0907"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GSPMDA" fast="false" reversible="false" name="Glutathionylspermidine amidase" metaid="R_GSPMDA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GSPAMID-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01918"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100437"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17175"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17173"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17174"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17176"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1972"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01404"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2988"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GSPMDS" fast="false" reversible="false" name="Glutathionylspermidine synthetase" metaid="R_GSPMDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GSPMDS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GSPSYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.1.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.1.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01917"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100438"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21272"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21273"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21274"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21275"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1971"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01403"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gtspmd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2988"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GUAD" fast="false" reversible="false" name="Guanine deaminase" metaid="R_GUAD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GUAD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GUANINE-DEAMINASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01676"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-74255"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-74255"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-74255"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-74255"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-74255"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-74255"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-74255"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-74255"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-74255"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14667"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14668"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14666"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/127"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01225"/>
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+        <listOfReactants>
+          <speciesReference species="M_gua_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xan_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2883"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THRESYN-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01466"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104846"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10842"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10841"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10843"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01069"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_phom_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thr__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0004"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13227"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_amp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100741"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22011"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22009"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22008"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01304"/>
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+          <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_suchms_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4013"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_PPNDH" fast="false" reversible="false" name="Prephenate dehydratase" metaid="R_PPNDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PREPHENATEDEHYDRAT-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21648"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21649"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21650"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21651"/>
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+          <speciesReference species="M_pphn_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_phpyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2599"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29281"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29282"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29280"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29279"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tmao_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tma_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0895"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0896"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0894"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1589"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1590"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1588"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1587"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30583"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30586"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30584"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30585"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09315"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tmao_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2dmmq8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tma_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0895"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0896"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0894"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DGK1" fast="false" reversible="true" name="Deoxyguanylate kinase (dGMP:ATP)" metaid="R_DGK1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12698"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12700"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/303"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01509"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_dgmp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dgdp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3648"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02094"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97804"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13517"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13519"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01513"/>
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+          <speciesReference species="M_dtmp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dtdp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1098"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2518"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.1.9"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02016"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/489"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05289"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0888"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3781"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2582"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0888"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DDPA" fast="false" reversible="false" name="3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase" metaid="R_DDPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97218"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MTU-964912"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14719"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14717"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14720"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01332"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dda7p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2601"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0754"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1704"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NMNDA" fast="false" reversible="false" name="Nicotinamide-nucleotide amidase" metaid="R_NMNDA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NMNDA"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:NMNAMIDOHYDRO-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02322"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101969"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12402"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12400"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12403"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12401"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01669"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nmn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nicrnt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2700"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NNAM" fast="false" reversible="false" name="Nicotinamidase" metaid="R_NNAM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NNAM"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:NICOTINAMID-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.19"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101977"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14545"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14547"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14546"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14548"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00938"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ncam_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1768"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_P5CD" fast="false" reversible="false" name="1-pyrroline-5-carboxylate dehydrogenase" metaid="R_P5CD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRROLINECARBDEHYDROG-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.12"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.88"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00707"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102301"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16417"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16418"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16419"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16420"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1083"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00503"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1014"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PGMT" fast="false" reversible="true" name="Phosphoglucomutase" metaid="R_PGMT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-16999"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PHOSPHOGLUCMUT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.2.2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.2.8"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12817"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7674"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00704"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2690"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0688"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1317"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FRUK" fast="false" reversible="false" name="Fructose-1-phosphate kinase" metaid="R_FRUK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_FRUK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.56"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99652"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14216"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14214"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14215"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7171"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01492"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_f1p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2168"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SPMDAT1" fast="false" reversible="false" name="Spermidine acetyltransferase" metaid="R_SPMDAT1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_SPMDAT1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SPMDAT1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SPERMACTRAN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.57"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104491"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-351208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28153"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28151"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28152"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28150"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7731"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09264"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_N1aspmd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1584"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_RHCCE" fast="false" reversible="false" name="S-ribosylhomocysteine cleavage enzyme" metaid="R_RHCCE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_RHCCE">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RIBOSYLHOMOCYSTEINASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.4.1.21"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01291"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104026"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17754"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17753"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17756"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17755"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/6873"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn14169"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05958"/>
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+          <speciesReference species="M_rhcys_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhptd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2687"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_dha_e" fast="false" reversible="false" name="Dihydroxyacetone exchange" metaid="R_EX_dha_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-559"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97367"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08325"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08326"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05532"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_dha_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_KG6PDC" fast="false" reversible="false" name="3-keto-L-gulonate 6-phosphate decarboxylase" metaid="R_KG6PDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.85"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07125"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100935"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14356"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14355"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7628"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04928"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3dhgulnp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xu5p__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4196"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3581"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SPMDAT2" fast="false" reversible="false" name="Spermidine acetyltransferase (N8)" metaid="R_SPMDAT2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104492"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28272"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28273"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28270"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28271"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09265"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_n8aspmd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1584"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TDPADGAT" fast="false" reversible="false" name="DTDP-4-amino-4,6-dideoxy-D-glucose acetyltransferase" metaid="R_TDPADGAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_TDPADGAT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TDPADGAT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TDPFUCACTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.210"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10142"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104757"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34445"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34443"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34446"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28763"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34444"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28766"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28764"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28765"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11409"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dtdp4addg_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dtdp4aaddg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3790"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALS" fast="false" reversible="false" name="Malate synthase" metaid="R_MALS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALSYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.3.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00472"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101347"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18181"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18182"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18184"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18183"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00330"/>
+                </rdf:Bag>
+              </bqbiol:is>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glx_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4014"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2976"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_X5PL3E" fast="false" reversible="false" name="L-xylulose 5-phosphate 3-epimerase" metaid="R_X5PL3E" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:LXULRU5P-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.22"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03244"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105224"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18498"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18500"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18499"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18497"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02321"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_xu5p__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ru5p__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4197"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3582"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-703"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.130"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02637"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97688"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21927"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21925"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21926"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21924"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01911"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_23doguln_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3dhguln_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3575"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TRE6PP" fast="false" reversible="false" name="Trehalose-phosphatase" metaid="R_TRE6PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_TRE6PP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TRE6PP"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TREHALOSEPHOSPHA-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.12"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02778"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06228"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104926"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MTU-868608"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23420"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23423"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23422"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23421"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02004"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tre6p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tre_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1897"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_fuc__L_e" fast="false" reversible="false" name="L-Fucose exchange" metaid="R_EX_fuc__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_fuc__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99704"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fuc__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_met__D_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101473"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34913"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34912"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34914"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34911"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08911"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_met__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_tartr__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104724"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09284"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tartr__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_BETALDHx">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02565"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96237"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-6797955"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-6797955"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-6797955"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15305"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15306"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15307"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2478"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01867"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_betald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glyb_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0312"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BETALDHy" fast="false" reversible="false" name="Betaine-aldehyde dehydrogenase" metaid="R_BETALDHy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_BETALDHy">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96238"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30070"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30069"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30068"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30067"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2479"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01868"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_betald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyb_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0312"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MLTG3" fast="false" reversible="false" name="Maltodextrin glucosidase (maltopentaose)" metaid="R_MLTG3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101621"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08934"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltpt_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltttr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0403"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_taur_e" fast="false" reversible="false" name="Taurine exchange" metaid="R_EX_taur_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_taur_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_taur_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104733"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09286"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13402"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_taur_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_maltpt_e" fast="false" reversible="false" name="Maltopentaose exchange" metaid="R_EX_maltpt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_maltpt_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_maltpt_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101356"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08873"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_maltpt_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_glyald_e" fast="false" reversible="false" name="D-Glyceraldehyde exchange" metaid="R_EX_glyald_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_glyald_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glyald_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100311"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08636"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08635"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10164"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glyald_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_glcur_e" fast="false" reversible="false" name="D-Glucuronate exchange" metaid="R_EX_glcur_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_glcur_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glcur_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100235"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08623"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glcur_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_ADPRDP" fast="false" reversible="false" name="ADPribose diphosphatase" metaid="R_ADPRDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ADPRDP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADPRDP"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.13"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95480"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_adprib_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3397"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3034"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DKGLCNR1" fast="false" reversible="false" name="2,5-diketo-D-gluconate reductase" metaid="R_DKGLCNR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_DKGLCNR1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DKGLCNR1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97489"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08345"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_25dkglcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dhguln_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3012"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0207"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NADTRHD" fast="false" reversible="false" name="NAD transhydrogenase" metaid="R_NADTRHD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRNUTRANSHYDROGEN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.3"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00112"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101898"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11692"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11695"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11694"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11693"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00083"/>
+                </rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3962"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AACPS2" fast="false" reversible="false" name="Acyl-[acyl-carrier-protein] synthetase  (n-C14:1)" metaid="R_AACPS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.20"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95141"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tdeACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1094"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FMNRx2" fast="false" reversible="false" name="FMN reductase" metaid="R_FMNRx2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_FMNRx2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FMNRx2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12444"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05706"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99597"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21625"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/50759"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/50756"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/50758"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21627"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21626"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21624"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/50757"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/5302"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13939"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03975"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13930"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3844"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0937"/>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2764"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2763"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACPS1" fast="false" reversible="false" name="Acyl-carrier protein synthase" metaid="R_ACPS1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.8.7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95403"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn06023"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_apoACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pap_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2563"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3475"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_nmn_e" fast="false" reversible="false" name="NMN exchange" metaid="R_EX_nmn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28483"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28482"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28484"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08995"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10181"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_nmn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+      <reaction id="R_EX_urea_e" fast="false" reversible="false" name="Urea exchange" metaid="R_EX_urea_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-507875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-507875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-507875"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32800"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05667"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09368"/>
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+          <speciesReference species="M_urea_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95922"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1860"/>
+                </rdf:Bag>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_arab__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_rbl__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0062"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_M1PD" fast="false" reversible="true" name="Mannitol-1-phosphate 5-dehydrogenase" metaid="R_M1PD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/M1PD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MANNPDEHYDROG-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02703"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101311"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19664"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19663"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19661"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19662"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_mnl1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3600"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_G3PD2" fast="false" reversible="true" name="Glycerol-3-phosphate dehydrogenase (NADP)" metaid="R_G3PD2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11099"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11098"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11097"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1184"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00612"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3608"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GALS3" fast="false" reversible="false" name="A-galactosidase (melibiose)" metaid="R_GALS3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ALPHAGALACTOSID-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.22"/>
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+          <speciesReference species="M_melib_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gal_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4119"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99468"/>
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+          <speciesReference species="M_fuc__L_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_fcl__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2802"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:FUCULOKIN-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12378"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12379"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12377"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02319"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fcl__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fc1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2803"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:FUCPALDOL-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99470"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12936"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12935"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01620"/>
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+          <speciesReference species="M_fc1p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lald__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2738"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2800"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100384"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11681"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/215"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00917"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xmp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2507"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AMPN" fast="false" reversible="false" name="AMP nucleosidase" metaid="R_AMPN" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1982"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GSNK" fast="false" reversible="false" name="Guanosine kinase" metaid="R_GSNK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100432"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27711"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27710"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27712"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27713"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00914"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_gsn_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0477"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_ACCOAL" fast="false" reversible="false" name="Acetate-CoA ligase (ADP-forming)" metaid="R_ACCOAL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.13"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95221"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppcoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4069"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0335"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GALUi" fast="false" reversible="false" name="UTP-glucose-1-phosphate uridylyltransferase (irreversible)" metaid="R_GALUi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_GALUi">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUC1PURIDYLTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.7.9"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19890"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19891"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/8973"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/68"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00213"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1236"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AACPS3" fast="false" reversible="false" name="Acyl-[acyl-carrier-protein] synthetase  (n-C16:0)" metaid="R_AACPS3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.2.1.20"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95142"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1094"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04550"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105007"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn06723"/>
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+          <speciesReference species="M_u3hga_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_u23ga_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0179"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_f6p_e" fast="false" reversible="false" name="D-fructose 6-phosphate exchange" metaid="R_EX_f6p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99076"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_f6p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_UAAGDS" fast="false" reversible="false" name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate synthetase" metaid="R_UAAGDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105013"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_26dap__M_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uamag_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ugmd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0085"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1094"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_uamr_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uama_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0091"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105038"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11252"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_glu__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uama_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uamag_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0088"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UGLYCH" fast="false" reversible="false" name="Ureidoglycolate hydrolase" metaid="R_UGLYCH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19810"/>
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+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_urdglyc_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glx_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0505"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22638"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01222"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dcmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2781"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1759"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14247"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00063"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0905"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2251"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3248"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22581"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22580"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22583"/>
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+          <speciesReference species="M_op4en_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4h2opntn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0350"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34998"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34996"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09229"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00540"/>
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+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0352"/>
+        </fbc:geneProductAssociation>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3248"/>
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+        </fbc:geneProductAssociation>
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+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0386"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CYANST" fast="false" reversible="false" name="Cyanide sulfurtransferase" metaid="R_CYANST" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THIOSULFATE-SULFURTRANSFERASE-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01931"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138187"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16883"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16884"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16882"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16881"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01416"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_cyan_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tsul_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tcynt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3425"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2668"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2521"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_ttdca_e" fast="false" reversible="false" name="Tetradecanoate (n-C14:0) exchange" metaid="R_EX_ttdca_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ttdca_e" stoichiometry="1" constant="true"/>
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+      <reaction id="R_DHPPDA2" fast="false" reversible="false" name="Diaminohydroxyphosphoribosylaminopryrimidine deaminase (25drapp)" metaid="R_DHPPDA2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RIBOFLAVINSYNDEAM-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.26"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03459"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97435"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21869"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21868"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21870"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_25drapp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_5apru_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0414"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_3HPPPNH" fast="false" reversible="false" name="3-(3-hydroxy-phenyl)propionate hydroxylase" metaid="R_3HPPPNH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MHPHYDROXY-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.13.127"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06786"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94903"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24786"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24787"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24788"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24785"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04601"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhpppn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0347"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_G5SADs" fast="false" reversible="false" name="L-glutamate 5-semialdehyde dehydratase (spontaneous)" metaid="R_G5SADs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SPONTPRO-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-70667"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28237"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28234"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28235"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28236"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11220"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02374"/>
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+          <speciesReference species="M_glu5sa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GMAND" fast="false" reversible="false" name="GDP-D-mannose dehydratase" metaid="R_GMAND" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GMAND"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GDPMANDEHYDRA-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.47"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00888"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100377"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23823"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23822"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23820"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23821"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/588"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00642"/>
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+          <speciesReference species="M_gdpmann_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_gdpddman_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2053"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PPCSCT" fast="false" reversible="false" name="Propanoyl-CoA: succinate CoA-transferase" metaid="R_PPCSCT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PPCSCT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103103"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_ppcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ppa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2920"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CYTD" fast="false" reversible="false" name="Cytidine deaminase" metaid="R_CYTD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CYTD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CYTIDEAM2-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01878"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97039"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16069"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16070"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16072"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16071"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/89"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01368"/>
+                </rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_cytd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uri_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2143"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AKGDH" fast="false" reversible="false" name="2-Oxogluterate dehydrogenase" metaid="R_AKGDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2OXOGLUTARATEDEH-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.52"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.61"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.1.4"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R08549"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-71401"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-71401"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-71401"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08094"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0727"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0116"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0726"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17905"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17908"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/426"/>
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+          <speciesReference species="M_hpyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glyc__R_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1033"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3553"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_GLYCDx" fast="false" reversible="false" name="Glycerol dehydrogenase" metaid="R_GLYCDx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13770"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13772"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13769"/>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dha_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3945"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ASPDECARBOX-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19499"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19498"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala_B_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0131"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_UGMDDS" fast="false" reversible="false" name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine synthetase" metaid="R_UGMDDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105094"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/4284"/>
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+          <speciesReference species="M_alaala_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ugmd_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ugmda_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0086"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CYTIDEAM-RXN"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2143"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97180"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15807"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15808"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15806"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/3011"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02277"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dann_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dtbt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0778"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DCTP-DEAM-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97201"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22681"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22680"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01672"/>
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+          <speciesReference species="M_dctp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dutp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2065"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UHGADA" fast="false" reversible="false" name="UDP-3-O-acetylglucosamine deacetylase" metaid="R_UHGADA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UHGADA"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:UDPACYLGLCNACDEACETYL-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.108"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04587"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105110"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25209"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25211"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25210"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03146"/>
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+          <speciesReference species="M_u3aga_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_u3hga_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0096"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AMANK" fast="false" reversible="false" name="N-acetyl-D-mannosamine kinase" metaid="R_AMANK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_AMANK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95805"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_acmana_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acmanap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3222"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_uacgam_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_u3aga_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0181"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2019"/>
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+          <speciesReference species="M_histd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="2" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_his__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="2" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2020"/>
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+          <speciesReference species="M_23dhdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2478"/>
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+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_gar_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1849"/>
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+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0337"/>
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+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3729"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2022"/>
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+          <speciesReference species="M_o2_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_so4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13286"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13288"/>
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+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glucys_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2688"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:HISTPRATPHYD-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04035"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103155"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22829"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22828"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22830"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22831"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02834"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_prbatp_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_prbamp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2026"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-70609"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-70609"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15889"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15891"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15890"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00189"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0485"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1524"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PRIBFAICARPISOM-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.16"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04640"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103169"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15471"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15472"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15469"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15470"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03175"/>
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+            </rdf:Description>
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+          <speciesReference species="M_prfp_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_prlp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2024"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01072"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-73815"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14908"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14906"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14907"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00790"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pram_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2312"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09644"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13641"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GMP-REDUCT-RXN"/>
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_imp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0104"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104275"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MTU-936615"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24560"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00423"/>
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+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_acser_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3607"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CYSS" fast="false" reversible="false" name="Cysteine synthase" metaid="R_CYSS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97007"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14829"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14831"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14830"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14832"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00649"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_acser_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2s_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2421"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2414"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NADS1" fast="false" reversible="false" name="NAD synthase (nh3)" metaid="R_NADS1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:NAD-SYNTH-NH3-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.5.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.1.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00189"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101897"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21188"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21190"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21191"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21189"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13688"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00138"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dnad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1740"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BPNT" fast="false" reversible="false" name="3',5'-bisphosphate nucleotidase" metaid="R_BPNT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:325-BISPHOSPHATE-NUCLEOTIDASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.97"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00188"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-176606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10041"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10040"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10043"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10042"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/736"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00137"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11357"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pap_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4214"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_2ddglcn_e" fast="false" reversible="false" name="2-Dehydro-3-deoxy-D-gluconate exchange" metaid="R_EX_2ddglcn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_2ddglcn_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_2ddglcn_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08320"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2ddglcn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_PAPSR" fast="false" reversible="false" name="Phosphoadenylyl-sulfate reductase (thioredoxin)" metaid="R_PAPSR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PAPSR">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAPSR"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:1.8.4.8-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.4.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02021"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102376"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05239"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_paps_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2582"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2762"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3781"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2762"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ASPK" fast="false" reversible="true" name="Aspartate kinase" metaid="R_ASPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ASPK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ASPARTATEKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.2.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00480"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96085"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23779"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23777"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23776"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23778"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/912"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00337"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4pasp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0002"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3940"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4024"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ASAD" fast="false" reversible="true" name="Aspartate-semialdehyde dehydrogenase" metaid="R_ASAD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ASAD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASAD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.11"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02291"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96039"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24285"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24284"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24286"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24287"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2255"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01643"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_aspsa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4pasp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3433"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DAPDC" fast="false" reversible="false" name="Diaminopimelate decarboxylase" metaid="R_DAPDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DAPDC">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DAPDC"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DIAMINOPIMDECARB-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.20"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00451"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97141"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15101"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15104"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15102"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15103"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00313"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_26dap__M_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2838"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_mmet_e" fast="false" reversible="false" name="S-Methyl-L-methionine exchange" metaid="R_EX_mmet_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_EX_mmet_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mmet_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-486"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101659"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08945"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mmet_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_NTRIR2x" fast="false" reversible="false" name="Nitrite Reductase (NADH)" metaid="R_NTRIR2x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00787"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102062"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24629"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24628"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24630"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24631"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00568"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11161"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="5" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_no2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
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+          <speciesReference species="M_nad_c" stoichiometry="3" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3365"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_3dhgulnp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b4192"/>
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+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_agdpcbi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1993"/>
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+          <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trp__L_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1260"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1261"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfProducts>
+          <speciesReference species="M_prfp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2026"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_rdmbzi_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_adocbl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1992"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03536"/>
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+          <speciesReference species="M_adocbip_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1993"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1007"/>
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+          <speciesReference species="M_thmpp_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0417"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hkndd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0348"/>
+        </fbc:geneProductAssociation>
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+        <listOfProducts>
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+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0331"/>
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+          <speciesReference species="M_dxyl_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dxyl5p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3564"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_inost_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3449"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_phthr_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pdx5p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2564"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0052"/>
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+        </fbc:geneProductAssociation>
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+        <listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppbng_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0369"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28567"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13827"/>
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+          <speciesReference species="M_seramp_c" stoichiometry="3" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="6" constant="true"/>
+          <speciesReference species="M_enter_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="9" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0583"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_h2s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="3" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2763"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08884"/>
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+          <speciesReference species="M_man6pglyc_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_man6p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0732"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_urdglyc_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oxur_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0517"/>
+        </fbc:geneProductAssociation>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0521"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_6pgc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ru5p__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2029"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104730"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15909"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15912"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15911"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/4928"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03630"/>
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+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_taur_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_aacald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0368"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DM_amob_c" fast="false" reversible="false" name="Sink needed to allow S-Adenosyl-4-methylthio-2-oxobutanoate to leave system" metaid="R_DM_amob_c" sboTerm="SBO:0000628" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19671"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19672"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19670"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/816"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00241"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4161"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4352"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2727"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2918"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2173"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3590"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4173"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PPM2" fast="false" reversible="true" name="Phosphopentomutase 2 (deoxyribose)" metaid="R_PPM2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:D-PPENTOMUT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.2.7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02749"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103116"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27660"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25206"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25205"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27661"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27658"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25207"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27659"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01986"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_2dr1p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dr5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4383"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MOAT2" fast="false" reversible="false" name="3-deoxy-D-manno-octulosonic acid transferase" metaid="R_MOAT2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.99.13"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05074"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06285"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101684"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28063"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28062"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28065"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28064"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03439"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_ckdo_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_kdolipid4_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_kdo2lipid4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3633"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11000"/>
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+          <speciesReference species="M_adn_e" stoichiometry="1" constant="true"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100849"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08754"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ins_e" stoichiometry="1" constant="true"/>
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+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_G6PDH2r">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G6PDH2r"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLU6PDEHYDROG-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.363"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.49"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00835"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99907"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15842"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15843"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15841"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15844"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1176"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/6509"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00604"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_6pgl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1852"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ME2" fast="false" reversible="false" name="Malic enzyme (NADP)" metaid="R_ME2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALIC-NADP-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.40"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101443"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18255"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18254"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18253"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00161"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2463"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00802"/>
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+      <reaction id="R_MOHMT" fast="false" reversible="false" name="3-methyl-2-oxobutanoate hydroxymethyltransferase" metaid="R_MOHMT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MOHMT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.2.11"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01226"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101702"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11824"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11827"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11825"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11826"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3mob_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dhp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0134"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_glyc3p_e" fast="false" reversible="false" name="Glycerol 3-phosphate exchange" metaid="R_EX_glyc3p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_glyc3p_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100308"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34969"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34967"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34968"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34970"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08643"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09749"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11234"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glyc3p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_MLTG2" fast="false" reversible="false" name="Maltodextrin glucosidase (maltotetraose)" metaid="R_MLTG2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MLTG2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTG2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALTET-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101620"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08933"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltttr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malttr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0403"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_but_e" fast="false" reversible="false" name="Butyrate (n-C4:0) exchange" metaid="R_EX_but_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_but_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_but_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96352"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_but_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_MLTG1" fast="false" reversible="false" name="Maltodextrin glucosidase (maltotriose)" metaid="R_MLTG1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MLTG1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTG1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5183"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.20"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101619"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05746"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malttr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0403"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AMALT3" fast="false" reversible="false" name="Amylomaltase (maltopentaose)" metaid="R_AMALT3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AMALT3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMALT3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14261"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.25"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95802"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08128"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_malt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltpt_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3416"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MLTP3" fast="false" reversible="true" name="Maltodextrin phosphorylase (maltoheptaose)" metaid="R_MLTP3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MLTP3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTP3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14286"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101634"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7988"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/10132"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08943"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_malthp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3417"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_lcts_e" fast="false" reversible="false" name="Lactose exchange" metaid="R_EX_lcts_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_lcts_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_lcts_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101027"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08780"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_lcts_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_ocdca_e" fast="false" reversible="false" name="Octadecanoate (n-C18:0) exchange" metaid="R_EX_ocdca_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_ocdca_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ocdca_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99109"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/39807"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/39808"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/39809"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/39810"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09034"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09669"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ocdca_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_cbl1_e" fast="false" reversible="false" name="Cob(I)alamin exchange" metaid="R_EX_cbl1_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_cbl1_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cbl1_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1565"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR123114"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29722"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29720"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29721"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29719"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cbl1_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_SPODM" fast="false" reversible="false" name="Superoxide dismutase" metaid="R_SPODM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_SPODM">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SPODM"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SUPEROX-DISMUT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.15.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00275"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104498"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20696"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20699"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20698"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20697"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_o2s_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3908"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1656"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AHCYSNS" fast="false" reversible="false" name="S-adenosylhomocysteine nucleosidase" metaid="R_AHCYSNS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AHCYSNS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AHCYSNS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00194"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95625"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17806"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17808"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17807"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00143"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rhcys_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0159"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACNML" fast="false" reversible="false" name="N-Acetylneuraminate lyase" metaid="R_ACNML" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ACNML">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACNML"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACNEULY-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.3.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01811"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23297"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23298"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23299"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7666"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01322"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acnam_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acmana_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28573"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28570"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28572"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09245"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00418"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_seramp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0586"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLCRD" fast="false" reversible="false" name="Glucarate dehydratase" metaid="R_GLCRD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUCARDEHYDRA-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14574"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14576"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14575"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2632"/>
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+        <listOfProducts>
+          <speciesReference species="M_5dh4dglc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2788"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2787"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_PPPNDO" fast="false" reversible="false" name="Phenylpropanoate Dioxygenase" metaid="R_PPPNDO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:HCAMULTI-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20359"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20357"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20360"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20358"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pppn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cechddd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2542"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2538"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2540"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2539"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_26DAHtex" fast="false" reversible="true" name="Meso-2,6-Diaminoheptanedioate transport via diffusion (extracellular to periplasm)" metaid="R_26DAHtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94741"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07931"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_26dap__M_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_26dap__M_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HCINNMtex" fast="false" reversible="true" name="3-hydroxycinnamic acid transport via diffusion (extracellular to periplasm)" metaid="R_HCINNMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_HCINNMtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HCINNMtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08702"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3hcinnm_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3hcinnm_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HPPPNtex" fast="false" reversible="true" name="3-(3-hydroxyphenyl)propionate transport via diffusion (extracellular to periplasm)" metaid="R_HPPPNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_HPPPNtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100697"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08726"/>
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+        <listOfReactants>
+          <speciesReference species="M_3hpppn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3hpppn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27814"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27816"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27815"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12184"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09787"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09866"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10904"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08063"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ac_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ac_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACALDtex" fast="false" reversible="true" name="Acetaldehyde transport via diffusion (extracellular to periplasm)" metaid="R_ACALDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95212"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09700"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08033"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08032"/>
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+        <listOfReactants>
+          <speciesReference species="M_acald_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acald_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHRPL"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CHORPYRLY-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.3.40"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01302"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96711"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16508"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16505"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16507"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16506"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00966"/>
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+        <listOfReactants>
+          <speciesReference species="M_chor_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4hbz_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4039"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1096"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_dtdp4d6dg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dtdp4addg_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3791"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_UACMAMO" fast="false" reversible="false" name="UDP-N-acetyl-D-mannosamine oxidoreductase" metaid="R_UACMAMO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.336"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03317"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25782"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25783"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25781"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02377"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="2" constant="true"/>
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+          <speciesReference species="M_nadh_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_uacmamu_c" stoichiometry="1" constant="true"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3845"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b4388"/>
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+          <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/766"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00194"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4abut_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3517"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1493"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACACT2r" fast="false" reversible="true" name="Acetyl-CoA C-acyltransferase (butanoyl-CoA) (r)" metaid="R_ACACT2r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ACACT2r">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACACT2r"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12565"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.16"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01177"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95196"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-77321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-77321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-77321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-77321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-77321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-77321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-77321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-77321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-77321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-77321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-77321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31114"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31113"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31111"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31112"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1414"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00874"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3ohcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2342"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3845"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BSORy" fast="false" reversible="false" name="Biotin sulfoxide reductase" metaid="R_BSORy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_BSORy">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BSORy"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.-.-.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R10127"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96326"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30538"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30537"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30535"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30536"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08179"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_btnso_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_btn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3551"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DMSOR2" fast="false" reversible="false" name="Dimethyl sulfoxide reductase (Demethylmenaquinol 8)" metaid="R_DMSOR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DMSOR2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DMSOR2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97531"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30589"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30587"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30590"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30588"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08356"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dmso_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dmmq8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dms_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0895"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0896"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0894"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ADSK" fast="false" reversible="false" name="Adenylyl-sulfate kinase" metaid="R_ADSK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ADSK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADSK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ADENYLYLSULFKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.25"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00509"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95159"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-174389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24155"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24152"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24154"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24153"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/237"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00361"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_aps_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_paps_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2750"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACACT3r" fast="false" reversible="true" name="Acetyl-CoA C-acyltransferase (hexanoyl-CoA) (r)" metaid="R_ACACT3r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ACACT3r">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACACT3r"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95197"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hxcoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3oocoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2342"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3845"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACACT4r" fast="false" reversible="true" name="Acetyl-CoA C-acyltransferase (octanoyl-CoA) (r)" metaid="R_ACACT4r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ACACT4r">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACACT4r"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-13617"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.16"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03778"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95198"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-77340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-77340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-77340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-77340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-77340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-77340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-77340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-77340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-77340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-77340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-77340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31087"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31089"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31088"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31090"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/3537"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02680"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_occoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3odcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2342"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3845"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SUCCt2_2pp" fast="false" reversible="false" name="Succinate transport via proton symport (2 H) (periplasm)" metaid="R_SUCCt2_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_SUCCt2_2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SUCCt2_2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-121"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104620"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29305"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29306"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29304"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29303"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10154"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09269"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3528"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0010"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SUCFUMtpp" fast="false" reversible="true" name="Succinate:fumarate antiporter (periplasm)" metaid="R_SUCFUMtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_SUCFUMtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SUCFUMtpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-106"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104633"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29326"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29323"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29325"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10159"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09712"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09273"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fum_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4123"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0621"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4138"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HSDy" fast="false" reversible="true" name="Homoserine dehydrogenase (NADPH)" metaid="R_HSDy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15764"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15762"/>
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+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_aspsa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3940"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0002"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CYSTL" fast="false" reversible="false" name="Cystathionine b-lyase" metaid="R_CYSTL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13965"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13968"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13966"/>
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+        <listOfProducts>
+          <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3008"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1622"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACMAMUT" fast="false" reversible="false" name="UDP-N-acetyl-D-mannosaminuronic acid transferase" metaid="R_ACMAMUT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28369"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28366"/>
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+          <speciesReference species="M_uacmamu_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_unaga_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_unagamu_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3794"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SHSL1" fast="false" reversible="false" name="O-succinylhomoserine lyase (L-cysteine)" metaid="R_SHSL1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:O-SUCCHOMOSERLYASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.48"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03260"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104380"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20398"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20399"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20400"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/3081"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_suchms_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cyst__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3939"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SSALy" fast="false" reversible="false" name="Succinate-semialdehyde dehydrogenase (NADP)" metaid="R_SSALy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00714"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13216"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13215"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13214"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1086"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00509"/>
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+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sucsal_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1525"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2661"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SUCptspp" fast="false" reversible="false" name="Sucrose transport via PEP:Pyr  (periplasm)" metaid="R_SUCptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104643"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05655"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09274"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sucr_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_suc6p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2417"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2429"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SULabcpp" fast="false" reversible="false" name="Sulfate transport via ABC system (periplasm)" metaid="R_SULabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104655"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10193#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10194#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10195#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09276"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05153"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so4_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2423"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2424"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2422"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2425"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0764"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0765"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0763"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2422"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2423"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2424"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3917"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104964"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29872#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29873#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29874#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29871#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05176"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09329"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tsul_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tsul_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2422"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2424"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3917"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2425"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2423"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29260"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29262"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29261"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10137"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09283"/>
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+          <speciesReference species="M_tartr__L_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_tartr__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3063"/>
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+      <reaction id="R_EX_dad_2_e" fast="false" reversible="false" name="Deoxyadenosine exchange" metaid="R_EX_dad_2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dad_2_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97081"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08293"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10939"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dad_2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_ser__D_e" fast="false" reversible="false" name="D-Serine exchange" metaid="R_EX_ser__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_ser__D_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ser__D_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-495"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97799"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29457"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29456"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29455"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29458"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08373"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10965"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ser__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_DDGALK" fast="false" reversible="false" name="2-dehydro-3-deoxygalactonokinase" metaid="R_DDGALK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DDGALK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DDGALK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DEHYDDEOXGALACTKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.58"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.178"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03387"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16527"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16525"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16526"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16528"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02429"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2dh3dgal_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dh3dgal6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3693"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_gam6p_e" fast="false" reversible="false" name="D-Glucosamine 6-phosphate exchange" metaid="R_EX_gam6p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_gam6p_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gam6p_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13642"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08591"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05568"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gam6p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_15dap_e" fast="false" reversible="false" name="1,5-Diaminopentane exchange" metaid="R_EX_15dap_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_15dap_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_15dap_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97147"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08305"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_15dap_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_AB6PGH" fast="false" reversible="false" name="Arbutin 6-phosphate glucohydrolase" metaid="R_AB6PGH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AB6PGH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AB6PGH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.86"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95165"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08025"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_arbt6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hqn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2901"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3721"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2716"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_ocdcea_e" fast="false" reversible="false" name="Octadecenoate (n-C18:1) exchange" metaid="R_EX_ocdcea_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_ocdcea_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ocdcea_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99110"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33658"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33655"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33656"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33657"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/10346"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ocdcea_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_cynt_e" fast="false" reversible="false" name="Cyanate exchange" metaid="R_EX_cynt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_cynt_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cynt_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-14"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96963"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08279"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cynt_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_galctn__D_e" fast="false" reversible="false" name="D-Galactonate exchange" metaid="R_EX_galctn__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_galctn__D_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_galctn__D_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99961"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08579"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_galctn__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_AMALT1" fast="false" reversible="false" name="Amylomaltase (maltotriose)" metaid="R_AMALT1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AMALT1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMALT1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:AMYLOMALT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.25"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95800"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08126"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_malt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malttr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltttr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3416"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_glyb_e" fast="false" reversible="false" name="Glycine betaine exchange" metaid="R_EX_glyb_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_glyb_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glyb_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-490"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100317"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6797957"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28945"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28944"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28946"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28943"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11693"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08639"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12430"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glyb_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_AHGDx" fast="false" reversible="true" name="(S)-alpha-hydroxyglutarate dehydrogenase" metaid="R_AHGDx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AHGDx">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AHGDx"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-16701"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.M7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.272"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.399"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95630"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/9820"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10432"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_S2hglut_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2913"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MLTP2" fast="false" reversible="true" name="Maltodextrin phosphorylase (maltohexaose)" metaid="R_MLTP2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MLTP2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTP2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14285"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101633"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29684"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29686"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29685"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/10080"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08942"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltpt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3417"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TAURabcpp" fast="false" reversible="false" name="Taurine transport via ABC system (periplasm)" metaid="R_TAURabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_TAURabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TAURabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-64-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.36-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.36"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104732"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14614#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14615#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14613#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14616#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09285"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05172"/>
+                </rdf:Bag>
+              </bqbiol:is>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+          <speciesReference species="M_pmtcoa_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2202"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2204"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2203"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_o2_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_octa_e" fast="false" reversible="false" name="Octanoate (n-C8:0) exchange" metaid="R_EX_octa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_octa_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_octa_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-272"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99126"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29761"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29762"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29759"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29760"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09036"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09840"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_octa_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_PHYTSpp" fast="false" reversible="false" name="Phytase (periplasm)" metaid="R_PHYTSpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PHYTSpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PHYTSpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102659"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09119"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="6" constant="true"/>
+          <speciesReference species="M_minohp_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_inost_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="6" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0980"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_gbbtn_e" fast="false" reversible="false" name="Gamma-butyrobetaine exchange" metaid="R_EX_gbbtn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_gbbtn_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gbbtn_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100053"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32838"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32837"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32835"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32836"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08595"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gbbtn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_PPTHpp" fast="false" reversible="false" name="Phosphonate hydrogenase (periplasm)" metaid="R_PPTHpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PPTHpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPTHpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103149"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29453"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29454"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29451"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29452"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09184"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppt_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PYRt2rpp" fast="false" reversible="true" name="Pyruvate reversible transport via proton symport (periplasm)" metaid="R_PYRt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PYRt2rpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYRt2rpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103385"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-372347"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-372342"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-372359"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05469"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09832"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09717"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09217"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_NO3R2pp" fast="false" reversible="false" name="Nitrate reductase (Menaquinol-8) (periplasm)" metaid="R_NO3R2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NO3R2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO3R2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101988"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29141#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29142#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29140#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29139#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09003"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10121"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_no3_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_no2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1467"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1468"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1466"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1465"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1224"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1227"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1226"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1225"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_xylu__L_e" fast="false" reversible="false" name="L-Xylulose exchange" metaid="R_EX_xylu__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_xylu__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_xylu__L_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138931"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09387"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_xylu__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_gdp_e" fast="false" reversible="false" name="GDP exchange" metaid="R_EX_gdp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_gdp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gdp_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100096"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-111812"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08600"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09815"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gdp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_gtp_e" fast="false" reversible="false" name="GTP exchange" metaid="R_EX_gtp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_gtp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gtp_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08680"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12663"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gtp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_NTP3pp" fast="false" reversible="false" name="Nucleoside-triphosphatase (GTP) (periplasm)" metaid="R_NTP3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTP3pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTP3pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.15"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.5.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00335"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102043"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19669"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19671"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19672"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19670"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/816"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00241"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gtp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gdp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0980"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NO3R2bpp" fast="false" reversible="false" name="Nitrate reductase (Menaquinol-8) (periplasm)" metaid="R_NO3R2bpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NO3R2bpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NO3R2bpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.7.99.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101989"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09002"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_no3_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2206"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2203"/>
+            </fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2202"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_THMabcpp" fast="false" reversible="false" name="Thiamine transport via ABC system (periplasm)" metaid="R_THMabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_THMabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THMabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138862"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05177"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09297"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thm_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thm_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0066"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0068"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0067"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_THMDt2pp_copy2" fast="false" reversible="true" name="Thymidine transport in via proton symport (periplasm)" metaid="R_THMDt2pp_copy2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29958"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29955"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29956"/>
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+          <speciesReference species="M_thymd_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thymd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2406"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thr__L_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thr__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3456"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3455"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3460"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3457"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3454"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_TREptspp" fast="false" reversible="false" name="Trehalose transport via PEP:Pyr PTS (periplasm)" metaid="R_TREptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02005"/>
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+          <speciesReference species="M_tre_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tre6p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2417"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4240"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_THD2pp" fast="false" reversible="false" name="NAD(P) transhydrogenase (periplasm)" metaid="R_THD2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_THD2pp">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10125"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09295"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1602"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1603"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TMAOR1pp" fast="false" reversible="false" name="Trimethylamine N-oxide reductase (menaquinol 8) (periplasm)" metaid="R_TMAOR1pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104879"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09314"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10127"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tmao_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tma_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0997"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0996"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1872"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1873"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TMAOR2pp" fast="false" reversible="false" name="Trimethylamine N-oxide reductase (demethylmenaquinol 8) (periplasm)" metaid="R_TMAOR2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104881"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09316"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10128"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tmao_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2dmmq8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tma_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0997"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0996"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b1872"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1873"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_XANtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09652"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09378"/>
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+          <speciesReference species="M_xan_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_xan_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97147"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08305"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_15dap_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_15dap_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28881"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28880"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28879"/>
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+          <speciesReference species="M_trp__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trp__L_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3709"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0112"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TYRt2rpp" fast="false" reversible="true" name="L-tyrosine reversible transport via proton symport (periplasm)" metaid="R_TYRt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+          <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0112"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_tma_e" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29954"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29951"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05199"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uri_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uri_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2964"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2393"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_URIt2pp_copy2" fast="false" reversible="true" name="Uridine transport in via proton symport (periplasm)" metaid="R_URIt2pp_copy2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29954"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29952"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29951"/>
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+          <speciesReference species="M_uri_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uri_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2406"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_VALabcpp" fast="false" reversible="false" name="L-valine transport via ABC system (periplasm)" metaid="R_VALabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-36-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105187"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29805#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29803#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29806#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29804#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05168"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09373"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_val__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3457"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3456"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3460"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3455"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3454"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_12PPDStex" fast="false" reversible="true" name="(S)-Propane-1,2-diol transport via diffusion (extracellular to periplasm)" metaid="R_12PPDStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_12PPDStex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/12PPDStex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94684"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_12ppd__S_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_12ppd__S_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DDGLCNtex" fast="false" reversible="true" name="2-dehydro-3-deoxy-D-gluconate transport via diffusion (extracellular to periplasm)" metaid="R_DDGLCNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DDGLCNtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DDGLCNtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08320"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2ddglcn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2ddglcn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_XTSNt2rpp" fast="false" reversible="true" name="Xanthosine transport via proton symport (periplasm)" metaid="R_XTSNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_XTSNt2rpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-31"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105246"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28940"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28942"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28941"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28939"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09381"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05680"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xtsn_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xtsn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2406"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_XYLabcpp" fast="false" reversible="false" name="D-xylose transport via ABC system (periplasm)" metaid="R_XYLabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_XYLabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XYLabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29902#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29900#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29899#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29901#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05167"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09383"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xyl__D_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xyl__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3568"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3566"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3567"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GMHEPK" fast="false" reversible="false" name="D-glycero-D-manno-heptose 7-phosphate kinase" metaid="R_GMHEPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_GMHEPK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GMHEPK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143147"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gmhep7p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gmhep17bp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3052"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_XYLUt2pp" fast="false" reversible="false" name="L-xylulose transport in via proton symport (periplasm)" metaid="R_XYLUt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_XYLUt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XYLUt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138930"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09386"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xylu__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xylu__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3577"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3578"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3579"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_THRt4pp" fast="false" reversible="false" name="L-threonine  via sodium symport (periplasm)" metaid="R_THRt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_THRt4pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRt4pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104842"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10186"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09306"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thr__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thr__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3089"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GALURtex" fast="false" reversible="true" name="D-galacturonate transport via diffusion (extracellular to periplasm)" metaid="R_GALURtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GALURtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALURtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100021"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08589"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_galur_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_galur_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GTPCI" fast="false" reversible="false" name="GTP cyclohydrolase I" metaid="R_GTPCI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_GTPCI">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GTPCI"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GTP-CYCLOHYDRO-I-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.4.16"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00424"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100453"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-1474146"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-1474146"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-1474146"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17476"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17473"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17474"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17475"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/9177"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00299"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11232"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ahdt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2153"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FDMO" fast="false" reversible="false" name="FMNH2-dependent monooxygenase" metaid="R_FDMO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-13418"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.14.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99485"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29718"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29715"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29716"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29717"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08467"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_isetac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gcald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0935"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FEOXAMabcpp" fast="false" reversible="false" name="Ferroxamine transport via ABC system (periplasm)" metaid="R_FEOXAMabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143100"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08509"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05558"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_feoxam_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_feoxam_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0152"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0153"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0151"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_fruur_e" fast="false" reversible="false" name="D-Fructuronate exchange" metaid="R_EX_fruur_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_fruur_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99659"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08539"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fruur_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_GALtex" fast="false" reversible="true" name="D-galactose transport via diffusion (extracellular to periplasm)" metaid="R_GALtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100025"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34918"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34917"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34916"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34915"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7001"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10911"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08585"/>
+                </rdf:Bag>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gal_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gal_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CBL1abcpp" fast="false" reversible="false" name="Cob(1)alamin transport via ABC system (periplasm)" metaid="R_CBL1abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CBL1abcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-5-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.33"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96471"/>
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+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cbl1_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cbl1_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1709"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0158"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1711"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_malttr_e" fast="false" reversible="false" name="Maltotriose exchange" metaid="R_EX_malttr_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_malttr_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101359"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08876"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_malttr_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_ACACt2pp" fast="false" reversible="true" name="Acetoacetate transport via proton symport  (periplasm)" metaid="R_ACACt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95207"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05484"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08029"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_acac_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2223"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACGAptspp" fast="false" reversible="false" name="N-Acetyl-D-glucosamine transport via PEP:Pyr PTS  (periplasm)" metaid="R_ACGAptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAptspp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95253"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08041"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05485"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_acgam_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acgam6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2417"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1101"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0679"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACMANAptspp" fast="false" reversible="false" name="N-acetyl-D-mannosamine transport via PTS  (periplasm)" metaid="R_ACMANAptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACMANAptspp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95275"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08046"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10183"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acmana_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acmanap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1818"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1817"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1819"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACNAMt2pp" fast="false" reversible="false" name="N-acetylneuraminate proton symport (periplasm)" metaid="R_ACNAMt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95291"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28990"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28989"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28988"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08050"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_acnam_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acnam_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3224"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GALCTtex" fast="false" reversible="true" name="D-galactarte transport via diffusion (extracellular to periplasm)" metaid="R_GALCTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-203"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99963"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28478"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28480"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28479"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28481"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12441"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08581"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_galct__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_galct__D_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GALCTNtex" fast="false" reversible="true" name="D-galactonate transport via diffusion (extracellular to periplasm)" metaid="R_GALCTNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GALCTNtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALCTNtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99961"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08579"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_galctn__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_galctn__D_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GALTtex" fast="false" reversible="true" name="Galactitol transport via diffusion (extracellular to periplasm)" metaid="R_GALTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GALTtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALTtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100019"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33146"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33144"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33143"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33145"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08587"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_galt_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_galt_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_cbi_e" fast="false" reversible="false" name="Cobinamide exchange" metaid="R_EX_cbi_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_cbi_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cbi_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-283"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR124011"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29695"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29697"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29696"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29698"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cbi_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_CHOLD" fast="false" reversible="false" name="Choline dehydrogenase" metaid="R_CHOLD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CHOLD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHOLD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-6021"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R08557"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96697"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33054"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33051"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33053"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10770"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_chol_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_betald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0311"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TRE6PS" fast="false" reversible="false" name="Alpha,alpha-trehalose-phosphate synthase (UDP-forming)" metaid="R_TRE6PS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_TRE6PS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TRE6PS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TREHALOSE6PSYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.15"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00836"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06043"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18890"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18891"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18889"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18892"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00605"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tre6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1896"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DRPA" fast="false" reversible="false" name="Deoxyribose-phosphate aldolase" metaid="R_DRPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DRPA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DRPA"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DEOXYRIBOSE-P-ALD-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01066"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97787"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-6787321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12823"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12822"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12821"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12824"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/64"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00784"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2dr5p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4381"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TKT2" fast="false" reversible="true" name="Transketolase" metaid="R_TKT2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_TKT2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TKT2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2TRANSKETO-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.2.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01830"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104869"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27627"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27628"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27626"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27629"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2935"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2465"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_arbtn_fe3_e" fast="false" reversible="false" name="Aerobactin exchange" metaid="R_EX_arbtn_fe3_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_arbtn_fe3_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_arbtn_fe3_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142930"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_arbtn_fe3_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_UDCPDP" fast="false" reversible="false" name="Undecaprenyl-diphosphatase" metaid="R_UDCPDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_UDCPDP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDCPDP"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105042"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17069"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17070"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17072"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17071"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/5225"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0841"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1278"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3057"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_cpgn_e" fast="false" reversible="false" name="Coprogen exchange" metaid="R_EX_cpgn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_cpgn_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cpgn_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142942"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cpgn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_ch4_e" fast="false" reversible="false" name="EX ch4 LPAREN e RPAREN " metaid="R_EX_ch4_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_ch4_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ch4_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-526"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96664"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13109"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10471"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ch4_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0592"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0590"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0588"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_adocbl_e" fast="false" reversible="false" name="Adenosylcobalamin exchange" metaid="R_EX_adocbl_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0152"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0151"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20869"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/6476"/>
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+          <speciesReference species="M_tre_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3519"/>
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+      <reaction id="R_GAMtex" fast="false" reversible="true" name="D-glucosamine transport via diffusion (extracellular to periplasm)" metaid="R_GAMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08173"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
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+                <fbc:geneProductRef fbc:geneProduct="G_b3733"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3735"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3734"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3732"/>
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+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b3738"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3736"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3737"/>
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+            <fbc:and>
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+                <fbc:geneProductRef fbc:geneProduct="G_b3735"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3734"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b3732"/>
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+                <fbc:geneProductRef fbc:geneProduct="G_b3737"/>
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+        </fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34988"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34990"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/10553"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11016"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08795"/>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_lac__L_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACt4pp" fast="false" reversible="false" name="Na+/Acetate symport (periplasm)" metaid="R_ACt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4067"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28720"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28719"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28721"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08064"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05491"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3654"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3714"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3664"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CO2tpp" fast="false" reversible="true" name="CO2 transporter via diffusion (periplasm)" metaid="R_CO2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09860"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_co2_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08325"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08326"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05532"/>
+                </rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_dha_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dha_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08355"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10129"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dmso_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dms_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1872"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1873"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ARGabcpp" fast="false" reversible="false" name="L-arginine transport via ABC system (periplasm)" metaid="R_ARGabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ARGabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29880#1"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05154"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2308"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2306"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2310"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2307"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0864"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0860"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0863"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0862"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0861"/>
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+          </fbc:or>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29990"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29989"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05318"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08068"/>
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+            </rdf:Description>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2406"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALAabcpp" fast="false" reversible="false" name="L-alanine transport via ABC system (periplasm)" metaid="R_ALAabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10170"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08097"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3454"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3456"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3455"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3460"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3457"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALLabcpp" fast="false" reversible="false" name="D-allose transport via ABC system (periplasm)" metaid="R_ALLabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08112"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_all__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4087"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4088"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4086"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALLTNt2rpp" fast="false" reversible="true" name="Allantoin transport in via proton symport (periplasm)" metaid="R_ALLTNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95770"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08116"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05682"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_alltn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0511"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ARBabcpp" fast="false" reversible="false" name="L-arabinose transport via ABC system (periplasm)" metaid="R_ARBabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-2-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.17"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_arab__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1901"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1900"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_ARGAGMt7pp" fast="false" reversible="true" name="Arginine/agmatine antiport (periplasm)" metaid="R_ARGAGMt7pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29653"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29652"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29651"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13809"/>
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+          <speciesReference species="M_arg__L_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_agm_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4115"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138069"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08158"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13758"/>
+                </rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_ascb__L_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ascb6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4195"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4193"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4194"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.4.25"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25094"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25095"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/84"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01219"/>
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+          <speciesReference species="M_dcmp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dcdp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0910"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05508"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08161"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13230"/>
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+        </listOfReactants>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1453"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08165"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0652"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0655"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0653"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05217"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09825"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13233"/>
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+        <listOfProducts>
+          <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4077"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ECOAH8" fast="false" reversible="true" name="3-hydroxyacyl-CoA dehydratase (3-hydroxyoctadecanoyl-CoA)" metaid="R_ECOAH8" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.17"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08413"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_3hodcoa_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_od2coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2341"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3846"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLCDpp" fast="false" reversible="false" name="Glucose dehydrogenase (ubiquinone-8 as acceptor) (periplasm)" metaid="R_GLCDpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100177"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08608"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10116"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_glc__D_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glcn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0124"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0837"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GUAtpp" fast="false" reversible="true" name="Guanine transport via diffusion (periplasm)" metaid="R_GUAtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-578"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10142"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09746"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gua_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gua_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4464"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4064"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ASPt2_2pp" fast="false" reversible="false" name="Aspartate transport via proton symport (2 H) (periplasm)" metaid="R_ASPt2_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-122A"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96104"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29288"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29289"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29287"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29290"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08169"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10151"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3528"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HYD2pp" fast="false" reversible="false" name="Hydrogenase (menaquinone8: 2 protons) (periplasm)" metaid="R_HYD2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_HYD2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100754"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29052#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29051#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29054#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29053#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08735"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10119"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0973"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0974"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0972"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2994"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2997"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2996"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2995"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GK1" fast="false" reversible="true" name="Guanylate kinase (GMP:ATP)" metaid="R_GK1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GK1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GUANYL-KIN-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00332"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100144"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20783"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20782"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20780"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20781"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/77"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00239"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3648"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HYXNtpp" fast="false" reversible="true" name="Hypoxanthine transport (periplasm)" metaid="R_HYXNtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-579"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-562"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100749"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10143"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08737"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08738"/>
+                </rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_hxan_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_hxan_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4064"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4464"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NACtpp" fast="false" reversible="false" name="Nicotinic acid uptake (periplasm)" metaid="R_NACtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_NACtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NACtpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101808"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-8869603"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05310"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08969"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_nac_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nac_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_ASPt2_3pp" fast="false" reversible="false" name="L-asparate transport via proton symport (3 H) (periplasm)" metaid="R_ASPt2_3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96105"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10155"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_asp__L_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="3" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4138"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4123"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HIStex" fast="false" reversible="true" name="L-histidine transport via diffusion (extracellular to periplasm)" metaid="R_HIStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_HIStex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HIStex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100649"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13472"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08721"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10932"/>
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+        </sbml:annotation>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_his__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FE3DCITabcpp" fast="false" reversible="false" name="Iron transport from ferric-dicitrate via ABC system (periplasm)" metaid="R_FE3DCITabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_FE3DCITabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FE3DCITabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99508"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08478"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe3dcit_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cit_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08610"/>
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+        <listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+        <listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10928"/>
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+        <listOfProducts>
+          <speciesReference species="M_gln__L_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05468"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09032"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09734"/>
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+        <listOfProducts>
+          <speciesReference species="M_o2_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3hhcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2341"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29762"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29759"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29760"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09036"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09840"/>
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+        <listOfProducts>
+          <speciesReference species="M_octa_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08351"/>
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+          <speciesReference species="M_lac__D_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_lac__D_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_dgmp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dgsn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10824"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09048"/>
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+          <speciesReference species="M_orn_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_orn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28457"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28455"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28456"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28454"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08534"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_frulys_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_frulys_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALTtexi" fast="false" reversible="false" name="MaltoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" metaid="R_MALTtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALTtexi">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTtexi"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14351"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-575"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1741"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101364"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33173"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33172"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33171"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33174"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11211"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08874"/>
+                </rdf:Bag>
+              </bqbiol:is>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_malt_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_malt_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4036"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ECOAH5" fast="false" reversible="true" name="3-hydroxyacyl-CoA dehydratase (3-hydroxydodecanoyl-CoA)" metaid="R_ECOAH5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.17"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.74"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04170"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97890"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-77256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31078"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31075"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31077"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31076"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/3890"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02911"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3hddcoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dd2coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2341"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3846"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHFS" fast="false" reversible="false" name="Dihydrofolate synthase" metaid="R_DHFS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DHFS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHFS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DIHYDROFOLATESYNTH-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.12"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.17"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02237"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR140043"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23585"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23587"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23584"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23586"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01603"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dhpt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dhf_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2315"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CITt7pp" fast="false" reversible="false" name="Citrate transport via succinate antiport (periplasm)" metaid="R_CITt7pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CITt7pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CITt7pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96752"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28837"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28836"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28838"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28835"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08216"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10150"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cit_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0612"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CRNt7pp" fast="false" reversible="false" name="Carnitine/butyrobetaine antiporter (periplasm)" metaid="R_CRNt7pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CRNt7pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNt7pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-100"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96908"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29427"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29430"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29429"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29428"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08263"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10149"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_crn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gbbtn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gbbtn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0040"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_ni2_e" fast="false" reversible="true" name="Ni2+ exchange" metaid="R_EX_ni2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_ni2_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ni2_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-141B"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101958"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29833"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29831"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29834"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29832"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ni2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_GLCtex_copy1" fast="false" reversible="false" name="Glucose transport via diffusion (extracellular to periplasm)" metaid="R_GLCtex_copy1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLCtex_copy1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-574"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100188"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7002"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/601"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09679"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08617"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glc__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glc__D_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4036"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_no_e" fast="false" reversible="false" name="Nitric oxide exchange" metaid="R_EX_no_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_no_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_no_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101998"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_no_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_CHLabcpp" fast="false" reversible="false" name="Choline transport via ABC system (periplasm)" metaid="R_CHLabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CHLabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CHLabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96691"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/38715#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/38718#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/38717#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/38716#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05159"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08212"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_chol_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_chol_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2129"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2128"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2131"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2130"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DGSNt2pp" fast="false" reversible="false" name="Deoxyguanosine transport in via proton symport (periplasm)" metaid="R_DGSNt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DGSNt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DGSNt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97325"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09688"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08323"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dgsn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dgsn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2964"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FE3DCITtonex" fast="false" reversible="false" name="Ferric-dicitrate transport via ton system (extracellular)" metaid="R_FE3DCITtonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2167"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2169"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4123"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0621"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27951"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99549"/>
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+        <listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3005"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3006"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29935"/>
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+        <listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0336"/>
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+      <reaction id="R_CYNTt2pp" fast="false" reversible="false" name="Cyanate transport via proton symport (periplasm)" metaid="R_CYNTt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29231"/>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0341"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29783#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32795#1"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1920"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1917"/>
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+          <speciesReference species="M_sbt__D_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sbt6p_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2704"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2703"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2702"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_glc__D_p" stoichiometry="2" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1197"/>
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+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0979"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0733"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4515"/>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYTDt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108B"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97044"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29985"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29983"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08289"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05198"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cytd_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cytd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2393"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2964"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CYTDt2pp_copy2" fast="false" reversible="true" name="Cytidine transport in via proton symport (periplasm)" metaid="R_CYTDt2pp_copy2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CYTDt2pp_copy2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29984"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29985"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cytd_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cytd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2406"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DADNt2pp" fast="false" reversible="false" name="Deoxyadenosine transport in via proton symport (periplasm)" metaid="R_DADNt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DADNt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108C"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97080"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29982"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29979"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29981"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05317"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08292"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dad_2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dad_2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2393"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2964"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DCYTt2pp" fast="false" reversible="false" name="Deoxycytidine transport in via proton symport (periplasm)" metaid="R_DCYTt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DCYTt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DCYTt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108D"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97209"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29975"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29976"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29978"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29977"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05205"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08316"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dcyt_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dcyt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2393"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2964"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CYTBD2pp" fast="false" reversible="false" name="Cytochrome oxidase bd (menaquinol-8: 2 protons) (periplasm)" metaid="R_CYTBD2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CYTBD2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYTBD2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97032"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08287"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10806"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="0.5" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0978"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0979"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACGAMK" fast="false" reversible="false" name="N-acetylglucosamine kinase" metaid="R_ACGAMK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ACGAMK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAMK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:N-ACETYLGLUCOSAMINE-KINASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.59"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01201"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95249"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17420"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17418"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17419"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17417"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1435"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00892"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acgam_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acgam6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1119"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACALDtpp" fast="false" reversible="true" name="Acetaldehyde reversible transport (periplasm)" metaid="R_ACALDtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ACALDtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACALDtpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-449872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09700"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08033"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08032"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acald_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACt2rpp" fast="false" reversible="true" name="Acetate reversible transport via proton symport (periplasm)" metaid="R_ACt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ACt2rpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACt2rpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95429"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08061"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05488"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ac_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0010"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DDGLCNt2rpp" fast="false" reversible="true" name="2-dehydro-3-deoxy-D-gluconate transport via proton symport, reversible (periplasm)" metaid="R_DDGLCNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DDGLCNt2rpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DDGLCNt2rpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-113"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138207"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29945"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29943"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29946"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29944"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05681"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08319"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2ddglcn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2ddglcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3909"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_RMNtex" fast="false" reversible="true" name="L-rhamnose transport via diffusion (extracellular to periplasm)" metaid="R_RMNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_RMNtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RMNtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104042"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34995"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34998"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34996"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09229"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_rmn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_rmn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_meoh_e" fast="false" reversible="false" name="Methanol exchange" metaid="R_EX_meoh_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_meoh_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_meoh_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-459"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101464"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34873"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34874"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10570"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_meoh_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_fe3dcit_e" fast="false" reversible="false" name="Fe(III)dicitrate exchange" metaid="R_EX_fe3dcit_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fe3dcit_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142958"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fe3dcit_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_fe3hox_e" fast="false" reversible="false" name="Fe(III)hydroxamate exchange" metaid="R_EX_fe3hox_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_fe3hox_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fe3hox_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142961"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fe3hox_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_fecrm_e" fast="false" reversible="false" name="Ferrichrome exchange" metaid="R_EX_fecrm_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_fecrm_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fecrm_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1701"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2241"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR123118"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fecrm_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_feenter_e" fast="false" reversible="false" name="Fe-enterobactin exchange" metaid="R_EX_feenter_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_feenter_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_feenter_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142965"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_feenter_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_feoxam_e" fast="false" reversible="false" name="Ferroxamine exchange" metaid="R_EX_feoxam_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_feoxam_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_feoxam_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99567"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_feoxam_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_MALTTRtexi" fast="false" reversible="false" name="Maltotriose transport via diffusion (extracellular to periplasm) irreversible" metaid="R_MALTTRtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALTTRtexi">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTTRtexi"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101359"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08876"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_malttr_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_malttr_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4036"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALTTTRtexi" fast="false" reversible="false" name="MaltotetraoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" metaid="R_MALTTTRtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALTTTRtexi">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTTTRtexi"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08878"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_maltttr_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_maltttr_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4036"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALTPTtexi" fast="false" reversible="false" name="MaltopentaoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" metaid="R_MALTPTtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALTPTtexi">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTPTtexi"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101356"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08873"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_maltpt_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_maltpt_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4036"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_METS" fast="false" reversible="false" name="Methionine synthase" metaid="R_METS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_METS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.1.13"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00946"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11173"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11175"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11174"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11172"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1260"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_5mthf_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4019"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3829"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ASPO3" fast="false" reversible="false" name="L-aspartate oxidase" metaid="R_ASPO3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ASPO3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96091"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28685"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28686"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28684"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08166"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iasp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2574"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ASPO5" fast="false" reversible="false" name="L-aspartate oxidase" metaid="R_ASPO5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96093"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30043"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30045"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30044"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30046"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08168"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iasp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2574"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ASPO4" fast="false" reversible="false" name="L-aspartate oxidase" metaid="R_ASPO4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ASPO4">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPO4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96092"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29192"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29193"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29191"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29194"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08167"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iasp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2574"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_3amp_e" fast="false" reversible="false" name="3'-AMP exchange" metaid="R_EX_3amp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_3amp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_3amp_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94857"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07973"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3amp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_3gmp_e" fast="false" reversible="false" name="3'-GMP exchange" metaid="R_EX_3gmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_3gmp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_3gmp_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94868"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07975"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3gmp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_3ump_e" fast="false" reversible="false" name="3'-UMP exchange" metaid="R_EX_3ump_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_3ump_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_3ump_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94983"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08005"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3ump_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_ASPO6" fast="false" reversible="false" name="L-aspartate oxidase" metaid="R_ASPO6" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ASPO6">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPO6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:L-ASPARTATE-OXID-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.3.16"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00481"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96094"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25879"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25878"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25877"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25876"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00338"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iasp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2574"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_cu2_e" fast="false" reversible="true" name="Cu2+ exchange" metaid="R_EX_cu2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_cu2_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cu2_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-14"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96951"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28705"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28706"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28704"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28703"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08274"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08273"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cu2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_LCTStex" fast="false" reversible="true" name="Lactose transport via diffusion (extracellular to periplasm)" metaid="R_LCTStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_LCTStex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LCTStex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101027"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08780"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_lcts_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_lcts_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LEUtex" fast="false" reversible="true" name="L-leucine transport via diffusion (extracellular to periplasm)" metaid="R_LEUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_LEUtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LEUtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-447"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101057"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13056"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08786"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11003"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_leu__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_leu__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LYStex" fast="false" reversible="true" name="L-lysine transport via diffusion (extracellular to periplasm)" metaid="R_LYStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_LYStex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYStex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-569"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101269"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7984"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10834"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08856"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_lys__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_lys__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_glyc__R_e" fast="false" reversible="false" name="(R)-Glycerate exchange" metaid="R_EX_glyc__R_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_glyc__R_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glyc__R_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-523"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100323"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08645"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glyc__R_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_eca4colipa_e" fast="false" reversible="false" name="(enterobacterial common antigen)x4 core oligosaccharide lipid A exchange" metaid="R_EX_eca4colipa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_eca4colipa_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_eca4colipa_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08406"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_eca4colipa_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_GLYOX3" fast="false" reversible="false" name="Glyoxalase III" metaid="R_GLYOX3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLYOX3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYOX3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLYOXIII-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.130"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09796"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27757"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27755"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27756"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27754"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08659"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mthgxl_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lac__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1967"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FDMO3" fast="false" reversible="false" name="FMNH2-dependent monooxygenase (ethanesulfonate)" metaid="R_FDMO3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FDMO3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FDMO3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99489"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29730"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29727"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29729"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29728"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08469"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ethso3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0935"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LYXtex" fast="false" reversible="true" name="L-Lyxose transport via diffusion (extracellular to periplasm)" metaid="R_LYXtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_LYXtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYXtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101272"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08859"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_lyx__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_lyx__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MANtex" fast="false" reversible="true" name="D-mannose transport via diffusion (extracellular to periplasm)" metaid="R_MANtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MANtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MANtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101402"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11452"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08886"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_man_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_man_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MAN6Ptex" fast="false" reversible="true" name="Mannose 6-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_MAN6Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MAN6Ptex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MAN6Ptex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101385"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13644"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08880"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_man6p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_man6p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FDMO4" fast="false" reversible="false" name="FMNH2-dependent monooxygenase (butanesulfonate)" metaid="R_FDMO4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FDMO4">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FDMO4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.14.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99491"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08470"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_butso3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_btal_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0935"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CYSabc2pp" fast="false" reversible="false" name="L-cysteine export via ABC system (cytoplasm to periplasm)" metaid="R_CYSabc2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CYSabc2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.21"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32796#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32797#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29783#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29786#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32798#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29784#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29785#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32795#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08280"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cys__L_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0887"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0886"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BUTSO3abcpp" fast="false" reversible="false" name="Butanesulfonate transport via ABC system (periplasm)" metaid="R_BUTSO3abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_BUTSO3abcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BUTSO3abcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96350"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05512"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08181"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_butso3_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_butso3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0934"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0933"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0936"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0366"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0365"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0367"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ETHSO3abcpp" fast="false" reversible="false" name="Ethanesulfonate transport via ABC system (periplasm)" metaid="R_ETHSO3abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ETHSO3abcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97977"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05552"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08425"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ethso3_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ethso3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0934"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0933"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0936"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MELIBtex" fast="false" reversible="true" name="Melibiose transport via diffusion (extracellular to periplasm)" metaid="R_MELIBtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MELIBtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MELIBtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138589"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_melib_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_melib_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DMSOtex" fast="false" reversible="true" name="Dimethyl sulfoxide transport via diffusion (extracellular to periplasm)" metaid="R_DMSOtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_DMSOtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DMSOtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-273"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97533"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29700"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29701"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29702"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29699"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08358"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dmso_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dmso_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DURItex" fast="false" reversible="true" name="Deoxyuridine transport via diffusion (extracellular to periplasm)" metaid="R_DURItex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DURItex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DURItex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97819"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10984"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08377"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_duri_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_duri_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0411"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_mal__D_e" fast="false" reversible="false" name="D-Malate exchange" metaid="R_EX_mal__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_mal__D_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mal__D_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101341"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08864"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mal__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_FRUtex" fast="false" reversible="true" name="D-fructose transport via diffusion (extracellular to periplasm)" metaid="R_FRUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FRUtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FRUtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99663"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-189222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12996"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08537"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fru_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fru_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FUCtex" fast="false" reversible="true" name="L-fucose transport via diffusion (extracellular to periplasm)" metaid="R_FUCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FUCtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FUCtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99704"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fuc__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fuc__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_sel_e" fast="false" reversible="true" name="Selenate exchange" metaid="R_EX_sel_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_sel_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_sel_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104327"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34889"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34887"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34888"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34890"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_sel_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_hg2_e" fast="false" reversible="false" name="Hg2+ exchange" metaid="R_EX_hg2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_hg2_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_hg2_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100625"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32815"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32817"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32816"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32818"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05586"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08717"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_hg2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_O16GLCT1" fast="false" reversible="false" name="Glucosyltransferase I (LPS O16 antigen biosynthesis)" metaid="R_O16GLCT1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_O16GLCT1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143258"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09028"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_aragund_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_garagund_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2032"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_O16AP2pp" fast="false" reversible="false" name="O16 antigen polymerase (periplasm)" metaid="R_O16AP2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_O16AP2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138661"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_o16a2und_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o16aund_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o16a3und_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2027"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2035"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_O16AP3pp" fast="false" reversible="false" name="O16 antigen polymerase (periplasm)" metaid="R_O16AP3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138662"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_o16a3und_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o16aund_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o16a4und_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2027"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2035"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FUMtex" fast="false" reversible="true" name="Fumarate transport via diffusion (extracellular to periplasm)" metaid="R_FUMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FUMtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FUMtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-553"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99715"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08544"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11013"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fum_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fum_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACACT5r" fast="false" reversible="true" name="Acetyl-CoA C-acyltransferase (decanoyl-CoA) (r)" metaid="R_ACACT5r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ACACT5r">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACACT5r"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95199"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dcacoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3oddcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3845"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2342"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_O16A4Lpp" fast="false" reversible="false" name="O16 anitgen (x4) ligase (periplasm)" metaid="R_O16A4Lpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_O16A4Lpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16A4Lpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143257"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_colipa_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o16a4und_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o16a4colipa_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3622"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PRASCSi" fast="false" reversible="false" name="Phosphoribosylaminoimidazolesuccinocarboxamide synthase" metaid="R_PRASCSi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PRASCSi">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PRASCSi"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SAICARSYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.2.6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04591"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR108987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-73805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-73805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-419223"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-73805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-73805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-73805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-73805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-73805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-73805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-73805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-73805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-73805"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22631"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22628"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22629"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22630"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_5aizc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_25aics_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2476"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALTATr" fast="false" reversible="true" name="Maltose O-acetyltransferase" metaid="R_MALTATr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALTATr">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTATr"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALTACETYLTRAN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.79"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01556"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06251"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101351"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01133"/>
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+              </bqbiol:is>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malt_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acmalt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0459"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHBSH" fast="false" reversible="false" name="2,3-dihydroxybenzoylserine hydrolase" metaid="R_DHBSH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DHBSH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHBSH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97370"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08328"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_23dhbzs_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_23dhb_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_MALDDH" fast="false" reversible="false" name="Malate decarboxylating oxidoreductase (decarboxylating)" metaid="R_MALDDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALDDH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:1.1.1.83-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.83"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00215"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101339"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18366"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18365"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18368"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18367"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/744"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00160"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_mal__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1800"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FE2tex" fast="false" reversible="true" name="Iron (II) transport via diffusion (extracellular to periplasm)" metaid="R_FE2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28487"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28489"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28486"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08476"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10963"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fe2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fe2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NMNtex" fast="false" reversible="true" name="NMN transport via diffusion (extracellular to periplasm)" metaid="R_NMNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NMNtex"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28483"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28482"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28484"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08995"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10181"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_nmn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nmn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ENTERES" fast="false" reversible="false" name="Enterochelin Esterase" metaid="R_ENTERES" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97934"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28021"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28019"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28020"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28018"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08421"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_enter_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="3" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_23dhbzs_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0585"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NO2tex" fast="false" reversible="true" name="Nitrite transport via diffusion (extracellular to periplasm)" metaid="R_NO2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-137"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101912"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28983"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28986"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28984"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28985"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10823"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08999"/>
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+        <listOfReactants>
+          <speciesReference species="M_no2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TRSARr" fast="false" reversible="true" name="Tartronate semialdehyde reductase" metaid="R_TRSARr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5289"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.60"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01745"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18846"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18845"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18847"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18848"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01280"/>
+                </rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_2h3oppan_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc__R_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0509"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3125"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHPS2" fast="false" reversible="false" name="Dihydropteroate synthase" metaid="R_DHPS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:H2PTEROATESYNTH-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.15"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03067"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR140085"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19950"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19949"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19952"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19951"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12954"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_4abz_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_6hmhptpp_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dhpt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3177"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FEOXAMUtex" fast="false" reversible="false" name="Ferroxamine (minus Fe3) secretion (to extracellular)" metaid="R_FEOXAMUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_FEOXAMUtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99554"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08515"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_feoxam_un_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_feoxam_un_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_ARBTNtpp" fast="false" reversible="false" name="Aerobactin secretion (to periplasm)" metaid="R_ARBTNtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ARBTNtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNtpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95931"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08150"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_arbtn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_arbtn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_MTHFC" fast="false" reversible="true" name="Methenyltetrahydrofolate cyclohydrolase" metaid="R_MTHFC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01655"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101748"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-6801462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23701"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23700"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23702"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23703"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/74"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01211"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0529"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ARBTNtex" fast="false" reversible="false" name="Aerobactin secretion (to extracellular)" metaid="R_ARBTNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ARBTNtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95929"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08148"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_arbtn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_arbtn_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_MTHFD" fast="false" reversible="true" name="Methylenetetrahydrofolate dehydrogenase (NADP)" metaid="R_MTHFD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01220"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101749"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22814"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22813"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22815"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22812"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0529"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LYXI" fast="false" reversible="false" name="Lyxose isomerase" metaid="R_LYXI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYXI"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01906"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138561"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01394"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_lyx__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_xylu__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3903"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BUTt2rpp" fast="false" reversible="true" name="Butyrate transport via proton symport, reversible (periplasm)" metaid="R_BUTt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_BUTt2rpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96353"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_but_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_but_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2223"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CADVtpp" fast="false" reversible="false" name="Lysine/Cadaverine antiporter (periplasm)" metaid="R_CADVtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_CADVtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96445"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08187"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10148"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_15dap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lys__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_15dap_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4132"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_QULNS" fast="false" reversible="false" name="Quinolinate synthase" metaid="R_QULNS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:QUINOLINATE-SYNTHA-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.72"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04292"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103400"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25889"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25891"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25890"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25888"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02988"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iasp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_quln_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0750"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_23CAMPtex" fast="false" reversible="true" name="23cAMP transport via diffusion (extracellular to periplasm)" metaid="R_23CAMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94718"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07925"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_23camp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_23camp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_23CCMPtex" fast="false" reversible="true" name="23cCMP transport via diffusion (extracellular to periplasm)" metaid="R_23CCMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/23CCMPtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94720"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07926"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_23ccmp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_23ccmp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_23CUMPtex" fast="false" reversible="true" name="23cUMP transport via diffusion (extracellular to periplasm)" metaid="R_23CUMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07928"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_23cump_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_23cump_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_23CGMPtex" fast="false" reversible="true" name="23cGMP transport via diffusion (extracellular to periplasm)" metaid="R_23CGMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_23CGMPtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/23CGMPtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94721"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07927"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_23cgmp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_23cgmp_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_3AMPtex" fast="false" reversible="true" name="3AMP transport via diffusion (extracellular to periplasm)" metaid="R_3AMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3AMPtex"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07973"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3amp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3amp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_3CMPtex" fast="false" reversible="true" name="3CMP transport via diffusion (extracellular to periplasm)" metaid="R_3CMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_3CMPtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3CMPtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94861"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07974"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3cmp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3cmp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LADGMDH" fast="false" reversible="false" name="L-alanyl-gamma-D-glutamyl-meso-diaminopimelate hydrolase" metaid="R_LADGMDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_LADGMDH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101002"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08773"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_LalaDgluMdap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_26dap__M_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_LalaDglu_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1326"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALKP" fast="false" reversible="false" name="Alkaline phosphatase" metaid="R_ALKP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-7249"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01010"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/51731"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/51728"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/51730"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/51729"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00743"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dha_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2690"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GDPtex" fast="false" reversible="true" name="GDP transport via diffusion (extracellular to periplasm)" metaid="R_GDPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100096"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08600"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09815"/>
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+          </rdf:RDF>
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+        <listOfReactants>
+          <speciesReference species="M_gdp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gdp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_cobalt2_e" fast="false" reversible="true" name="Co2+ exchange" metaid="R_EX_cobalt2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28580"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28578"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12148"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08241"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08242"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10474"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_cobalt2_e" stoichiometry="1" constant="true"/>
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+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95690"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28395"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28396"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7810"/>
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+        <listOfProducts>
+          <speciesReference species="M_LalaLglu_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1325"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FEENTERtpp" fast="false" reversible="false" name="Enterochelin transport (secretion)" metaid="R_FEENTERtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29437"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29436"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_enter_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0591"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_TMAtex" fast="false" reversible="true" name="Trimethylamine transport via diffusion (extracellular to periplasm)" metaid="R_TMAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104884"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09318"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tma_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_tma_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_pheme_e" fast="false" reversible="false" name="Protoheme exchange" metaid="R_EX_pheme_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-917892"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-917892"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-917892"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-917892"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-917892"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_pheme_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_TMAOtex" fast="false" reversible="true" name="Trimethylamine N-oxide transport via diffusion (extracellular to periplasm)" metaid="R_TMAOtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104882"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tmao_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_tmao_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TREtex" fast="false" reversible="true" name="Trehalose transport via diffusion (extracellular to periplasm)" metaid="R_TREtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17631"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17632"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17630"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17629"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09323"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_tre_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_tre_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_L_LACD3" fast="false" reversible="false" name="L-Lactate dehydrogenase (menaquinone)" metaid="R_L_LACD3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.2.3"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08793"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_lac__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0306"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0308"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0307"/>
+            </fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3605"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08506"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_enter_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FE3HOXUtpp" fast="false" reversible="false" name="Fe(III)hydroxamate unloaded secretion (extracellular)" metaid="R_FE3HOXUtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99518"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08490"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fe3hox_un_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_FEOXAMUtpp" fast="false" reversible="false" name="Ferroxamine (minus Fe3) secretion (to periplasm)" metaid="R_FEOXAMUtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FEOXAMUtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEOXAMUtpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99555"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08516"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_feoxam_un_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_feoxam_un_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_FECRMUtpp" fast="false" reversible="false" name="Ferrichrome (minus Fe) secretion (to periplasm)" metaid="R_FECRMUtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99534"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08500"/>
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+        <listOfProducts>
+          <speciesReference species="M_fecrm_un_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_FE3HOXR2" fast="false" reversible="false" name="Fe(III)hydroxamate reductase" metaid="R_FE3HOXR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08486"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_fe3hox_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe3hox_un_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101273"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08792"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_lac__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0308"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0306"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0307"/>
+            </fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3605"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31092"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31091"/>
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+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ddcacoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3otdcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2342"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3845"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-449"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104949"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/14017"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13425"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09327"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05222"/>
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+          <speciesReference species="M_trp__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_trp__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28892"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28894"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28893"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09215"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ptrc_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0692"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1296"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2014"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GGGABAH" fast="false" reversible="false" name="Gamma-glutamyl-gamma-aminobutyric acid hydrolase" metaid="R_GGGABAH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100114"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19740"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19739"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19738"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19737"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05128"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_gg4abut_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4abut_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1298"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34975"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34976"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34977"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09166"/>
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+          <speciesReference species="M_pnto__R_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pnto__R_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_frulys_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_frulysp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3374"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99495"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29312"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29311"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29314"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29313"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08471"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sulfac_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glx_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0935"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32807"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32809"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09330"/>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_tsul_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10974"/>
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+          <speciesReference species="M_tyr__L_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ura_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+        </fbc:geneProductAssociation>
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+        <listOfProducts>
+          <speciesReference species="M_urea_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        <listOfProducts>
+          <speciesReference species="M_uri_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0411"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09277"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sulfac_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sulfac_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0933"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0936"/>
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+        <listOfProducts>
+          <speciesReference species="M_ethso3_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29758"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29756"/>
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+          <speciesReference species="M_lipoate_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_lipoate_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+          <speciesReference species="M_cyan_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tsul_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so3_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tcynt_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1308"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29703"/>
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+          <speciesReference species="M_val__L_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_val__L_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09652"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09378"/>
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+        <listOfReactants>
+          <speciesReference species="M_xan_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_xan_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MERCAPYSTRANS-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03106"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138585"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21741"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21740"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2944"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02230"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cyan_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mercppyr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tcynt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2521"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_XYLtex" fast="false" reversible="true" name="D-xylose transport via diffusion (extracellular to periplasm)" metaid="R_XYLtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09650"/>
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+          <speciesReference species="M_xyl__D_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_xyl__D_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_PPPNtex" fast="false" reversible="true" name="3-phenylpropionate transport via diffusion (extracellular to periplasm)" metaid="R_PPPNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103136"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29748"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29750"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29749"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29747"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09183"/>
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+          <speciesReference species="M_pppn_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_pppn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-888592"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35036"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35037"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35038"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13098"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08028"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11326"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09795"/>
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+          <speciesReference species="M_4abut_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4abut_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29680"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29679"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12483"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08526"/>
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+        </sbml:annotation>
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+        <listOfProducts>
+          <speciesReference species="M_for_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0904"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2492"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19262#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19264#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19263#1"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pheme_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pheme_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2198"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2199"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2197"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2200"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2201"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-511"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101482"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08914"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05613"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_metsox_S__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_metsox_S__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09185"/>
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+          <speciesReference species="M_ppt_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ppt_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GALBDtex" fast="false" reversible="true" name="Beta D-galactose transport via diffusion (extracellular to periplasm)" metaid="R_GALBDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08574"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_gal_bD_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gal_bD_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LIPAHT2ex" fast="false" reversible="false" name="Core oligosaccharide lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" metaid="R_LIPAHT2ex" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_colipa_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdca_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hacolipa_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0622"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DATPHs" fast="false" reversible="false" name="DATP amine hydrolysis (spontaneous)" metaid="R_DATPHs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97174"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08313"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ditp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLCTR1" fast="false" reversible="false" name="Glucosyltransferase I (LPS core synthesis)" metaid="R_GLCTR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143137"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_icolipa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gicolipa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3631"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LIPAabcpp" fast="false" reversible="false" name="Lipid A transport via ABC system (periplasm)" metaid="R_LIPAabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101082"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35251#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35254#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35253#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35252#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08787"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0914"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LIPAHTex" fast="false" reversible="false" name="Lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" metaid="R_LIPAHTex" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101079"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08790"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdca_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_halipa_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0622"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LIPACabcpp" fast="false" reversible="false" name="Lipid (cold) A transport via ABC system (periplasm)" metaid="R_LIPACabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_LIPACabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101077"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08788"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_cold_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_cold_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0914"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ECAP1pp" fast="false" reversible="false" name="Enterobacterial common antigen polymerase (periplasm)" metaid="R_ECAP1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ECAP1pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ECAP1pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97874"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_unagamuf_p" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_eca2und_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3785"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3793"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PTRCtex" fast="false" reversible="true" name="Putrescine transport via diffusion (extracellular to periplasm)" metaid="R_PTRCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PTRCtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PTRCtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103339"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09216"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13393"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ptrc_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ptrc_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UDCPDPpp" fast="false" reversible="false" name="Undecaprenyl-diphosphatase (periplasm)" metaid="R_UDCPDPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_UDCPDPpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDCPDPpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105042"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17069"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17070"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17072"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17071"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/5225"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1278"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3057"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0841"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GGGABADr" fast="false" reversible="true" name="Gamma-glutamyl-gamma aminobutyric acid dehydrogenase" metaid="R_GGGABADr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07418"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100113"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28410"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28412"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28411"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28413"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05127"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ggbutal_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gg4abut_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1300"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_mso3_e" fast="false" reversible="false" name="Methanesulfonate exchange" metaid="R_EX_mso3_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08960"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mso3_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_23camp_e" fast="false" reversible="false" name="2',3'-Cyclic AMP exchange" metaid="R_EX_23camp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_23camp_e"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07925"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_23camp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_23cgmp_e" fast="false" reversible="false" name="2',3'-Cyclic GMP exchange" metaid="R_EX_23cgmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94721"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07927"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_23cgmp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_23cump_e" fast="false" reversible="false" name="2',3'-Cyclic UMP exchange" metaid="R_EX_23cump_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_23cump_e"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07928"/>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_23cump_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_ECAP2pp" fast="false" reversible="false" name="Enterobacterial common antigen polymerase (periplasm)" metaid="R_ECAP2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+          <speciesReference species="M_eca2und_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_unagamuf_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_eca3und_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3785"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3793"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ECA4OALpp" fast="false" reversible="false" name="Enterobacterial common antigen (x4) O-antigen ligase (periplasm)" metaid="R_ECA4OALpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142825"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_colipa_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_eca4und_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_eca4colipa_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3622"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_FE3Ri" fast="false" reversible="false" name="Fe(III) reduction" metaid="R_FE3Ri" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30157"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30158"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30156"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08491"/>
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+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe3_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3844"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FE3HOXR3" fast="false" reversible="false" name="Fe(III)hydroxamate reductase" metaid="R_FE3HOXR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99516"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_fe3hox_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe3hox_un_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_FEENTERR1" fast="false" reversible="false" name="Fe-enterobactin reduction (Fe(III)-unloading)" metaid="R_FEENTERR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99543"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_feenter_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_enter_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_NODOy" fast="false" reversible="false" name="Nitric oxide dioxygenase" metaid="R_NODOy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.12.17"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05725"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19465"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19467"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19466"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19468"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_no_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_no3_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2552"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PYRtex" fast="false" reversible="true" name="Pyruvate transport via diffusion (extracellular to periplasm)" metaid="R_PYRtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-506"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-570"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103384"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12168"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10929"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09218"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pyr_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pyr_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GALM2pp" fast="false" reversible="false" name="Aldose-1-epimerase" metaid="R_GALM2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_GALM2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALM2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ALDOSE1EPIM-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28677"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28675"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28676"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28678"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7775"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08582"/>
+                </rdf:Bag>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_gal_bD_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gal_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0756"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CU1abcpp" fast="false" reversible="false" name="Copper (Cu +1) ABC transporter (periplasm)" metaid="R_CU1abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-207"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.54"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96949"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25795#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25794#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25793#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25792#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12237#1"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cu_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cu_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0484"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HG2abcpp" fast="false" reversible="false" name="Mercury (Hg+2) ABC transporter (periplasm)" metaid="R_HG2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100623"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10343"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08715"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hg2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hg2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3469"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FEENTERR3" fast="false" reversible="false" name="Fe-enterobactin reduction (Fe(III)-unloading)" metaid="R_FEENTERR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_feenter_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_enter_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_SULFACtex" fast="false" reversible="true" name="Sulfoaceate transport via diffusion (extracellular to periplasm)" metaid="R_SULFACtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09278"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_sulfac_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_sulfac_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_sulfac_e" fast="false" reversible="false" name="Sulfoacetate exchange" metaid="R_EX_sulfac_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_butso3_e" fast="false" reversible="false" name="Butanesulfonate exchange" metaid="R_EX_butso3_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_butso3_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+      <reaction id="R_GLCTR3" fast="false" reversible="false" name="Glucosyltransferase III (LPS core synthesis)" metaid="R_GLCTR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08620"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_ggagicolipa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_gggagicolipa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3626"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HEPT4" fast="false" reversible="false" name="Heptosyltransferase IV (LPS core synthesis)" metaid="R_HEPT4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08713"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_gggagicolipa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_colipa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3623"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_ethso3_e" fast="false" reversible="false" name="Ethanesulfonate exchange" metaid="R_EX_ethso3_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08426"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_ethso3_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+      <reaction id="R_DSERtex" fast="false" reversible="true" name="D-serine transport via diffusion (extracellular to periplasm)" metaid="R_DSERtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29456"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29455"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29458"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08373"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10965"/>
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+            </rdf:Description>
+          </rdf:RDF>
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+        <listOfReactants>
+          <speciesReference species="M_ser__D_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ser__D_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LA4NTpp" fast="false" reversible="false" name="4-amino-4-deoxy-L-arabinotransferase (LPS lipid A modification, periplasmic face of membrane))" metaid="R_LA4NTpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100954"/>
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+          <speciesReference species="M_uLa4n_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_acolipa_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2257"/>
+        </fbc:geneProductAssociation>
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19469"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19470"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19471"/>
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+          <speciesReference species="M_no_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_no3_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2552"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35031"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13973"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09248"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13110"/>
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+        <listOfProducts>
+          <speciesReference species="M_ser__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:or>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101998"/>
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+          <speciesReference species="M_no_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_no_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <listOfProducts>
+          <speciesReference species="M_no_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101954"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29607"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29608"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_no_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_n2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2711"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2710"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_N2Otpp" fast="false" reversible="true" name="Nitrious oxide transport (diffusion)" metaid="R_N2Otpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08967"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08264"/>
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+          <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0040"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12605"/>
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+        <listOfProducts>
+          <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4111"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_CRNDt2rpp" fast="false" reversible="true" name="D-carnitine outward transport (H+ antiport)" metaid="R_CRNDt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        <listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4111"/>
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+      <reaction id="R_CTBTt2rpp" fast="false" reversible="true" name="Cronobetaine outward transport (H+ antiport)" metaid="R_CTBTt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ctbt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4111"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_42A12BOOXpp" fast="false" reversible="false" name="4-(2-Aminoethyl)-1,2-benzenediol:oxygen oxidoreductase(deaminating)(flavin-containing)" metaid="R_42A12BOOXpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27948"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/4000"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02993"/>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_34dhpac_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1386"/>
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+      <reaction id="R_TYROXDApp" fast="false" reversible="false" name="Tyramine:oxygen oxidoreductase(deaminating)(flavin-containing) (periplasm)" metaid="R_TYROXDApp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_o2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tym_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_4hoxpacd_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1386"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pacald_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pacald_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29746"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29743"/>
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+        <listOfProducts>
+          <speciesReference species="M_peamn_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipoate_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipoate_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_AGM4PA" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase" metaid="R_AGM4PA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AGM4PA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95546"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08076"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anhgm4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_LalaDgluMdapDala_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anhgm_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0110"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_RNDR3b" fast="false" reversible="false" name="Ribonucleoside-diphosphate reductase (CDP) (glutaredoxin)" metaid="R_RNDR3b" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_RNDR3b">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNDR3b"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104065"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09233"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_grxrd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dcdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_grxox_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0849"/>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2675"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2676"/>
+              </fbc:and>
+            </fbc:and>
+            <fbc:and>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2675"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2676"/>
+              </fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3610"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2675"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2676"/>
+              </fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1064"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2675"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2676"/>
+              </fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1654"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_RNDR4b" fast="false" reversible="false" name="Ribonucleoside-diphosphate reductase (UDP) (glutaredoxin)" metaid="R_RNDR4b" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_RNDR4b">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNDR4b"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104067"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09234"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_grxrd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dudp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_grxox_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0849"/>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2675"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2676"/>
+              </fbc:and>
+            </fbc:and>
+            <fbc:and>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2675"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2676"/>
+              </fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3610"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2675"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2676"/>
+              </fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1654"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2675"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2676"/>
+              </fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1064"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACGAL1Ptex" fast="false" reversible="true" name="N-acetyl-D-galactosamine 1-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_ACGAL1Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ACGAL1Ptex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAL1Ptex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95234"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08036"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acgal1p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acgal1p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACGALtex" fast="false" reversible="true" name="N-acetyl-D-galactosamine transport via diffusion (extracellular to periplasm)" metaid="R_ACGALtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ACGALtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGALtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95244"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08037"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acgal_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acgal_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLCUR1Ptex" fast="false" reversible="true" name="D-glucuronate 1-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_GLCUR1Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_GLCUR1Ptex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCUR1Ptex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100231"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08621"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glcur1p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glcur1p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UDPGLCURtex" fast="false" reversible="true" name="UDP-D-glucuronate transport via diffusion (extracellular to periplasm)" metaid="R_UDPGLCURtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_UDPGLCURtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPGLCURtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105066"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09352"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_udpglcur_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_udpglcur_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UDPGALPpp" fast="false" reversible="false" name="UDPgalactose pyrophosphohydrolase" metaid="R_UDPGALPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_UDPGALPpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPGALPpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.45"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09348"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpgal_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gal1p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UACGAMPpp" fast="false" reversible="false" name="UDP-N-acetyl-D-glucosamine pyrophosphohydrolase (periplasm)" metaid="R_UACGAMPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_UACGAMPpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UACGAMPpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.45"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105020"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09341"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uacgam_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acgam1p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UACGALPpp" fast="false" reversible="false" name="UDP-N-acetyl-D-galactosamine pyrophosphohydrolase (periplasm)" metaid="R_UACGALPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_UACGALPpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UACGALPpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.45"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09340"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpacgal_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acgal1p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UGLCURPpp" fast="false" reversible="false" name="UDP-D-glucuronate pyrophosphohydrolase (periplasm)" metaid="R_UGLCURPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UGLCURPpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105055"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29562"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29559"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29561"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29560"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09355"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpglcur_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glcur1p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FEROpp" fast="false" reversible="false" name="Ferroxidase" metaid="R_FEROpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FEROpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11437"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11149"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11438"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11151"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11436"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11150"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11148"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/665"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00056"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fe2_p" stoichiometry="4" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="4" constant="true"/>
+          <speciesReference species="M_o2_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fe3_p" stoichiometry="4" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0123"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3336"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ISETACabcpp" fast="false" reversible="false" name="Isethionate transport via ABC system (periplasm)" metaid="R_ISETACabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100880"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08758"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05594"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_isetac_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_isetac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0365"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0366"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0367"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0933"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0934"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0936"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ISETACtex" fast="false" reversible="true" name="Isethionate transport via diffusion (extracellular to periplasm)" metaid="R_ISETACtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ISETACtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100881"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08759"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_isetac_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_isetac_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GUR1PPpp" fast="false" reversible="false" name="Glucuronate 1-phosphate phosphatase (periplasm)" metaid="R_GUR1PPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GUR1PPpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GUR1PPpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100480"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08684"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glcur1p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glcur_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_UDPGtex" fast="false" reversible="true" name="UDPglucose transport via diffusion (extracellular to periplasm)" metaid="R_UDPGtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_UDPGtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143086"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11025"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09353"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_udpg_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_udpg_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACGAL1PPpp" fast="false" reversible="false" name="N-acetyl-D-galactosamine 1-phosphatase (periplasm)" metaid="R_ACGAL1PPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ACGAL1PPpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAL1PPpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95233"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08035"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_acgal1p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acgal_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_UDPGALtex" fast="false" reversible="true" name="UDPgalactose transport via diffusion (extracellular to periplasm)" metaid="R_UDPGALtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPGALtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105061"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09349"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13413"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_udpgal_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_udpgal_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACGAM1Ptex" fast="false" reversible="true" name="N-acetyl-D-glucosamine 1-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_ACGAM1Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ACGAM1Ptex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ACGAM1Ptex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95246"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08039"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acgam1p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acgam1p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UACGAMtex" fast="false" reversible="true" name="UDP-N-acetyl-D-glucosamine transport via diffusion (extracellular to periplasm)" metaid="R_UACGAMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105021"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-742354"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09342"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_uacgam_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_uacgam_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UDPACGALtex" fast="false" reversible="true" name="UDP-N-acetyl-D-galactosamine transport via diffusion (extracellular to periplasm)" metaid="R_UDPACGALtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_UDPACGALtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPACGALtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105046"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09347"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_udpacgal_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_udpacgal_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AM4PCP" fast="false" reversible="false" name="Anhydrous-N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase" metaid="R_AM4PCP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AM4PCP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AM4PCP"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95794"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08125"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anhm4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anhm3p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1192"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AM3PA" fast="false" reversible="false" name="Anhydrous-N-Acetylmuramyl-tripeptide amidase" metaid="R_AM3PA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AM3PA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AM3PA"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95792"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08123"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anhm3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_LalaDgluMdap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anhm_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0110"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UM4PCP" fast="false" reversible="false" name="UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine L,D-carboxypeptidase" metaid="R_UM4PCP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105116"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_um4p_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ala__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ugmd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1192"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CBLAT" fast="false" reversible="true" name="Cob(I)alamin adenosyltransferase" metaid="R_CBLAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CBLAT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:COBALADENOSYLTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.17"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01492"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96476"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_cbl1_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adocbl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1270"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTRIR4pp" fast="false" reversible="false" name="Nitrite Reductase (Menaquinole-8, periplasm)" metaid="R_NTRIR4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102065"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29164"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29166"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29165"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29163"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09019"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mql8_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_nh4_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4070"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4071"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4072"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4073"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTRIR3pp" fast="false" reversible="false" name="Nitrite Reductase (Ubiquinole-8, periplasm)" metaid="R_NTRIR3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102064"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29157"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29155"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29156"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29158"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09018"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="3" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nh4_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8_c" stoichiometry="3" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4070"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4071"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4072"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4073"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_INOSTt4pp" fast="false" reversible="false" name="Na+/myo-inositol symporter (periplasm)" metaid="R_INOSTt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_INOSTt4pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INOSTt4pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08752"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_inost_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_inost_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3679"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PHEMEtiex" fast="false" reversible="false" name="Protoheme transport irreversible out via diffusion (periplasm to extracellular)" metaid="R_PHEMEtiex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PHEMEtiex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102625"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-917892"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-917892"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-917892"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-917892"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-917892"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-917892"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-917892"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-917892"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-917892"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pheme_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pheme_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_AGM3PA" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide amidase" metaid="R_AGM3PA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_AGM3PA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95543"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08073"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anhgm3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_LalaDgluMdap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anhgm_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0110"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CYANtex" fast="false" reversible="true" name="Cyanide transport via diffusion (extracellular to periplasm)" metaid="R_CYANtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CYANtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYANtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96957"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08276"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cyan_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cyan_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SO3tex" fast="false" reversible="true" name="Sulfite transport via diffusion (extracellular to periplasm)" metaid="R_SO3tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SO3tex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104460"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12453"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09260"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_so3_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_so3_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TCYNTtex" fast="false" reversible="true" name="Thiocyanate transport via diffusion (extracellular to periplasm)" metaid="R_TCYNTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_TCYNTtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TCYNTtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104749"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09287"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tcynt_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_tcynt_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACANTHAT" fast="false" reversible="false" name="Acetyl-CoA:anthranilate acetyltransferase" metaid="R_ACANTHAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28551"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28550"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28552"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08034"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anth_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acanth_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1463"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_METSOX2abcpp" fast="false" reversible="false" name="L-methionine R-oxide transport via ABC system (periplasm)" metaid="R_METSOX2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-7185"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138592"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08916"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_metsox_R__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_metsox_R__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_METSOX1tex" fast="false" reversible="true" name="L-methionine S-oxide diffusion (extracellular)" metaid="R_METSOX1tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_metsox_S__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_metsox_S__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_METSOX2tex" fast="false" reversible="true" name="L-methionine R-oxide diffusion (extracellular)" metaid="R_METSOX2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138593"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08917"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_metsox_R__L_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_metsox_R__L_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_3UMPtex" fast="false" reversible="true" name="3UMP transport via diffusion (extracellular to periplasm)" metaid="R_3UMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94983"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08005"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3ump_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3ump_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MSO3abcpp" fast="false" reversible="false" name="Methanesulfonate transport via ABC system (periplasm)" metaid="R_MSO3abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_MSO3abcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MSO3abcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101741"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05621"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08959"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mso3_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mso3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0933"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0936"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0934"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MSO3tex" fast="false" reversible="true" name="Methanesulfonate transport via diffusion (extracellular to periplasm)" metaid="R_MSO3tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MSO3tex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MSO3tex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101742"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08960"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mso3_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_mso3_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FECRMR1" fast="false" reversible="false" name="Ferrichrome reductase" metaid="R_FECRMR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FECRMR1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FECRMR1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99530"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08495"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fecrm_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fecrm_un_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_FECRMR2" fast="false" reversible="false" name="Ferrichrome reductase" metaid="R_FECRMR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_FECRMR2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FECRMR2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99531"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08496"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fecrm_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fecrm_un_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_TDP" fast="false" reversible="false" name="Thiamin pyrophosphatase" metaid="R_TDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_TDP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TDP"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-3542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.15"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00615"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104756"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27998"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28000"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28001"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27999"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00436"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thmpp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thmmp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1134"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_3PEPTabcpp" fast="false" reversible="false" name="Tripeptide (LalaDgluMdap) transport via ABC system (periplasm)" metaid="R_3PEPTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_3PEPTabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3PEPTabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94970"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08003"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_LalaDgluMdap_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_LalaDgluMdap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1245"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1247"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1244"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1329"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1246"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2177"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2180"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2178"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2179"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1245"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1247"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1246"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1244"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1243"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_4PEPTabcpp" fast="false" reversible="false" name="Tetrapeptide (LalaDgluMdapDala) transport via ABC system (periplasm)" metaid="R_4PEPTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_4PEPTabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4PEPTabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95050"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08008"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_LalaDgluMdapDala_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_LalaDgluMdapDala_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1243"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1247"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1244"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1245"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1246"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2177"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2180"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2178"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2179"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_3GMPtex" fast="false" reversible="true" name="3GMP transport via diffusion (extracellular to periplasm)" metaid="R_3GMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_3GMPtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3GMPtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94868"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07975"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3gmp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3gmp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FALDtpp" fast="false" reversible="true" name="Formaldehyde transport via diffusion (periplasm)" metaid="R_FALDtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_FALDtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FALDtpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99238"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08461"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08462"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fald_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fald_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_tym_e" fast="false" reversible="false" name="Tyramine exchange" metaid="R_EX_tym_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_tym_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09335"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tym_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_AGM3Pt2pp" fast="false" reversible="false" name="GlcNAc-anhMurNAc tripeptide transport in via proton symport (periplasm)" metaid="R_AGM3Pt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_AGM3Pt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95545"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08075"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anhgm3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_anhgm3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0433"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SO4tex" fast="false" reversible="true" name="Sulfate transport via diffusion (extracellular to periplasm)" metaid="R_SO4tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104469"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-8875871"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34983"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34984"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34986"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34985"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09261"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05238"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_so4_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_so4_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AGM4Pt2pp" fast="false" reversible="false" name="GlcNAc-anhMurNAc tetrapeptide transport in via proton symport (periplasm)" metaid="R_AGM4Pt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AGM4Pt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM4Pt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95549"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08079"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anhgm4p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_anhgm4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0433"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AGMt2pp" fast="false" reversible="false" name="GlcNAc-anhMurNAc transport in via proton symport (periplasm)" metaid="R_AGMt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AGMt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95555"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08081"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anhgm_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_anhgm_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0433"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FECRMexs" fast="false" reversible="false" name="Ferrichrome Fe(III)-loading reaction (spontaneous)" metaid="R_FECRMexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FECRMexs">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FECRMexs"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99536"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08494"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fecrm_un_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fecrm_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ARBTNR1" fast="false" reversible="false" name="Aerobactin reductase" metaid="R_ARBTNR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ARBTNR1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNR1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95924"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08145"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_arbtn_fe3_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_arbtn_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_ARBTNR2" fast="false" reversible="false" name="Aerobactin reductase" metaid="R_ARBTNR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ARBTNR2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNR2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95925"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08146"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_arbtn_fe3_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_arbtn_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_METSOXR1" fast="false" reversible="false" name="L-methionine-S-oxide reductase" metaid="R_METSOXR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02025"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101484"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn06077"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08918"/>
+                </rdf:Bag>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_metsox_S__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2582"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4219"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3781"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4219"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3551"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2582"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3551"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3781"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_METSOXR2" fast="false" reversible="false" name="L-methionine-R-sulfoxide reductase" metaid="R_METSOXR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_METSOXR2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.4.14"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07608"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138594"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08919"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07439"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_metsox_R__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2582"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1778"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3781"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1778"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1832"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3781"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1832"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2582"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DAPAL" fast="false" reversible="false" name="2,3-diaminopropionate amonnia lyase" metaid="R_DAPAL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00195"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97138"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22085"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22087"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22084"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22086"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/741"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/9888"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00144"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_23dappa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nh4_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2871"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AMPTASECG" fast="false" reversible="false" name="Alanyl aminopeptidase (cys-gly)" metaid="R_AMPTASECG" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AMPTASECG">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-6622"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.11.23"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.11.1"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-1247910"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-1247910"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-1247910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-1247910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-1247910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-1247910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-1247910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-1247910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-1247910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28786"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28785"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28784"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28783"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1221"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00650"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cgly_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0932"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4260"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2523"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0237"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_imp_e" fast="false" reversible="false" name="IMP exchange" metaid="R_EX_imp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_imp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_imp_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-566"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100831"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08749"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_imp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_DOPAtex" fast="false" reversible="true" name="Dopamine transport via diffusion (extracellular to periplasm)" metaid="R_DOPAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DOPAtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DOPAtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97758"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-372542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-372542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-372542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-372542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-372542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-372542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-372542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-372542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-372542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-372542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-372542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-351596"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7032"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08363"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dopa_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dopa_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_4HOXPACDtex" fast="false" reversible="true" name="4-hydroxyphenylacetaldehyde transport via diffusion (extracellular to periplasm)" metaid="R_4HOXPACDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_4HOXPACDtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4HOXPACDtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95017"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08006"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_4hoxpacd_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4hoxpacd_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ARBTNR3" fast="false" reversible="false" name="Aerobactin reductase" metaid="R_ARBTNR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ARBTNR3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNR3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95926"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08147"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_arbtn_fe3_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_arbtn_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_ARBTNexs" fast="false" reversible="false" name="Aerobactin Fe-loading reaction (spontaneous)" metaid="R_ARBTNexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ARBTNexs">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ARBTNexs"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95928"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08144"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_arbtn_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_arbtn_fe3_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FEOXAMexs" fast="false" reversible="false" name="Ferroxamine Fe3-loading reaction (spontaneous)" metaid="R_FEOXAMexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FEOXAMexs">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FEOXAMexs"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143101"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08510"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_feoxam_un_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_feoxam_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LACZpp" fast="false" reversible="false" name="B-galactosidase" metaid="R_LACZpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_LACZpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LACZpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.23"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.108"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06114"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01100"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101000"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10077"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10078"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10076"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10079"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/9724"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00816"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11244"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lcts_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gal_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glc__D_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2132"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SPMDtex" fast="false" reversible="true" name="Spermidine transport via diffusion (extracellular to periplasm)" metaid="R_SPMDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_SPMDtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SPMDtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104495"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35040"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35039"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35042"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35041"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13767"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09266"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_spmd_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_spmd_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GPDDA1pp" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphocholine)" metaid="R_GPDDA1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GPDDA1pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GPDDA1pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.1.4.2-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.46"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.4.2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01030"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100410"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-6814137"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-1483116"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6814132"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-1483112"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16061"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16063"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16062"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16064"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1318"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00758"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_g3pc_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_chol_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2239"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GPDDA5pp" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoinositol)" metaid="R_GPDDA5pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_inost_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
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+          <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2763"/>
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+        </fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_fe3hox_un_c" stoichiometry="2" constant="true"/>
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+              </bqbiol:is>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_enter_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_feenter_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SUCRtex" fast="false" reversible="true" name="Sucrose transport transport via diffusion (extracellular to periplasm)" metaid="R_SUCRtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09275"/>
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+          <speciesReference species="M_sucr_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FE3HOXexs" fast="false" reversible="false" name="Fe(III) hydroxamate Fe-loading reaction (spontaneaous)" metaid="R_FE3HOXexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_fe3hox_un_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_fe3hox_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_FECRMR3" fast="false" reversible="false" name="Ferrichrome reductase" metaid="R_FECRMR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fecrm_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fecrm_un_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_FDMO2" fast="false" reversible="false" name="FMNH2-dependent monooxygenase (methanesulfonate)" metaid="R_FDMO2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_mso3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_fald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0935"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LALGP" fast="false" reversible="false" name="L-alanyl-gamma-L-glutamate peptidase" metaid="R_LALGP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29337"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29335"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29338"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0237"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AGM4PApp" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase (periplasm)" metaid="R_AGM4PApp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            </rdf:Description>
+          </rdf:RDF>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_LalaDgluMdapDala_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anhgm_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2817"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4169"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2435"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0867"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DARABISOM-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95909"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13852"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13851"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13850"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01152"/>
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+          <speciesReference species="M_arab__D_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_rbl__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2802"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AGt3" fast="false" reversible="false" name="Silver transport out via proton antiport" metaid="R_AGt3" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95620"/>
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+          <speciesReference species="M_ag_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ag_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0572"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0574"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0573"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0575"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28742"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28739"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08196"/>
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+          <speciesReference species="M_cd2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cd2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3915"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0752"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ZNabcpp" fast="false" reversible="false" name="Zinc (Zn+2) transport via ABC system (periplasm)" metaid="R_ZNabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09392"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_zn2_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_zn2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1858"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1857"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10827"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09256"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_skm_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_skm_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1981"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FE2t2pp" fast="false" reversible="false" name="Iron (II) transport in via proton symport (periplasm)" metaid="R_FE2t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2421"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99501"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29579"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29582"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29581"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29580"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08473"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fe2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fe2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2392"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLYC2Ptex" fast="false" reversible="true" name="Glycerol-2-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_GLYC2Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLYC2Ptex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100319"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08640"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glyc2p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc2p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PSERtex" fast="false" reversible="true" name="Phospho-L-serine transport via diffusion (extracellular to periplasm)" metaid="R_PSERtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PSERtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSERtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103246"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09204"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pser__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pser__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TARTRtex" fast="false" reversible="true" name="Tartrate transport via diffusion (extracellular to periplasm)" metaid="R_TARTRtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_TARTRtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TARTRtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104724"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09284"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tartr__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_tartr__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_R5Ptex" fast="false" reversible="true" name="Ribose 5-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_R5Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_R5Ptex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/R5Ptex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103411"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_r5p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_r5p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_THRPtex" fast="false" reversible="true" name="Phospho-L-threonine transport via diffusion (extracellular to periplasm)" metaid="R_THRPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_THRPtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRPtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104845"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09303"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_thrp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_thrp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TYRPtex" fast="false" reversible="true" name="Phopho-L-tyrosine transport via diffusion (extracellular to periplasm)" metaid="R_TYRPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_TYRPtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TYRPtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104999"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09337"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tyrp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_tyrp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_R5PPpp" fast="false" reversible="false" name="Ribose 5-phosphate phosphatase" metaid="R_R5PPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_R5PPpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/R5PPpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103410"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_r5p_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rib__D_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PSP_Lpp" fast="false" reversible="false" name="Phospho-L-serine phosphatase (periplasmic)" metaid="R_PSP_Lpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PSP_Lpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSP_Lpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5114"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00582"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103260"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-977324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21208"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21211"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21210"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21209"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/10330"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/983"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00420"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pser__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ser__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TYRPpp" fast="false" reversible="false" name="Phospho-L-tyrosine phosphatase (periplasmic)" metaid="R_TYRPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_TYRPpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TYRPpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14534"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104998"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30866"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30863"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30865"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30864"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/9571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09336"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tyrp_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tyr__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_R1PK" fast="false" reversible="false" name="Ribose 1-phosphokinase" metaid="R_R1PK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_R1PK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/R1PK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1402"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103408"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29776"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29775"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29777"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29778"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09221"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_r1p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_r15bp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_PAPSR2" fast="false" reversible="false" name="Phosphoadenylyl-sulfate reductase (glutaredoxin)" metaid="R_PAPSR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2762"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b1654"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2762"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GRXR" fast="false" reversible="false" name="Glutaredoxin reductase" metaid="R_GRXR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <fbc:geneProductRef fbc:geneProduct="G_b0849"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_RNDR1b" fast="false" reversible="false" name="Ribonucleoside-diphosphate reductase (ADP) (glutaredoxin)" metaid="R_RNDR1b" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_grxrd_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_grxox_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b1064"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0849"/>
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+                <fbc:geneProductRef fbc:geneProduct="G_b2675"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2676"/>
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+                <fbc:geneProductRef fbc:geneProduct="G_b2676"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b1654"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20110"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20111"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20109"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20112"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04651"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4094"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16779#1"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10168"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10558"/>
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+          <speciesReference species="M_k_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_k_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0698"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0697"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0697"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4513"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
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+          <speciesReference species="M_grxrd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dgdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_grxox_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3610"/>
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+        </fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0452"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tdcoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0452"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LEUabcpp" fast="false" reversible="false" name="L-leucine transport via ABC system (periplasm)" metaid="R_LEUabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_LEUabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LEUabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-35-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101054"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29810#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29808#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29809#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29807#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05161"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08784"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_leu__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_leu__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3455"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3460"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3457"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3454"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3456"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3458"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3456"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3455"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3457"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3454"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_L_LACt2rpp" fast="false" reversible="true" name="L-lactate reversible transport via proton symport (periplasm)" metaid="R_L_LACt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_L_LACt2rpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/L_LACt2rpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-104"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101277"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373889"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-373875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-373867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-373875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-373867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-373867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373887"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-373875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-373875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-373867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-373867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-373867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-373867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-373867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-373875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-373867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-373867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-373875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-373875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-373875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-373875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-373875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29418"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29417"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05602"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08794"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13334"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lac__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lac__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3603"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2975"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALt2_2pp" fast="false" reversible="false" name="Malate transport via proton symport (2 H) (periplasm)" metaid="R_MALt2_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALt2_2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALt2_2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-121A"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101370"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29341"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29340"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29342"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29339"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08865"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10153"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mal__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3528"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CPGNR1" fast="false" reversible="false" name="Coprogen(Fe(III)) reductase" metaid="R_CPGNR1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CPGNR1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNR1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96868"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08247"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cpgn_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cpgn_un_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_CPGNR2" fast="false" reversible="false" name="Coprogen(Fe(III)) reductase" metaid="R_CPGNR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CPGNR2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNR2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96869"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08248"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cpgn_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cpgn_un_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_THRtex" fast="false" reversible="true" name="L-threonine transport via diffusion (extracellular to periplasm)" metaid="R_THRtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_THRtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104852"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35022"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35020"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35019"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35021"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13464"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09307"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13117"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10898"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_thr__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_thr__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CPGNR3" fast="false" reversible="false" name="Coprogen(Fe(III)) reductase" metaid="R_CPGNR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CPGNR3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNR3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96870"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08249"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cpgn_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cpgn_un_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_CPGNUtpp" fast="false" reversible="false" name="Coprogen unloaded secretion" metaid="R_CPGNUtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CPGNUtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNUtpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08252"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cpgn_un_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cpgn_un_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_CPGNUtex" fast="false" reversible="false" name="Coprogen unloaded secretion (extracellular)" metaid="R_CPGNUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CPGNUtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNUtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08251"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cpgn_un_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cpgn_un_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_MALt2_3pp" fast="false" reversible="false" name="Malate transport via proton symport (3 H) (periplasm)" metaid="R_MALt2_3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALt2_3pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALt2_3pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101371"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10156"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08866"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_mal__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4123"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4138"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALTabcpp" fast="false" reversible="false" name="Maltose transport via ABC system (periplasm)" metaid="R_MALTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALTabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.19-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-16-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.19"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101362"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22134#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22135#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22132#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22133#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12365#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05170"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malt_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4033"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4035"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4032"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4034"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALTHXabcpp" fast="false" reversible="false" name="Maltohexaose transport via ABC system (periplasm)" metaid="R_MALTHXabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALTHXabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTHXabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101353"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08869"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10174"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malthx_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4034"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4032"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4033"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4035"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALTPTabcpp" fast="false" reversible="false" name="Maltopentaose transport via ABC system (periplasm)" metaid="R_MALTPTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALTPTabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTPTabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101355"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10172"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltpt_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltpt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4035"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4032"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4033"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4034"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AAMYL" fast="false" reversible="false" name="Alpha-amylase" metaid="R_AAMYL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AAMYL">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AAMYL"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95153"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_14glucan_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1927"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AAMYLpp" fast="false" reversible="false" name="Alpha-amylase (periplasm)" metaid="R_AAMYLpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AAMYLpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AAMYLpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95153"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_14glucan_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_malthx_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3571"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALTTRabcpp" fast="false" reversible="false" name="Maltotriose transport via ABC system (periplasm)" metaid="R_MALTTRabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALTTRabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTTRabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-503"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101358"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05608"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08875"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malttr_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malttr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4034"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4035"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4033"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4032"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_THMDtex" fast="false" reversible="true" name="Thymidine transport via diffusion (extracellular to periplasm)" metaid="R_THMDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_THMDtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THMDtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104821"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10916"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09299"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_thymd_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_thymd_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALTTTRabcpp" fast="false" reversible="false" name="Maltotetraose transport via ABC system (periplasm)" metaid="R_MALTTTRabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MALTTTRabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALTTTRabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-504"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101360"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08877"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10173"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltttr_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltttr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4033"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4032"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4034"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4035"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MAN6Pt6_2pp" fast="false" reversible="false" name="Mannose-6-phosphate transport via phosphate antiport (periplasm)" metaid="R_MAN6Pt6_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MAN6Pt6_2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MAN6Pt6_2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101384"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10187"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08879"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_man6p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_man6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3666"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FACOAL80t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (octanoate transport via vectoral Co-A coupling)" metaid="R_FACOAL80t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FACOAL80t2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FACOAL80t2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99206"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/51824"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/51825"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/51827"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/51826"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_octa_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_occoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1805"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1701"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PPGPPDP" fast="false" reversible="false" name="Guanosine-3',5'-bis(diphosphate) 3'-diphosphatase" metaid="R_PPGPPDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PPGPPDP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPGPPDP"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PPGPPSYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.7.2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00336"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103109"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14254"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14255"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14253"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00242"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppgpp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3650"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CPGNabcpp" fast="false" reversible="false" name="Coprogen transport via ABC system (periplasm)" metaid="R_CPGNabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CPGNabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPGNabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96873"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08245"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cpgn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cpgn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0151"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0153"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0152"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CPGNexs" fast="false" reversible="false" name="Coprogen Fe-loading reaction (spontaneaous)" metaid="R_CPGNexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08246"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cpgn_un_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cpgn_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MANGLYCptspp" fast="false" reversible="false" name="2-O-alpha-mannosyl-D-glycerate transport via PEP:Pyr PTS (periplasm)" metaid="R_MANGLYCptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101394"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08882"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_manglyc_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_man6pglyc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0731"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MELIBt2pp" fast="false" reversible="false" name="Melibiose transport in via symport (periplasm)" metaid="R_MELIBt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MELIBt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-94"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138587"/>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_melib_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_melib_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4120"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0343"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CBIuabcpp" fast="false" reversible="false" name="Cobinamide transport via ABC system (uptake, periplasm)" metaid="R_CBIuabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_CBIuabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.33"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96467"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cbi_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cbi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1711"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0158"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1709"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_METabcpp" fast="false" reversible="false" name="L-methionine transport via ABC system (periplasm)" metaid="R_METabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_METabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/METabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-4522"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29780#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29779#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29782#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29781#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32829#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32827#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32830#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32828#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05219"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08909"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11151"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0198"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0197"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0199"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CITtex" fast="false" reversible="true" name="Citrate transport via diffusion (extracellular to periplasm)" metaid="R_CITtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CITtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CITtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96756"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33184"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33186"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33183"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33185"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10946"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08217"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cit_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cit_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACGAtex" fast="false" reversible="true" name="N-Acetyl-D-glucosamine transport via diffusion (extracellular to periplasm)" metaid="R_ACGAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ACGAtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95252"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08042"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acgam_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acgam_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DDCAtexi" fast="false" reversible="false" name="Fatty acid (dodecanoate) transport via facilitated irreversible diffusion (extracellular to periplasm)" metaid="R_DDCAtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_DDCAtexi">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97211"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ddca_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2344"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TTDCAtexi" fast="false" reversible="false" name="Tetradecanoate transport via facilitated irreversible diffusion (extracellular to periplasm)" metaid="R_TTDCAtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99092"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ttdca_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2344"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HDCAtexi" fast="false" reversible="false" name="Hexadecanoate transport via facilitated irreversible diffusion (extracellular to periplasm)" metaid="R_HDCAtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/45258"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/45259"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08704"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09848"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09676"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_hdca_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2344"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GUACYC" fast="false" reversible="false" name="Guanylate cyclase" metaid="R_GUACYC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GUANYLCYC-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00434"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13667"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13665"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00307"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_35cgmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_EX_fe3hox_un_e" fast="false" reversible="false" name="Fe(III)hydoxamate, unloaded exchange" metaid="R_EX_fe3hox_un_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_na1_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_na1_p" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1186"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ATPHs" fast="false" reversible="false" name="ATP amine hydrolysis (spontaneous)" metaid="R_ATPHs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ATP-DEAMINASE-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13040"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13039"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_itp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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+      <reaction id="R_SARCOX" fast="false" reversible="false" name="Sarcosine oxidase" metaid="R_SARCOX" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13314"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13313"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13316"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1001"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00433"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sarcs_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1059"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GTPHs" fast="false" reversible="false" name="GTP amine hydrolysis (spontaneous)" metaid="R_GTPHs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100459"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08679"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xtp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MN6PP" fast="false" reversible="false" name="Mannose 6-phosphate phosphatase" metaid="R_MN6PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101671"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28556"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28557"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28555"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28554"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7278"/>
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+          <speciesReference species="M_man6p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_man_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0822"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1727"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3697"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3826"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NAt3_2pp" fast="false" reversible="false" name="Sodium proton antiporter (H:NA is 2) (periplasm)" metaid="R_NAt3_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29251"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29254"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29253"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10178"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08983"/>
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+          <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0019"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NH4tpp" fast="false" reversible="true" name="Ammonia reversible transport (periplasm)" metaid="R_NH4tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28747"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08986"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09736"/>
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+        <listOfProducts>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0451"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07127"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94909"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28223"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28225"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28224"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04930"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3dhgulnp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3580"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13461"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08920"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10976"/>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_met__L_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28708"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_fru_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3697"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2690"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2293"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3826"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NMNPtpp" fast="false" reversible="false" name="NMN permease (periplasm)" metaid="R_NMNPtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_NMNPtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28483"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28482"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28484"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08995"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10181"/>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nmn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0751"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NO2t2rpp" fast="false" reversible="true" name="Nitrite transport in via proton symport, reversible (periplasm)" metaid="R_NO2t2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101984"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05625"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08998"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_no2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1223"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3367"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NO3t7pp" fast="false" reversible="false" name="Nitrate transport in via nitrite antiport (periplasm)" metaid="R_NO3t7pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101995"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28746"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28743"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28744"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28745"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09004"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10177"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_no3_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_no2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_no3_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1223"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1469"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ORNabcpp" fast="false" reversible="false" name="Ornithine transport via ABC system (periplasm)" metaid="R_ORNabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ORNabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-37-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.21"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29883#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29885#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29886#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29884#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09046"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05156"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_orn_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2307"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2308"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2306"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2310"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PIuabcpp" fast="false" reversible="false" name="Phosphate transport via ABC system (uptake, periplasm)" metaid="R_PIuabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PIuabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-27-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.27"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102870"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24441#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24442#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24443#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24440#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05145"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09122"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3725"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3727"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3728"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3726"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PNTOt4pp" fast="false" reversible="false" name="Pantothenate sodium symporter (periplasm)" metaid="R_PNTOt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-117"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103054"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29930"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29929"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29928"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09165"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10180"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
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+          <speciesReference species="M_pnto__R_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pnto__R_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3258"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FRULYSDG" fast="false" reversible="true" name="Fructoselysine phosphate deglycase" metaid="R_FRULYSDG" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_FRULYSDG">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99653"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08530"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3371"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_METDabcpp" fast="false" reversible="false" name="D-methionine transport via ABC system (periplasm)" metaid="R_METDabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_METDabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-202"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101472"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29770#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29767#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29769#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29768#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05183"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__D_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0198"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0199"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0197"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GDPMNH" fast="false" reversible="false" name="GDP-mannose mannosyl hydrolase" metaid="R_GDPMNH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100091"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28102"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28104"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28103"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28105"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08599"/>
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+          <speciesReference species="M_gdpmann_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_man_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2051"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_FACOAL60t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (hexanoate transport via vectoral Co-A coupling)" metaid="R_FACOAL60t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hxa_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hxcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1805"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1701"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_IDONt2rpp" fast="false" reversible="true" name="L-idonate transport via proton symport, reversible (periplasm)" metaid="R_IDONt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29573"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29571"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29574"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08742"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10167"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_idon__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_idon__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4265"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ILEabcpp" fast="false" reversible="false" name="L-isoleucine transport via ABC system (periplasm)" metaid="R_ILEabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ILEabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-15-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100821"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29820#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29819#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29821#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29822#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08745"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05179"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ile__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ile__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3456"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3455"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3460"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3457"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3454"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_INDOLEt2pp" fast="false" reversible="false" name="Indole transport via proton symport, irreversible (periplasm)" metaid="R_INDOLEt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_INDOLEt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INDOLEt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-142"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100835"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29228"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29227"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29230"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29229"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08750"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10176"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_indole_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_indole_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3266"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3265"/>
+            </fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_INSt2pp" fast="false" reversible="false" name="Inosine transport in via proton symport (periplasm)" metaid="R_INSt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_INSt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INSt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-108G"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100850"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29965"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29964"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29966"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29963"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05316"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08753"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ins_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ins_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2964"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2406"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2393"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PROabcpp" fast="false" reversible="false" name="L-proline transport via ABC system (periplasm)" metaid="R_PROabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PROabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PROabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-26-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103210"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29816#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29817#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29815#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29818#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09187"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05165"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pro__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2677"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2678"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2679"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PROt2rpp" fast="false" reversible="true" name="L-proline reversible transport via proton symport (periplasm)" metaid="R_PROt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PROt2rpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PROt2rpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-29"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103211"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28963"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28964"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28965"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28966"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11167"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09191"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05638"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pro__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4111"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0402"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MNLtex" fast="false" reversible="true" name="Mannitol transport via diffusion (extracellular to periplasm)" metaid="R_MNLtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MNLtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MNLtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101678"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08950"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mnl_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_mnl_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PROt4pp" fast="false" reversible="false" name="Na+/Proline-L symporter (periplasm)" metaid="R_PROt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PROt4pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PROt4pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-118"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103197"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-352052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-352052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-352052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-352052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-352052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-352052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-352052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-352052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-352052"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28968"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28969"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28970"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28967"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05221"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09192"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pro__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1015"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PTRCabcpp" fast="false" reversible="false" name="Putrescine transport via ABC system (periplasm)" metaid="R_PTRCabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PTRCabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PTRCabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-25-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.31"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103338"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29998#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29996#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29995#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29997#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11263"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05163"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09213"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ptrc_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0854"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0855"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0857"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0856"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1440"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1442"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1441"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1443"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1125"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1126"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1124"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1123"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LYXt2pp" fast="false" reversible="false" name="L-Lyxose transport via proton symport (periplasm)" metaid="R_LYXt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_LYXt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LYXt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-236"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101271"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08858"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05692"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lyx__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lyx__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3907"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GDPPYPHOSKIN-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28098"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28101"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28099"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28100"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08598"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppgpp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2784"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3650"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_OCDCAtexi" fast="false" reversible="false" name="Octadecanoate transport via facilitated irreversible diffusion (extracellular to periplasm)" metaid="R_OCDCAtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/39808"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/39809"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/39810"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09034"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09669"/>
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+        <listOfProducts>
+          <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2344"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99110"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33655"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33656"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33657"/>
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+        <listOfProducts>
+          <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2344"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ASPARAGHYD-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-6797627"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21016"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21018"/>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_asp__L_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2957"/>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUTAMIN-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-70609"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15889"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15890"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/762"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00189"/>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glu__L_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2957"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08570"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09644"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13641"/>
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+          <speciesReference species="M_g6p_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_g6p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29385"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11288"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_din_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2744"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2291"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3399"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2361"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tungs_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tungs_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0765"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0763"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <listOfProducts>
+          <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22021#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22022#1"/>
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+          <speciesReference species="M_mobd_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mobd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:and>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0765"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0763"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2422"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2423"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2424"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3917"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2425"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2422"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2423"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2424"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34908"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+          <speciesReference species="M_ni2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3476"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3479"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3477"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3478"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4242"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3005"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3006"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0150"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_arbtn_fe3_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_adocbl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1709"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0158"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1711"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08211"/>
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+          <speciesReference species="M_cgly_e" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NI2tex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-141B"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101958"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29833"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29831"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29834"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29832"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ni2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ni2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD10pp" fast="false" reversible="false" name="5'-nucleotidase (XMP)" metaid="R_NTD10pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD10pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:XMPXAN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02719"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102029"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28532"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28530"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28531"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28533"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/129"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01961"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xmp_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xtsn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD1pp" fast="false" reversible="false" name="5'-nucleotidase (dUMP)" metaid="R_NTD1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD1pp">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14143"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02102"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102028"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29358"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29355"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29357"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29356"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/501"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01521"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dump_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_duri_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_chtbs_e" fast="false" reversible="false" name="Chitobiose exchange" metaid="R_EX_chtbs_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_chtbs_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138171"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_chtbs_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_gmp_e" fast="false" reversible="false" name="GMP exchange" metaid="R_EX_gmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_gmp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_gmp_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-565"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100386"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08664"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gmp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_NTD2pp" fast="false" reversible="false" name="5'-nucleotidase (UMP)" metaid="R_NTD2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14025"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00963"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102032"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29362"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29360"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29359"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/210"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00708"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uri_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NACtex" fast="false" reversible="true" name="Nicotinic acid transport via diffusion (extracellular to periplasm)" metaid="R_NACtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NACtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NACtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101808"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-8869603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08970"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05310"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08969"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_nac_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nac_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD3pp" fast="false" reversible="false" name="5'-nucleotidase (dCMP)" metaid="R_NTD3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD3pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5292"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.89"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01664"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102033"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29364"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29365"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29366"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29363"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/480"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01218"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dcmp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dcyt_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD4pp" fast="false" reversible="false" name="5'-nucleotidase (CMP)" metaid="R_NTD4pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD4pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14026"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.91"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00511"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102034"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29370"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29368"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29369"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29367"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/211"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00363"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cmp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cytd_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD5pp" fast="false" reversible="false" name="5'-nucleotidase (dTMP)" metaid="R_NTD5pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THYMIDYLATE-5-PHOSPHATASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.35"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11081"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11083"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11082"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11080"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/479"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01145"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dtmp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thymd_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_h2o2_e" fast="false" reversible="false" name="Hydrogen peroxide exchange" metaid="R_EX_h2o2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_h2o2_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-284"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-572"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR98640"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13308"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08685"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_ump_e" fast="false" reversible="false" name="UMP exchange" metaid="R_EX_ump_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_ump_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ump_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105127"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27927"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27929"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27926"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27928"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09808"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09361"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ump_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_pydam_e" fast="false" reversible="false" name="Pyridoxamine exchange" metaid="R_EX_pydam_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_pydam_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pydam_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103358"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28468"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28467"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28469"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28466"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pydam_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_CRNabcpp" fast="false" reversible="false" name="L-carnitine transport via ABC system (periplasm)" metaid="R_CRNabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CRNabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96905"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/38719#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/38722#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/38720#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/38721#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05180"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08253"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_crn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2679"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2677"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2678"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CRNDabcpp" fast="false" reversible="false" name="D-carnitine transport via ABC system (periplasm)" metaid="R_CRNDabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CRNDabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNDabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96902"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08259"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_crn__D_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_crn__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2679"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2677"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2678"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DNTPPA" fast="false" reversible="false" name="Dihydroneopterin triphosphate pyrophosphatase" metaid="R_DNTPPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DNTPPA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DNTPPA"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.67"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04638"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97680"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25302"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25305"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25303"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25304"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/10428"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03173"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ahdt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhpmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1865"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0099"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD6pp" fast="false" reversible="false" name="5'-nucleotidase (dAMP)" metaid="R_NTD6pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD6pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD6pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14161"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.89"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02088"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102036"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29371"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29374"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29372"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29373"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/282"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13134"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01507"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_damp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dad_2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD7pp" fast="false" reversible="false" name="5'-nucleotidase (AMP)" metaid="R_NTD7pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD7pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD7pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:AMP-DEPHOSPHORYLATION-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00183"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102037"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-109415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-109415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-109415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-109415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-109415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-109415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-109415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-109415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-109415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-109415"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29376"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29378"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29375"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29377"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/295"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00132"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_amp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CTBTabcpp" fast="false" reversible="false" name="Crotonobetaine transport via ABC system (periplasm)" metaid="R_CTBTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CTBTabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CTBTabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96938"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ctbt_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ctbt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2678"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2677"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2679"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD9pp" fast="false" reversible="false" name="5'-nucleotidase (GMP)" metaid="R_NTD9pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD9pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD9pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-7609"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01227"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100381"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27715"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27716"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27717"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27714"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/186"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00913"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gmp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gsn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NH4tex" fast="false" reversible="true" name="Ammonia transport via diffusion (extracellular to periplasm)" metaid="R_NH4tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NH4tex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NH4tex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-206"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9615"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-544"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101950"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-444416"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-444416"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ARGDECARBOX-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00566"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-350598"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-350598"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-350598"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-350598"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-350598"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17641"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17642"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17644"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17643"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/594"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00405"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_arg__L_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_agm_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2938"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_URIH" fast="false" reversible="false" name="Uridine hydrolase" metaid="R_URIH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URIH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:URIDINE-NUCLEOSIDASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01080"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105161"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15580"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15578"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15579"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15577"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00797"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uri_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_rib__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ura_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2162"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0651"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0030"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALLPI" fast="false" reversible="true" name="Allose 6-phosphate isomerase" metaid="R_ALLPI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09030"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95766"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28430"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28433"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28431"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28432"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08113"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_all6p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_allul6p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4090"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALLK" fast="false" reversible="false" name="Allose kinase" metaid="R_ALLK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ALLK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.55"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03576"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95765"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02552"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_all__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_all6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4084"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALLULPE" fast="false" reversible="true" name="Allulose 6-phosphate epimerase" metaid="R_ALLULPE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ALLULPE">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALLULPE"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-304"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95774"/>
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+              </bqbiol:is>
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+        </sbml:annotation>
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+          <speciesReference species="M_allul6p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4085"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ADEtex" fast="false" reversible="true" name="Adenine transport via diffusion (extracellular to periplasm)" metaid="R_ADEtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADEtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-577"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10918"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08065"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09786"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ade_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ade_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ADNtex" fast="false" reversible="true" name="Adenosine transport via diffusion (extracellular to periplasm)" metaid="R_ADNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ADNtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08069"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11000"/>
+                </rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_adn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0411"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NADPHQR2" fast="false" reversible="false" name="NADPH Quinone Reductase (Ubiquinone-8)" metaid="R_NADPHQR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29112"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29113"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29111"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08977"/>
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+            </rdf:Description>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3028"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NADPHQR3" fast="false" reversible="false" name="NADPH Quinone Reductase (Menaquinone-8)" metaid="R_NADPHQR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101892"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29115"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29117"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29118"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08978"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3028"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NADPHQR4" fast="false" reversible="false" name="NADPH Quinone Reductase (2-Demethylmenaquinone-8)" metaid="R_NADPHQR4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101893"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30514"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30512"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3028"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLBRAN2" fast="false" reversible="false" name="1,4-alpha-glucan branching enzyme (glycogen -&gt; bglycogen)" metaid="R_GLBRAN2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08605"/>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_bglycogen_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3432"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_gthrd_c" stoichiometry="2" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_aso3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1064"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3503"/>
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+        </fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        <listOfProducts>
+          <speciesReference species="M_agm_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_ALAtex" fast="false" reversible="true" name="L-alanine transport via diffusion (extracellular to periplasm)" metaid="R_ALAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95706"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/10375"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08104"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10921"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13221"/>
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+          <speciesReference species="M_ala__L_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ala__L_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95682"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08175"/>
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+          <speciesReference species="M_ala_B_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ala_B_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_DALAtex" fast="false" reversible="true" name="D-Alanine transport via diffusion (extracellular to periplasm)" metaid="R_DALAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95702"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08302"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10991"/>
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+        <listOfProducts>
+          <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MANGLYCtex" fast="false" reversible="true" name="2-O-alpha-mannosyl-D-glycerate transport via diffusion (extracellular to periplasm)" metaid="R_MANGLYCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101395"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08883"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_manglyc_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_manglyc_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28455"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28456"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28454"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08534"/>
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+          <speciesReference species="M_frulys_e" stoichiometry="1" constant="true"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08134"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13227"/>
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+        <listOfProducts>
+          <speciesReference species="M_amp_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_metsox_S__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27995"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27996"/>
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+          <speciesReference species="M_xtsn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_rib__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xan_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0030"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_metsox_R__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99658"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4321"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_ARBtex" fast="false" reversible="true" name="L-arabinose transport via diffusion (extracellular to periplasm)" metaid="R_ARBtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32143"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32144"/>
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+          <speciesReference species="M_arg__L_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+          <speciesReference species="M_ins_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_hxan_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rib__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0030"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_dca_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dcacoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1701"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05160"/>
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+          <speciesReference species="M_rib__D_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rib__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b4230"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4227"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4485"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4231"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3750"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3751"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3749"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3748"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b4088"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4086"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4087"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_unagamuf_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3792"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_O16AT" fast="false" reversible="false" name="Rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate O-acetyltransferase (LPS O16 antigen biosynthesis)" metaid="R_O16AT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102081"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09025"/>
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+          <speciesReference species="M_ragund_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_aragund_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2033"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_O16GALFT" fast="false" reversible="false" name="Galactofuranosyltransferase (LPS O16 antigen biosynthesis)" metaid="R_O16GALFT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09027"/>
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+          <speciesReference species="M_garagund_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpgalfur_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_gfgaragund_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2034"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_O16GLCT2" fast="false" reversible="false" name="Glucosyltransferase II (LPS O16 antigen biosynthesis)" metaid="R_O16GLCT2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+          <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o16aund_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+      <reaction id="R_O16AUNDtpp" fast="false" reversible="false" name="O16 antigen (flippase, cytoplasm to periplasm)" metaid="R_O16AUNDtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09026"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_o16aund_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_o16aund_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2037"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_O16AP1pp" fast="false" reversible="false" name="O16 antigen polymerase (periplasm)" metaid="R_O16AP1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_o16aund_p" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o16a2und_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2027"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2035"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GPDDA3pp" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoserine)" metaid="R_GPDDA3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29877"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29878"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29876"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08668"/>
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+        </sbml:annotation>
+        <listOfReactants>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ser__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2239"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GPDDA4pp" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoglycerol)" metaid="R_GPDDA4pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13035"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08669"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2239"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GPDDA2pp" fast="false" reversible="false" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoethanolamine)" metaid="R_GPDDA2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GPDDA2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14160"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01470"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100411"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29320"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29322"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29321"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29319"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01073"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_etha_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2239"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FACOAL120t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (dodecanoate transport via vectoral Co-A coupling)" metaid="R_FACOAL120t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99144"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ddcacoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1701"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1805"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLYCAt2rpp" fast="false" reversible="true" name="D-glycerate transport via proton symport, reversible (periplasm)" metaid="R_GLYCAt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLYCAt2rpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100322"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08644"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13711"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_glyc__R_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc__R_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3127"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2789"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLYCAtex" fast="false" reversible="true" name="D-glycerate transport via diffusion (extracellular to periplasm)" metaid="R_GLYCAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_GLYCAtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYCAtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-523"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100323"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08645"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glyc__R_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc__R_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FACOAL140t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (tetradecanoate transport via vectoral Co-A coupling)" metaid="R_FACOAL140t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_FACOAL140t2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99147"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tdcoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1701"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1805"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_enlipa_e" fast="false" reversible="false" name="Phosphoethanolamine KDO(2)-lipid (A) exchange" metaid="R_EX_enlipa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_enlipa_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_enlipa_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97923"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08419"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_enlipa_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_BUTtex" fast="false" reversible="true" name="Butyrate transport via diffusion (extracellular to periplasm)" metaid="R_BUTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_BUTtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96352"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_but_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_but_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_hacolipa_e" fast="false" reversible="false" name="Hepta-acylated core oligosaccharide lipid A (E. coli) exchange" metaid="R_EX_hacolipa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_hacolipa_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143008"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_hacolipa_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_AGM4PCP" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase" metaid="R_AGM4PCP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AGM4PCP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM4PCP"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95547"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08077"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anhgm4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anhgm3p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1192"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_ala__D_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_fe3hox_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b1252"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3005"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3006"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0150"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_cu2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3469"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32780#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32781#2"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_cobalt2_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3469"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15557#2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15558#2"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ni2_p" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3469"/>
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+          <speciesReference species="M_mg2_p" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b4242"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2175"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_his__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_his__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0112"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CBIAT" fast="false" reversible="true" name="Cobinamide adenyltransferase" metaid="R_CBIAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:BTUR2-RXN"/>
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+          <speciesReference species="M_cbi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adocbi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1270"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLUt4pp" fast="false" reversible="false" name="Na+/glutamate symport (periplasm)" metaid="R_GLUt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29033"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29032"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05298"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08632"/>
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+          <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3653"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLYALDtpp" fast="false" reversible="true" name="Glyceraldehyde facilitated diffusion (periplasm)" metaid="R_GLYALDtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100311"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08635"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10164"/>
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+          <speciesReference species="M_glyald_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyald_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3927"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CRNtex" fast="false" reversible="true" name="L-carnitine transport via diffusion (extracellular to periplasm)" metaid="R_CRNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96906"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34962"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34960"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34959"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34961"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09773"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09858"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09691"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08265"/>
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+          <speciesReference species="M_crn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_crn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_etha_e" fast="false" reversible="false" name="Ethanolamine exchange" metaid="R_EX_etha_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97974"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32750"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32749"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32747"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32748"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08424"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10841"/>
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+          <speciesReference species="M_etha_e" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ACETYLGLUTKIN-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02649"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95256"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2545"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01917"/>
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+          <speciesReference species="M_acglu_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acg5p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3959"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LYSabcpp" fast="false" reversible="false" name="L-lysine transport via ABC system (periplasm)" metaid="R_LYSabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-3-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.21"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29887#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29888#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29890#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29889#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05151"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08853"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lys__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2308"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2306"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2310"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2307"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_COBALT2tex" fast="false" reversible="true" name="Cobalt (Co+2) transport via diffusion (extracellular to periplasm)" metaid="R_COBALT2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-141A"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96821"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28580"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28581"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28578"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12148"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08241"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08242"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10474"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_cobalt2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cobalt2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101026"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28864"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28866"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28865"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28863"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08779"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_lcts_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lcts_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1528"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2170"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0070"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PPK2" fast="false" reversible="false" name="Polyphosphate kinase" metaid="R_PPK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </listOfReactants>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2501"/>
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+      </reaction>
+      <reaction id="R_ARBt3ipp" fast="false" reversible="false" name="L-arabinose transport via proton antiport (periplasm)" metaid="R_ARBt3ipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95937"/>
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+            </rdf:Description>
+          </rdf:RDF>
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+          <speciesReference species="M_arab__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_arab__L_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1528"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_14GLUCANabcpp" fast="false" reversible="false" name="1,4-alpha-D-glucan transport via ABC system (periplasm)" metaid="R_14GLUCANabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_14GLUCANabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/14GLUCANabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94693"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_14glucan_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_14glucan_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4032"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4034"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4035"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4033"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_14GLUCANtexi" fast="false" reversible="false" name="1,4-alpha-D-glucan transport via diffusion (extracellular to periplasm) irreversible" metaid="R_14GLUCANtexi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_14GLUCANtexi">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/14GLUCANtexi"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.161"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94694"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_14glucan_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_14glucan_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4036"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DINStex" fast="false" reversible="true" name="Deoxyinosine transport via diffusion (extracellular to periplasm)" metaid="R_DINStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_DINStex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DINStex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97466"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08344"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_din_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_din_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHPTPE" fast="false" reversible="true" name="Dihydroneopterin triphosphate 2'-epimerase" metaid="R_DHPTPE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DHPTPE">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHPTPE"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.99.d"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08341"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ahdt_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhmptp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2303"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PPDOy" fast="false" reversible="false" name="Propane-1,2-diol:NADP+ 1-oxidoreductase" metaid="R_PPDOy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PPDOy">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPDOy"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-15743"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103108"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lald__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_12ppd__R_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0325"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FALGTHLs" fast="false" reversible="true" name="Formaldehyde glutathione ligase (spontaneous)" metaid="R_FALGTHLs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FALGTHLs">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FALGTHLs"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-2961"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.4.1.22"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06982"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99239"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22488"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22490"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22491"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22489"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7488"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08463"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04791"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_hmgth_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTD12pp" fast="false" reversible="false" name="5'-nucleotidase (dIMP) (periplasm)" metaid="R_NTD12pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTD12pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTD12pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29386"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29384"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29383"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29385"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11288"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09010"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dimp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_din_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PPA2" fast="false" reversible="false" name="Inorganic triphosphatase" metaid="R_PPA2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PPA2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPA2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRIPHOSPHATASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.25"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00138"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103069"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14158"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14160"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14157"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14159"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/707"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00106"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2502"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2744"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DIMPtex" fast="false" reversible="true" name="DIMP transport via diffusion (extracellular to periplasm)" metaid="R_DIMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DIMPtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DIMPtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97463"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08342"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dimp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dimp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_hdca_e" fast="false" reversible="false" name="Hexadecanoate (n-C16:0) exchange" metaid="R_EX_hdca_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_hdca_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_hdca_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99101"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/45257"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/45256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/45258"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/45259"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08704"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09848"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09676"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_hdca_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_glcr_e" fast="false" reversible="false" name="D-Glucarate exchange" metaid="R_EX_glcr_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_glcr_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glcr_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-204"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100222"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28477"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28476"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28474"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28475"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12442"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08614"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glcr_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_GNK" fast="false" reversible="false" name="Gluconokinase" metaid="R_GNK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GNK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUCONOKIN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.12"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01737"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100390"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19434"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19436"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19433"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19435"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1845"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01275"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glcn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_6pgc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3437"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4268"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HMBS" fast="false" reversible="false" name="Hydroxymethylbilane synthase" metaid="R_HMBS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+          <speciesReference species="M_uri_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rml_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rml1p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3904"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:FHLMULTI-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27610"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27613"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27612"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08518"/>
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+          <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b4079"/>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2489"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2487"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2485"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2482"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2483"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2486"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2490"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2488"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2484"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2481"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b4079"/>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2722"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2723"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2724"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2720"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2721"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2719"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyam5p_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pydam_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13429"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13432"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13431"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03907"/>
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+          <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_4c2me_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2747"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUTDEHYD-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.1.4"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100086"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11613"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11614"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11612"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11615"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/757"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00184"/>
+                </rdf:Bag>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1761"/>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3213"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3212"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94722"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27886"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27887"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27889"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27888"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02521"/>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3amp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4213"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_GALTptspp" fast="false" reversible="false" name="Galactitol transport via PEP:Pyr PTS (periplasm)" metaid="R_GALTptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100018"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08586"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05567"/>
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+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_galt1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2092"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2094"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2093"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100020"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08588"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05673"/>
+                </rdf:Bag>
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+          <speciesReference species="M_galur_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_galur_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3093"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_ZN2abcpp" fast="false" reversible="false" name="Zinc (Zn+2) ABC transporter, efflux (periplasm)" metaid="R_ZN2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20624"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20621"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13430#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13918"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09388"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_zn2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_zn2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3469"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CSNtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96928"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08267"/>
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+        </sbml:annotation>
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+        <listOfProducts>
+          <speciesReference species="M_csn_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-389826"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-389826"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-389826"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-389826"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10995"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10994"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10992"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyclt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1033"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3553"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101256"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22353"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22352"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22355"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00322"/>
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+          <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_15dap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0186"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4131"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97073"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08291"/>
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+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1189"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28831"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28833"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28832"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4476"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3415"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4265"/>
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+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1621"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2417"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1101"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2417"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1819"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1818"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1817"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
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+          </fbc:or>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glcr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2789"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2943"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09368"/>
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+        <listOfProducts>
+          <speciesReference species="M_urea_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3927"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29665"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29666"/>
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+        <listOfProducts>
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+          <speciesReference species="M_xan_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3654"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2888"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21670#1"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08641"/>
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+          <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3451"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3453"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3450"/>
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+        </fbc:geneProductAssociation>
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+        <listOfProducts>
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+          <speciesReference species="M_pppn_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2536"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11262"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09263"/>
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+              </bqbiol:is>
+            </rdf:Description>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_spmd_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1123"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1125"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1124"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1126"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1443"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1442"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1441"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1440"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32817"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32816"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32818"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08717"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28335"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28334"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2781"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104806"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17327"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17326"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17328"/>
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+          <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thdp_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sl2a6o_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0166"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95383"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14970"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14969"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/14972"/>
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+        </listOfReactants>
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+          <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1519"/>
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+        <listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29656"/>
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+        <listOfProducts>
+          <speciesReference species="M_cys__L_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_NADPPPS" fast="false" reversible="false" name="NADP phosphatase" metaid="R_NADPPPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THREDEHYD-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22111"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22110"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00737"/>
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+        <listOfProducts>
+          <speciesReference species="M_2obut_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3772"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3117"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33172"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33171"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33174"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11211"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_dcyt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2291"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2361"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfProducts>
+          <speciesReference species="M_cytd_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/283"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01274"/>
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+          <speciesReference species="M_lgt__S_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lac__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0212"/>
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+          <speciesReference species="M_dad_2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0411"/>
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+          <speciesReference species="M_LalaDgluMdapDala_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_nac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nicrnt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0931"/>
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+      </reaction>
+      <reaction id="R_EX_pnto__R_e" fast="false" reversible="false" name="(R)-Pantothenate exchange" metaid="R_EX_pnto__R_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34975"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34976"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34977"/>
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+        </listOfReactants>
+      </reaction>
+      <reaction id="R_SELNPS" fast="false" reversible="false" name="Selenophosphate synthase" metaid="R_SELNPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18739"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18737"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18738"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02569"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_seln_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_selnp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1764"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_DHAtex" fast="false" reversible="true" name="Dihydroxyacetone transport via diffusion (extracellular to periplasm)" metaid="R_DHAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08326"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05532"/>
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+        <listOfReactants>
+          <speciesReference species="M_dha_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dha_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ETOHtex" fast="false" reversible="true" name="Ethanol transport via diffusion (extracellular to periplasm)" metaid="R_ETOHtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-546"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97980"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35267"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35270"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08428"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09764"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_etoh_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_etoh_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MTRPOX" fast="false" reversible="false" name="N-methyltryptophan oxidase" metaid="R_MTRPOX" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-301"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28008"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28006"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28007"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7294"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08965"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_Nmtrp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trp__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1059"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AGM4PCPpp" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase (periplasmic)" metaid="R_AGM4PCPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_AGM4PCPpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95547"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anhgm3p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2175"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GTPDPDP" fast="false" reversible="false" name="Guanosine-5'-triphosphate,3'-diphosphate diphosphatase" metaid="R_GTPDPDP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PPPGPPHYDRO-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.40"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13073"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13075"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13076"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02449"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_gdptp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppgpp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3779"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CRNCAR" fast="false" reversible="true" name="Carnitine-CoA racemase" metaid="R_CRNCAR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CRNCAR"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CARNCOARACE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96896"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30539"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30540"/>
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+          <speciesReference species="M_crncoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_crnDcoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0036"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GALabcpp" fast="false" reversible="false" name="D-galactose transport via ABC system (periplasm)" metaid="R_GALabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_GALabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ABC-18-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100023"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08573"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05162"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gal_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gal_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2148"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2149"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2150"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b4227"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4230"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4485"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4231"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLYCLTt2rpp" fast="false" reversible="true" name="Glycolate transport via proton symport, reversible (periplasm)" metaid="R_GLYCLTt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29413"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29411"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29412"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05470"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyclt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2975"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GUAt2pp" fast="false" reversible="false" name="Guanine transport in via proton symport (periplasm)" metaid="R_GUAt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08681"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05203"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_gua_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gua_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3654"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HPPPNt2rpp" fast="false" reversible="true" name="3-(3-hydroxyphenyl)propionate transport via proton symport, reversible (periplasm)" metaid="R_HPPPNt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28907"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28909"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28908"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08725"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10134"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_3hpppn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3hpppn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0353"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_RNDR2" fast="false" reversible="false" name="Ribonucleoside-diphosphate reductase (GDP)" metaid="R_RNDR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02019"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104062"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05233"/>
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+          <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dgdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3781"/>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2234"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2235"/>
+              </fbc:and>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2582"/>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b2234"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b2235"/>
+              </fbc:and>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_asn__L_e" fast="false" reversible="false" name="L-Asparagine exchange" metaid="R_EX_asn__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_asn__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05220"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08162"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+      <reaction id="R_ANHMK" fast="false" reversible="false" name="1,6-anhydrous-N-Acetylmuramate kinase" metaid="R_ANHMK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ANHMK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ANHMK"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08136"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anhm_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acmum6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1640"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DCAtex" fast="false" reversible="true" name="Decanoate transport via diffusion (extracellular to periplasm)" metaid="R_DCAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DCAtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DCAtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97181"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dca_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHFR" fast="false" reversible="true" name="Dihydrofolate reductase" metaid="R_DHFR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DHFR">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.5.1.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00939"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97401"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-197972"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-197972"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-197972"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-197972"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-197972"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-197972"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-197972"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-197972"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-197972"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-197972"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-197972"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15010"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15009"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15012"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15011"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/100"/>
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+            </rdf:Description>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1606"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0048"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_cit_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cit_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96756"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33184"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33186"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33183"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33185"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10946"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08217"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cit_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PRAIi">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PRAISOM-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.24"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03509"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103156"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21543"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21540"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21541"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02508"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pran_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2cpr5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1262"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_mal__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mal__L_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-225"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-224"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101367"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13793"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10967"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08868"/>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mal__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NMNN">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.14"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101971"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nmn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ncam_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_XAND">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16672"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16671"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/196"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01522"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xan_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_urate_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2866"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2867"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2868"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_3hocoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3846"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2341"/>
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+        </fbc:geneProductAssociation>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TYROSINE-AMINOTRANSFERASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.57"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15095"/>
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+          <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_34hpp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4054"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0928"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3770"/>
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+          <speciesReference species="M_skm_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_skm5p_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0388"/>
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+          <speciesReference species="M_dcyt_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dcyt_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0411"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfProducts>
+          <speciesReference species="M_acac_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28991"/>
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+        <listOfProducts>
+          <speciesReference species="M_acnam_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4311"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08143"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_arbtn_fe3_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_arbtn_fe3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0151"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0153"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0152"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_inost_e" fast="false" reversible="false" name="Myo-Inositol exchange" metaid="R_EX_inost_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_inost_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_inost_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100848"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32869"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32870"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32868"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08755"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_inost_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_mobd_e" fast="false" reversible="true" name="Molybdate exchange" metaid="R_EX_mobd_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_mobd_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mobd_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101690"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34909"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34907"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34910"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34908"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08956"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mobd_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_NNDMBRT" fast="false" reversible="false" name="Nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase" metaid="R_NNDMBRT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NNDMBRT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NNDMBRT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DMBPPRIBOSYLTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.21"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04148"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101979"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11196"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11197"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11199"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11198"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02897"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dmbzid_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nicrnt_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_5prdmbz_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nac_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1991"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DGSNtex" fast="false" reversible="true" name="Deoxyguanosine transport via diffusion (extracellular to periplasm)" metaid="R_DGSNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DGSNtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DGSNtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97324"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08324"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dgsn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dgsn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_THRA2" fast="false" reversible="false" name="L-allo-Threonine Aldolase" metaid="R_THRA2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_THRA2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THRA2"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_athr__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2551"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0870"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ASO3t8pp" fast="false" reversible="false" name="Arsenite efflux via ATP hydrolysis (periplasm)" metaid="R_ASO3t8pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ASO3t8pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASO3t8pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.16-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.16"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96072"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11351#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11348#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11350#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11349#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08163"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_aso3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_aso3_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3502"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_H2Stex" fast="false" reversible="true" name="H2s transport via diffusion (extracellular to periplasm)" metaid="R_H2Stex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_H2Stex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/H2Stex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-310"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100494"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08690"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08689"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10541"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2s_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2s_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PPK" fast="false" reversible="false" name="Polyphosphate kinase" metaid="R_PPK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PPK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPK"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2501"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_so4_e" fast="false" reversible="true" name="Sulfate exchange" metaid="R_EX_so4_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_so4_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_so4_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104469"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-PFA-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-8875871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34983"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34984"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34986"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34985"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09261"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05238"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_so4_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_SADH" fast="false" reversible="false" name="Succinylarginine dihydrolase" metaid="R_SADH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_SADH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SADH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SUCCARGDIHYDRO-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.3.23"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04189"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104239"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19534"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19535"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19533"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19536"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02927"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_sucarg_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_sucorn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1745"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLUSy" fast="false" reversible="false" name="Glutamate synthase (NADPH)" metaid="R_GLUSy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLUSy">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLUSy"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUTAMATESYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.4.1.13"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00114"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100291"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15503"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15501"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15504"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15502"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/694"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00085"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glu__L_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3213"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3212"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GUAPRT" fast="false" reversible="false" name="Guanine phosphoribosyltransferase" metaid="R_GUAPRT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_GUAPRT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GUANPRIBOSYLTRAN-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25427"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25426"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25424"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25425"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/195"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00915"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gua_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0125"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0238"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_phe__L_e" fast="false" reversible="false" name="L-Phenylalanine exchange" metaid="R_EX_phe__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-445"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102637"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27952"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27951"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27950"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27953"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13470"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/14018"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11018"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09118"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_phe__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104852"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35020"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35019"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35021"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13464"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09307"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13117"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10898"/>
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+            </rdf:Description>
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+          <speciesReference species="M_thr__L_e" stoichiometry="1" constant="true"/>
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+      <reaction id="R_EX_uri_e" fast="false" reversible="false" name="Uridine exchange" metaid="R_EX_uri_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_uri_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_uri_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105165"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09372"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_uri_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_OMCDC" fast="false" reversible="false" name="2-Oxo-4-methyl-3-carboxypentanoate decarboxylation" metaid="R_OMCDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_OMCDC">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-7800"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.85"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01652"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102180"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25078"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25080"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25081"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25079"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01208"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_3c4mop_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4mop_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ABUTD" fast="false" reversible="false" name="Aminobutyraldehyde dehydrogenase" metaid="R_ABUTD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:AMINOBUTDEHYDROG-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.19"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02549"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95191"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19108"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19105"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19106"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2464"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01851"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_4abutn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_4abut_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1444"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ERYTH4PDEHYDROG-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.72"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01825"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97842"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12058"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12057"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12059"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12056"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1909"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01331"/>
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+            </rdf:Description>
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+          <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4per_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2927"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1779"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUTAMIDOTRANS-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.3.-"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04558"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24796"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24794"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24793"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24795"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/4234"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03135"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_prlp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_aicar_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_eig3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2023"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2025"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PDH" fast="false" reversible="false" name="Pyruvate dehydrogenase" metaid="R_PDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PDH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PDH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRUVDEH-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.1.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.51"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.4.1"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00209"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373177"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-71397"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-71397"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-71397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28043"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28045"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28044"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28042"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/523"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00154"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0115"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0116"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0114"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MTHFR2" fast="false" reversible="false" name="5,10-methylenetetrahydrofolate reductase (NADH)" metaid="R_MTHFR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MTHFR2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07168"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101751"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19822"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19823"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19821"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19824"/>
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_5mthf_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3941"/>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1873"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08689"/>
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+          <speciesReference species="M_h2s_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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+          <speciesReference species="M_damp_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0474"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_dump_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3640"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2251"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2997"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2996"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2995"/>
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+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b1467"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1468"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1466"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1465"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1224"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1227"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1226"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1225"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NTP5" fast="false" reversible="false" name="Nucleoside-triphosphatase (CTP)" metaid="R_NTP5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NTP5">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NTP5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12195"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.15"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00569"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102045"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29389"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29387"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29388"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29390"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00408"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4161"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CELBpts" fast="false" reversible="false" name="Cellobiose transport via PEPPyr PTS" metaid="R_CELBpts" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CELBpts">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CELBpts"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96586"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cellb_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_6pgg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2715"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+              <fbc:and>
+                <fbc:geneProductRef fbc:geneProduct="G_b1738"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b1737"/>
+                <fbc:geneProductRef fbc:geneProduct="G_b1736"/>
+              </fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FORt2pp" fast="false" reversible="false" name="Formate transport via proton symport (uptake only, periplasm)" metaid="R_FORt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FORt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FORt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99621"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08524"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05559"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_for_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0904"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2492"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_r5p_e" fast="false" reversible="false" name="Alpha-D-Ribose 5-phosphate exchange" metaid="R_EX_r5p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_r5p_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_r5p_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103411"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_r5p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_glyc2p_e" fast="false" reversible="false" name="Glycerol 2-phosphate exchange" metaid="R_EX_glyc2p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_glyc2p_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glyc2p_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100319"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08640"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glyc2p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_MTAN" fast="false" reversible="false" name="Methylthioadenosine nucleosidase" metaid="R_MTAN" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MTAN">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MTAN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:METHYLTHIOADENOSINE-NUCLEOSIDASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.2.16"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01401"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101744"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13620"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13619"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13617"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13618"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1593"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01021"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_5mta_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_5mtr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0159"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DPR" fast="false" reversible="false" name="2-dehydropantoate 2-reductase" metaid="R_DPR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DPR">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DPR"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2-DEHYDROPANTOATE-REDUCT-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.169"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02472"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97779"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16233"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16234"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16235"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16236"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2405"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01790"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2dhp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pant__R_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0425"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3774"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_halipa_e" fast="false" reversible="false" name="Hepta-acylated KDO(2)-lipid (A) exchange" metaid="R_EX_halipa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_halipa_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_halipa_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143009"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_halipa_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_AACPS5" fast="false" reversible="false" name="Acyl-[acyl-carrier-protein] synthetase  (n-C18:1)" metaid="R_AACPS5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AACPS5">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AACPS5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95144"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_octeACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1094"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MANptspp" fast="false" reversible="false" name="D-mannose transport via PEP:Pyr PTS (periplasm)" metaid="R_MANptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MANptspp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MANptspp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101401"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05610"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08885"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_man_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_man6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1819"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1818"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1817"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_cmp_e" fast="false" reversible="false" name="CMP exchange" metaid="R_EX_cmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_cmp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cmp_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96806"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08236"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09776"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cmp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_NTD8" fast="false" reversible="false" name="5'-nucleotidase (dGMP)" metaid="R_NTD8" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14142"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01968"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102038"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29382"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29380"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29381"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29379"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/304"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01445"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dgmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dgsn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2744"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2291"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3399"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2361"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GALCTD" fast="false" reversible="false" name="Galactarate dehydratase" metaid="R_GALCTD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GALCTD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GALCTD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GALACTARDEHYDRA-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.42"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R05608"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99955"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16008"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16006"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16005"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16007"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03887"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_galct__D_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_5dh4dglc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3128"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_malthx_e" fast="false" reversible="false" name="Maltohexaose exchange" metaid="R_EX_malthx_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_malthx_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_malthx_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08870"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_malthx_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_MLTG4" fast="false" reversible="false" name="Maltodextrin glucosidase (maltohexaose)" metaid="R_MLTG4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MLTG4">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTG4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-14282"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.2.1.20"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101622"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08935"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltpt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0403"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UDPGDC" fast="false" reversible="false" name="UDP-glucuronate C-4'' decarboxylase" metaid="R_UDPGDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_UDPGDC">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/UDPGDC"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1861"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.305"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07658"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105064"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24703"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24705"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24704"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24702"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12883"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07473"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09351"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpglcur_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpLa4o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2255"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PUNP4" fast="false" reversible="true" name="Purine-nucleoside phosphorylase (Deoxyguanosine)" metaid="R_PUNP4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PUNP4">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PUNP4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DEOXYGUANPHOSPHOR-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01969"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103346"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27741"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27738"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27740"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27739"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/360"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01446"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dgsn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dr1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gua_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2407"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4384"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AMAOTr" fast="false" reversible="true" name="Adenosylmethionine-8-amino-7-oxononanoate transaminase" metaid="R_AMAOTr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AMAOTr">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AMAOTr"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DAPASYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.62"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03231"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95806"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16863"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16861"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16862"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16864"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/3057"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02312"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_8aonn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amob_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dann_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0774"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_csn_e" fast="false" reversible="false" name="Cytosine exchange" metaid="R_EX_csn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_csn_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_csn_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96928"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08267"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_csn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_etoh_e" fast="false" reversible="false" name="Ethanol exchange" metaid="R_EX_etoh_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_etoh_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_etoh_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-546"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97980"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35269"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35267"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35270"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08428"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09764"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_etoh_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_G6PP" fast="false" reversible="false" name="Glucose-6-phosphate phosphatase" metaid="R_G6PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_G6PP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G6PP"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN66-526"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.58"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00303"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99912"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16691"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16689"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16692"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16690"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/7713"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/796"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00220"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0822"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3826"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2293"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MMCD" fast="false" reversible="false" name="Methylmalonyl-CoA decarboxylase" metaid="R_MMCD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MMCD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MMCD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:METHYLMALONYL-COA-DECARBOXYLASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.41"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00923"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101656"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21398"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21397"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21399"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21396"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00672"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mmcoa__S_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppcoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2919"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLNS" fast="false" reversible="false" name="Glutamine synthetase" metaid="R_GLNS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLNS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLNS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLUTAMINESYN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/6.3.1.2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00253"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100024"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-70606"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-70606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-70606"/>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_aacoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2224"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2342"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3845"/>
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+          <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_orn_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1605"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29750"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29749"/>
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+        <listOfProducts>
+          <speciesReference species="M_anhgm_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05607"/>
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+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_malt6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1621"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2417"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105133"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_udcpp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpLa4fn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_uLa4fn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2254"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UPLA4FNF" fast="false" reversible="false" name="Undecaprenyl phosphate-L-Ara4FN formylase" metaid="R_UPLA4FNF" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105132"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09363"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uLa4fn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uLa4n_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2256"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ULA4Ntppi" fast="false" reversible="false" name="Transport (cytoplasm to periplasm)" metaid="R_ULA4Ntppi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105114"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09357"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_uLa4n_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_uLa4n_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2258"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4544"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HEPT1" fast="false" reversible="false" name="Heptosyltransferase I (LPS core synthesis)" metaid="R_HEPT1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100602"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28404"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28405"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28402"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28403"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08710"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_adphep_LD_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hlipa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3621"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FALDtex" fast="false" reversible="true" name="Formaldehyde transport via diffusion (extracellular to periplasm)" metaid="R_FALDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FALDtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99238"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08461"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08462"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fald_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fald_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MCITD" fast="false" reversible="false" name="2-methylcitrate dehydratase" metaid="R_MCITD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MCITD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2-METHYLCITRATE-DEHYDRATASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.79"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04424"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101413"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17725"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17728"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17726"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17727"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/4111"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03060"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2mcit_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2mcacn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0334"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CU2tex" fast="false" reversible="true" name="Copper (Cu+2) transport via diffusion (extracellular to periplasm)" metaid="R_CU2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CU2tex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96951"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28705"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28706"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28704"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28703"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08274"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08273"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cu2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cu2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_glcur1p_e" fast="false" reversible="false" name="D-Glucuronate 1-phosphate exchange" metaid="R_EX_glcur1p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_EX_glcur1p_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_glcur1p_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100231"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08621"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glcur1p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_GLCATr" fast="false" reversible="true" name="D-glucose O-acetyltransferase" metaid="R_GLCATr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_GLCATr">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLCATr"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.79"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143129"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08607"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acglc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0459"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALR2" fast="false" reversible="false" name="Aldose reductase (methylglyoxal)" metaid="R_ALR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ALR2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALR2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-4281"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02528"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95788"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27986"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27988"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27987"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27989"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2450"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01832"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mthgxl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acetol_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3012"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0207"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1781"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3001"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AMALT2" fast="false" reversible="false" name="Amylomaltase (maltotetraose)" metaid="R_AMALT2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08127"/>
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+          <speciesReference species="M_malt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltttr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_maltpt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3416"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MLTP1" fast="false" reversible="true" name="Maltodextrin phosphorylase (maltopentaose)" metaid="R_MLTP1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29649"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/6523"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/10119"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08941"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cys__D_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cys__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_HXAND" fast="false" reversible="false" name="Hypoxanthine dehydrogenase" metaid="R_HXAND" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100747"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24670"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24673"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/323"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01297"/>
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+          <speciesReference species="M_hxan_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xan_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2866"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2867"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2868"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08462"/>
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+          <speciesReference species="M_fald_e" stoichiometry="1" constant="true"/>
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+      <reaction id="R_EX_pydxn_e" fast="false" reversible="false" name="Pyridoxine exchange" metaid="R_EX_pydxn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_pydxn_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-205"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103364"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28472"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28470"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28473"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28471"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13097"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pydxn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_acgal_e" fast="false" reversible="false" name="N-Acetyl-D-galactosamine exchange" metaid="R_EX_acgal_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_acgal_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_acgal_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95244"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08037"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acgal_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_so2_e" fast="false" reversible="false" name="Sulfur dioxide exchange" metaid="R_EX_so2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_so2_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09258"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09259"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_so2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_dms_e" fast="false" reversible="false" name="Dimethyl sulfide exchange" metaid="R_EX_dms_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10500"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dms_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_GMPtex" fast="false" reversible="true" name="GMP transport via diffusion (extracellular to periplasm)" metaid="R_GMPtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_GMPtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-565"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08664"/>
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+        <listOfProducts>
+          <speciesReference species="M_gmp_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08749"/>
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+        <listOfProducts>
+          <speciesReference species="M_imp_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_G3PItex" fast="false" reversible="true" name="Glycero-3-phospho-1-inositol transport via diffusion (extracellular to periplasm)" metaid="R_G3PItex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32917"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32916"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32915"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13292"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08564"/>
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+          <speciesReference species="M_g3pi_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_g3pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12133#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12132#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05516"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08195"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_cd2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cd2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3469"/>
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+        <listOfProducts>
+          <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_G3PEtex" fast="false" reversible="true" name="Glycero-3-phosphoethanolamine transport via diffusion (extracellular to periplasm)" metaid="R_G3PEtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08560"/>
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+        <listOfProducts>
+          <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32911"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32913"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32914"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_kphphhlipa_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_g1p_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
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+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0474"/>
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+        <listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0574"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0573"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0575"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_zn2_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_zn2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0752"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <listOfProducts>
+          <speciesReference species="M_skm_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29010"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mn2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2392"/>
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+          <speciesReference species="M_kphphhlipa_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_dtdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_icolipa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3629"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2148"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2150"/>
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+          <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gagicolipa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3628"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MNtex" fast="false" reversible="true" name="Manganese (Mn+2) transport via diffusion (extracellular to periplasm)" metaid="R_MNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MNtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-16"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-487"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101670"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28702"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28699"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28700"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28701"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08952"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08947"/>
+                </rdf:Bag>
+              </bqbiol:is>
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+        </sbml:annotation>
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+          <speciesReference species="M_mn2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_mn2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GAL1Ptex" fast="false" reversible="true" name="D-galactose 1-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_GAL1Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99923"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08572"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gal1p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gal1p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLCTR2" fast="false" reversible="false" name="Glucosyltransferase II (LPS core synthesis)" metaid="R_GLCTR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_GLCTR2">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143138"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08619"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gagicolipa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ggagicolipa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3627"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_G2PPpp" fast="false" reversible="false" name="Glycerol 2-phosphate phosphatase (periplasmic)" metaid="R_G2PPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLYCEROL-2-PHOSPHATASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.19"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01043"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99852"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13106"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13108"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13107"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13105"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1325"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00766"/>
+                </rdf:Bag>
+              </bqbiol:is>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_glyc2p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4055"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_UDPGPpp" fast="false" reversible="false" name="UDPglucose pyrophosphohydrolase" metaid="R_UDPGPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_UDPGPpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.45"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00287"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143430"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-6810464"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-6810464"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-6810464"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-6810464"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-6810464"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-6810464"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-6810464"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29558"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29557"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29555"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29556"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/446"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00212"/>
+                </rdf:Bag>
+              </bqbiol:is>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udpg_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g1p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ump_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0480"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_acgal1p_e" fast="false" reversible="false" name="N-Acetyl-D-galactosamine 1-phosphate exchange" metaid="R_EX_acgal1p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_acgal1p_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_acgal1p_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95234"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08036"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_acgal1p_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_cyan_e" fast="false" reversible="false" name="Hydrogen cyanide exchange" metaid="R_EX_cyan_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_cyan_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cyan_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96957"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08276"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cyan_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_tyrp_e" fast="false" reversible="false" name="Phosphotyrosine exchange" metaid="R_EX_tyrp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_tyrp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104999"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09337"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tyrp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_O2Stex" fast="false" reversible="true" name="Superoxide anion transport via diffusion (extracellular to periplasm)" metaid="R_O2Stex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_O2Stex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O2Stex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102089"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-1222342"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_o2s_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_o2s_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HEPK1" fast="false" reversible="false" name="LPS heptose kinase I (LPS core synthesis)" metaid="R_HEPK1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_HEPK1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HEPK1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138511"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08708"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hhlipa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_phhlipa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3630"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HEPT3" fast="false" reversible="false" name="Heptosyltransferase III (LPS core synthesis)" metaid="R_HEPT3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_HEPT3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100606"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08712"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_adphep_LD_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_phhlipa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hphhlipa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3632"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HEPK2" fast="false" reversible="false" name="LPS heptose kinase II (LPS core synthesis)" metaid="R_HEPK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08709"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hphhlipa_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_phphhlipa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3625"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALDD3y" fast="false" reversible="false" name="Aldehyde dehydrogenase (propanal, NADP)" metaid="R_ALDD3y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_ALDD3y">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALDD3y"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95754"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppal_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3588"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4269"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3011"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_uacgam_e" fast="false" reversible="false" name="UDP-N-acetyl-D-glucosamine exchange" metaid="R_EX_uacgam_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_uacgam_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_uacgam_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105021"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-742354"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09342"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_uacgam_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_Kt3pp" fast="false" reversible="false" name="Potassium transport out via proton antiport (periplasm)" metaid="R_Kt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_Kt3pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/Kt3pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-42"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100939"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29470"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29467"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29468"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29469"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05596"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08770"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_k_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_k_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3350"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0047"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1216"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0842"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_udpacgal_e" fast="false" reversible="false" name="UDP-N-acetyl-D-galactosamine exchange" metaid="R_EX_udpacgal_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_udpacgal_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_udpacgal_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105046"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09347"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_udpacgal_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_udpg_e" fast="false" reversible="false" name="UDPglucose exchange" metaid="R_EX_udpg_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_udpg_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_udpg_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143086"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11025"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09353"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_udpg_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_udpgal_e" fast="false" reversible="false" name="UDPgalactose exchange" metaid="R_EX_udpgal_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_udpgal_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_udpgal_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105061"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09349"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13413"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_udpgal_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_udpglcur_e" fast="false" reversible="false" name="UDP-D-glucuronate exchange" metaid="R_EX_udpglcur_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_udpglcur_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_udpglcur_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105066"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09352"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_udpglcur_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_14glucan_e" fast="false" reversible="false" name="1,4-alpha-D-glucan exchange" metaid="R_EX_14glucan_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_14glucan_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_14glucan_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.161"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94694"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_14glucan_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_pser__L_e" fast="false" reversible="false" name="O-Phospho-L-serine exchange" metaid="R_EX_pser__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_pser__L_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pser__L_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103246"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09204"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pser__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_R5PP" fast="false" reversible="false" name="Ribose 5-phosphate phosphatase" metaid="R_R5PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_R5PP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/R5PP"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103410"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rib__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0822"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2690"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0675"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2293"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3697"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_xmp_e" fast="false" reversible="false" name="Xanthosine 5'-phosphate exchange" metaid="R_EX_xmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_xmp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_xmp_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105231"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09380"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_xmp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_damp_e" fast="false" reversible="false" name="DAMP exchange" metaid="R_EX_damp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_damp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_damp_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97136"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08303"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_damp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_CYSSADS" fast="false" reversible="false" name="L-cysteine sulfinic acid desulfurase" metaid="R_CYSSADS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CYSSADS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYSSADS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.12"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.4.1.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00863"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97008"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1198"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00624"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3sala_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_so2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2810"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1680"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_dimp_e" fast="false" reversible="false" name="DIMP exchange" metaid="R_EX_dimp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_dimp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dimp_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97463"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08342"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dimp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_CPPPGO2" fast="false" reversible="false" name="Oxygen Independent coproporphyrinogen-III oxidase" metaid="R_CPPPGO2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CPPPGO2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPPPGO2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:HEMN-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.98.3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.22"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06895"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96881"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15425"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15427"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15428"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15426"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04704"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_amet_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_cpppg3_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_dad_5_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_met__L_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pppg9_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3867"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_isetac_e" fast="false" reversible="false" name="Isethionic acid exchange" metaid="R_EX_isetac_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_isetac_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_isetac_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100881"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08759"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_isetac_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_AGM3PH" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide beta -1,4-N-acetylglucosaminidase" metaid="R_AGM3PH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AGM3PH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM3PH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95544"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08074"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anhgm3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acgam_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anhm3p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1107"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HOMt2pp" fast="false" reversible="false" name="L-homoserineserine efflux via proton symport" metaid="R_HOMt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_HOMt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HOMt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-242"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100676"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29004"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29003"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29005"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29006"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08722"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hom__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hom__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0813"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3824"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_aso3_e" fast="false" reversible="false" name="Arsenite exchange" metaid="R_EX_aso3_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_aso3_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_aso3_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-551"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96073"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05507"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08164"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_aso3_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_tcynt_e" fast="false" reversible="false" name="Thiocyanate exchange" metaid="R_EX_tcynt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_tcynt_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_tcynt_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104749"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09287"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tcynt_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_fe3dhbzs_e" fast="false" reversible="false" name="Ferric 2,3-dihydroxybenzoylserine exchange" metaid="R_EX_fe3dhbzs_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_fe3dhbzs_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_fe3dhbzs_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142960"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fe3dhbzs_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_AGM3PApp" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide amidase (periplasm)" metaid="R_AGM3PApp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AGM3PApp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AGM3PApp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95543"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08073"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_anhgm3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_LalaDgluMdap_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anhgm_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4169"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2435"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2817"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0867"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PPPGO" fast="false" reversible="false" name="Protoporphyrinogen oxidase (aerobic)" metaid="R_PPPGO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PPPGO">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PPPGO"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.3.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103128"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-421452"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/3048"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09179"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02304"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_o2_c" stoichiometry="1.5" constant="true"/>
+          <speciesReference species="M_pppg9_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_ppp9_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3850"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_feoxam_un_e" fast="false" reversible="false" name="Ferroxamine minus Fe(3) exchange" metaid="R_EX_feoxam_un_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_feoxam_un_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_feoxam_un_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142966"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_feoxam_un_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_HOMtex" fast="false" reversible="true" name="L-homoserine transport via diffusion (extracellular to periplasm)" metaid="R_HOMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_HOMtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HOMtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100678"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08723"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_hom__L_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_hom__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SO2tex" fast="false" reversible="true" name="SO2 transport via diffusion (extracellular to periplasm)" metaid="R_SO2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_SO2tex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SO2tex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104456"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09258"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09259"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_so2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_so2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SO2tpp" fast="false" reversible="true" name="SO2 transport via diffusion (periplasm)" metaid="R_SO2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_SO2tpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SO2tpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104456"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09258"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09259"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_so2_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_so2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LDH_D2" fast="false" reversible="false" name="D-lactate dehydrogenase" metaid="R_LDH_D2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_LDH_D2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LDH_D2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101039"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29081"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29080"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29082"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29079"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08783"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_lac__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2133"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_g3pc_e" fast="false" reversible="false" name="Sn-Glycero-3-phosphocholine exchange" metaid="R_EX_g3pc_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_g3pc_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_g3pc_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99874"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32912"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32911"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32913"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32914"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08554"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13291"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_g3pc_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_g3pg_e" stoichiometry="1" constant="true"/>
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+      <reaction id="R_EX_g3pi_e" fast="false" reversible="false" name="Sn-Glycero-3-phospho-1-inositol exchange" metaid="R_EX_g3pi_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32917"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32916"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32915"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13292"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08564"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:SIROHEME-FERROCHELAT-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02864"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24360"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24362"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24363"/>
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+          <speciesReference species="M_fe2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_scl_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_sheme_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3368"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SUCOAS" fast="false" reversible="true" name="Succinyl-CoA synthetase (ADP-forming)" metaid="R_SUCOAS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0729"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0728"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17011"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17009"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17010"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02831"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sucbz_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sbzcoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2260"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:DCYSDESULF-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01874"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96992"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11269"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11270"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11271"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/11268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01365"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cys__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1919"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CYStpp" fast="false" reversible="false" name="L-cysteine export via facilitated transport" metaid="R_CYStpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CYStpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CYStpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-1924"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97029"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29655"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29656"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29658"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29657"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13465"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08284"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10998"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08286"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cys__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2578"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1533"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_g3ps_e" fast="false" reversible="false" name="Glycerophosphoserine exchange" metaid="R_EX_g3ps_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_g3ps_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99893"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08566"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_g3ps_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_peamn_e" fast="false" reversible="false" name="Phenethylamine exchange" metaid="R_EX_peamn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29745"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29744"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29746"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29743"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11405"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09080"/>
+                </rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_peamn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_34dhpac_e" fast="false" reversible="false" name="3,4-Dihydroxyphenylacetaldehyde exchange" metaid="R_EX_34dhpac_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94848"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07972"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_34dhpac_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_NTP1" fast="false" reversible="false" name="Nucleoside-triphosphatase (ATP)" metaid="R_NTP1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4394"/>
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+        <listOfProducts>
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+          <speciesReference species="M_air_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2499"/>
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+          <speciesReference species="M_glyc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+          <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gal1p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0757"/>
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+          <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+          <speciesReference species="M_dca_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dcaACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_octa_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocACP_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_LPLIPAL2G181" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C18:1)" metaid="R_LPLIPAL2G181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+          <speciesReference species="M_hxa_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hxcoa_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2221"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ocdcaACP_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
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+          <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pe160_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
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+          <speciesReference species="M_ddcaACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pant__R_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pnto__R_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0133"/>
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+          <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3451"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3453"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3452"/>
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+        </fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3452"/>
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdd2coa_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3846"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_G1PPpp" fast="false" reversible="false" name="Glucose-1-phosphatase" metaid="R_G1PPpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
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+        </fbc:geneProductAssociation>
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+        <listOfProducts>
+          <speciesReference species="M_2dh3dgal_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4478"/>
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+      <reaction id="R_GCALDD" fast="false" reversible="false" name="Glycolaldehyde dehydrogenase" metaid="R_GCALDD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glyclt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1415"/>
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+      <reaction id="R_HISTP" fast="false" reversible="false" name="Histidinol-phosphatase" metaid="R_HISTP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2022"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_G3PSabcpp" fast="false" reversible="false" name="Sn-glycerol-3-phosphoserine transport via ABC system (periplasm)" metaid="R_G3PSabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08565"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_g3ps_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3450"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3451"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3453"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3452"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29177"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29175"/>
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+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_o2s_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3029"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_QMO3" fast="false" reversible="false" name="Quinol monooxygenase (menaquinol 8)" metaid="R_QMO3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29185"/>
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+        </listOfReactants>
+        <listOfProducts>
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+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2s_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3029"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LPLIPAL2E141" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C14:1)" metaid="R_LPLIPAL2E141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_LPLIPAL2E161" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C16:1)" metaid="R_LPLIPAL2E161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1380"/>
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+      <reaction id="R_AMALT4" fast="false" reversible="false" name="Amylomaltase (maltohexaose)" metaid="R_AMALT4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malthp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3416"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27718"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27720"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27719"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/124"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00831"/>
+                </rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_imp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ins_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2744"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3399"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_LPLIPAL2E181" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C18:1)" metaid="R_LPLIPAL2E181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101189"/>
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+            </rdf:Description>
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+          <speciesReference species="M_2agpe181_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_YUMPS" fast="false" reversible="true" name="YUMP synthetase" metaid="R_YUMPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103310"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ura_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_psd5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2165"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_LPLIPAL2G180" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C18:0)" metaid="R_LPLIPAL2G180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101195"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2agpg180_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LPLIPAL2G141" fast="false" reversible="false" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C14:1)" metaid="R_LPLIPAL2G141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_LPLIPAL2G141">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101192"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2agpg141_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_2AGPA120tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphatidate (n-C12:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPA120tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_2AGPA120tipp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94743"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07932"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_2ddecg3p_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2ddecg3p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2835"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_2AGPG180tipp" fast="false" reversible="false" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0) transporter via facilitated diffusion (periplasm)" metaid="R_2AGPG180tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_2AGPG180tipp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94769"/>
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+            </rdf:Description>
+          </rdf:RDF>
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+          <speciesReference species="M_2agpg180_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2agpg180_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2835"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_IPDDI" fast="false" reversible="true" name="Isopentenyl-diphosphate D-isomerase" metaid="R_IPDDI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:IPPISOM-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100796"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-191382"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23285"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23284"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00830"/>
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+          <speciesReference species="M_ipdp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dmpp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2889"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ORNDC" fast="false" reversible="false" name="Ornithine Decarboxylase" metaid="R_ORNDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ORNDECARBOX-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00670"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-70692"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-70692"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22966"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00470"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2965"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0693"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03194"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105137"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32461"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32459"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32460"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02287"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_amet_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_uppg3_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ahcys_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_dscl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3368"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_KAS15" fast="false" reversible="false" name="Beta-ketoacyl-ACP synthase (2)" metaid="R_KAS15" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_actACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1091"/>
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+      </reaction>
+      <reaction id="R_ALAALAtex" fast="false" reversible="true" name="D-alanyl-D-alanine (DalaDala) transport via diffusion (extracellular to periplasm)" metaid="R_ALAALAtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        <listOfProducts>
+          <speciesReference species="M_alaala_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_FACOAL181t2pp" fast="false" reversible="false" name="Fatty-acid-CoA ligase (octadecenoate transport via vectoral Co-A coupling)" metaid="R_FACOAL181t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_odecoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+          <fbc:or>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1701"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_T2DECAI" fast="false" reversible="true" name="Trans-2-decenoyl-ACP isomerase" metaid="R_T2DECAI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        <listOfProducts>
+          <speciesReference species="M_cdec3eACP_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0954"/>
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+      <reaction id="R_2AGPGAT180" fast="false" reversible="false" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C18:0)" metaid="R_2AGPGAT180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg180_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
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+      <reaction id="R_2AGPGAT181" fast="false" reversible="false" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C18:1)" metaid="R_2AGPGAT181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg181_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_3OAS161" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:1)" metaid="R_3OAS161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tdeACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3ocpalm9eACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2323"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3-DEHYDROQUINATE-SYNTHASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.3.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03083"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21968"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21970"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21971"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21969"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2923"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02212"/>
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+          <speciesReference species="M_2dda7p_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3dhq_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3389"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EAR141y" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C14:1)" metaid="R_EAR141y" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_t3c7mrseACP_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tdeACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1288"/>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_t3c9palmeACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1288"/>
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+          <speciesReference species="M_2agpg141_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2835"/>
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+          <speciesReference species="M_2agpg181_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_2agpg181_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2835"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg141_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0452"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_LPLIPAL2ATG140" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C14:0)" metaid="R_LPLIPAL2ATG140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_pg140_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_apg140_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+      <reaction id="R_LPLIPAL2ATG141" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C14:1)" metaid="R_LPLIPAL2ATG141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101178"/>
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+            </rdf:Description>
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+          <speciesReference species="M_pg141_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_apg141_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+                <rdf:Bag>
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+          <speciesReference species="M_pg160_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_apg160_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_LPLIPAL2ATG180" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C18:0)" metaid="R_LPLIPAL2ATG180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_LPLIPAL2ATG180">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101181"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_pg180_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_apg180_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+      <reaction id="R_LPLIPAL2ATG161" fast="false" reversible="false" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C16:1)" metaid="R_LPLIPAL2ATG161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_LPLIPAL2ATG161">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+          <speciesReference species="M_pg161_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_apg161_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pg181_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_apg181_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3pg_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+      <reaction id="R_FACOAE100" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (decanoate)" metaid="R_FACOAE100" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99127"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dca_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0452"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FACOAE80" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (octanoate)" metaid="R_FACOAE80" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30144"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30145"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30146"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/6581"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08447"/>
+                </rdf:Bag>
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+          <speciesReference species="M_occoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_octa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0452"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FACOAE60" fast="false" reversible="false" name="Fatty-acid-CoA thioesterase (hexanoate)" metaid="R_FACOAE60" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
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+          <speciesReference species="M_hxcoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hxa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0452"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CLPNS180pp" fast="false" reversible="true" name="Cardiolipin synthase (periplasmic, n-C18:0)" metaid="R_CLPNS180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CLPNS180pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96787"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pg180_p" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_clpn180_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1249"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0789"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PLIPA1E120pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylethanolamine, n-C12:0) (periplasm)" metaid="R_PLIPA1E120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102974"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_pe120_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2agpe120_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CLPNS181pp" fast="false" reversible="true" name="Cardiolipin synthase (periplasmic, n-C18:1)" metaid="R_CLPNS181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                <rdf:Bag>
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+        <listOfProducts>
+          <speciesReference species="M_clpn181_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:or>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0789"/>
+          </fbc:or>
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+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_cpg160_c" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05197"/>
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+          <speciesReference species="M_ura_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1006"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0452"/>
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+      <reaction id="R_CLPNS120pp" fast="false" reversible="true" name="Cardiolipin synthase (periplasmic, n-C12:0)" metaid="R_CLPNS120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        <listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1249"/>
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+        <listOfProducts>
+          <speciesReference species="M_2agpe160_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0657"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_hdcoa_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0452"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2344"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2344"/>
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+        <listOfProducts>
+          <speciesReference species="M_2agpg160_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lpp_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0657"/>
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+          <speciesReference species="M_ddca_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg120_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
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+          <speciesReference species="M_pg120_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_apg120_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+        <listOfProducts>
+          <speciesReference species="M_ala__D_c" stoichiometry="2" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1488"/>
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+          <speciesReference species="M_pe180_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
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+          <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+          <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+          <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+          <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pe181_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
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+      <reaction id="R_2AGPGAT140" fast="false" reversible="false" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C14:0)" metaid="R_2AGPGAT140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_2AGPGAT140">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94772"/>
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+          <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
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+          <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+          <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tdecoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1805"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_hdcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1701"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0914"/>
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+          <speciesReference species="M_pg181_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2agpg181_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALAALAabcpp" fast="false" reversible="false" name="D-alanyl-D-alanine (DalaDala) transport via ABC system (periplasm)" metaid="R_ALAALAabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08098"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_alaala_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3544"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3542"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3543"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3540"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3541"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1487"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1486"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1483"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1485"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1484"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HEXt2rpp" fast="false" reversible="true" name="Hexanoate transport via proton symport, reversible (periplasm)" metaid="R_HEXt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100622"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12596"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08714"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_hxa_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hxa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2223"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_G3PEabcpp" fast="false" reversible="false" name="Sn-glycerol-3-phosphoethanolamine transport via ABC system (periplasm)" metaid="R_G3PEabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_G3PEabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/G3PEabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99883"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08559"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3450"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3451"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3453"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3452"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_G3PCabcpp" fast="false" reversible="false" name="Sn-glycerol-3-phosphocholine transport via ABC system (periplasm)" metaid="R_G3PCabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99873"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08553"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_g3pc_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3pc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3450"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3451"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3453"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3452"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_2AGPGAT161" fast="false" reversible="false" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C16:1)" metaid="R_2AGPGAT161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_2AGPGAT161">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94775"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2agpg161_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg161_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PA181abcpp" fast="false" reversible="false" name="Phosphatidate transport via ABC system (n-C18:1, periplasm)" metaid="R_PA181abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102310"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09059"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa181_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa181_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0914"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_12DGR141tipp" fast="false" reversible="false" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:1)" metaid="R_12DGR141tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_12DGR141tipp">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94677"/>
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+            </rdf:Description>
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+          <speciesReference species="M_12dgr141_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_12dgr141_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_AMPTASEPG" fast="false" reversible="false" name="Aminopeptidase (pro-gly)" metaid="R_AMPTASEPG" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95829"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28802"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28799"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28801"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28800"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08133"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_progly_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2523"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0932"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4260"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0237"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ADSL1r" fast="false" reversible="true" name="Adenylsuccinate lyase" metaid="R_ADSL1r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16855"/>
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+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1131"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PROGLYabcpp" fast="false" reversible="false" name="L-Prolinylglycine (Pro-Gly) transport via ABC system (periplasm)" metaid="R_PROGLYabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103190"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09189"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_progly_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_progly_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3544"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3542"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3541"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3543"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GTHRDabcpp" fast="false" reversible="false" name="Reduced glutathione via ABC system (periplasm)" metaid="R_GTHRDabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29789#2"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13306"/>
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+          <speciesReference species="M_gthrd_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0830"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0829"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0832"/>
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+        </fbc:geneProductAssociation>
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+        </fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1278"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2835"/>
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+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2366"/>
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+          <speciesReference species="M_pa141_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg141_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pg160_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pg161_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa181_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg181_p" stoichiometry="1" constant="true"/>
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+      </reaction>
+      <reaction id="R_D_LACt2pp" fast="false" reversible="true" name="D-lactate transport via proton symport (periplasm)" metaid="R_D_LACt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09772"/>
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+        <listOfProducts>
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+          <speciesReference species="M_lac__D_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2975"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_PLIPA1E180pp" fast="false" reversible="false" name="Phospholipase A1 (phosphatidylethanolamine, n-C18:0) (periplasm)" metaid="R_PLIPA1E180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_pe180_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2agpe180_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+      <reaction id="R_RIBtex" fast="false" reversible="true" name="Ribose transport via diffusion (extracellular to periplasm)" metaid="R_RIBtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_FLVRx" fast="false" reversible="false" name="Flavin reductase (NAD)" metaid="R_FLVRx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ribflv_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rbflvrd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3844"/>
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+      <reaction id="R_THMtex" fast="false" reversible="true" name="Thiamine transport via diffusion (extracellular to periplasm)" metaid="R_THMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09300"/>
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+        <listOfProducts>
+          <speciesReference species="M_thm_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        <listOfProducts>
+          <speciesReference species="M_xylu__L_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+          <speciesReference species="M_pg140_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2agpg140_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+        <listOfProducts>
+          <speciesReference species="M_2agpg161_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+        <listOfProducts>
+          <speciesReference species="M_clpn160_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1249"/>
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+          <speciesReference species="M_clpn161_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0789"/>
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+        <listOfProducts>
+          <speciesReference species="M_all__D_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+      <reaction id="R_PG160abcpp" fast="false" reversible="false" name="Phosphatidylglycerol transport via ABC system (n-C16:0, periplasm)" metaid="R_PG160abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+              <fbc:and>
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+                <fbc:geneProductRef fbc:geneProduct="G_b3006"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0805"/>
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+            <fbc:and>
+              <fbc:and>
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+                <fbc:geneProductRef fbc:geneProduct="G_b3006"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2155"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mthgxl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07930"/>
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+          <speciesReference species="M_23dappa_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_unagamuf_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_eca4und_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3793"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143102"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_feoxam_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b1252"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3005"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3006"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15117"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15120"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09320"/>
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+          <speciesReference species="M_dpcoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2tpr3dpcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0613"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_dgmp_e" stoichiometry="1" constant="true"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08592"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05569"/>
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+          <speciesReference species="M_gam_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_gam6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1819"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1817"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1818"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GSNt2pp" fast="false" reversible="false" name="Guanosine transport in via proton symport (periplasm)" metaid="R_GSNt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09747"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+          <speciesReference species="M_gsn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2964"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn03974"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fmnh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0937"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3844"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_3hpppn_e" fast="false" reversible="false" name="3-(3-hydroxy-phenyl)propionate exchange" metaid="R_EX_3hpppn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+      <reaction id="R_EX_man6p_e" fast="false" reversible="false" name="D-Mannose 6-phosphate exchange" metaid="R_EX_man6p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08880"/>
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+      <reaction id="R_GSNtex" fast="false" reversible="true" name="Guanosine transport via diffusion (extracellular to periplasm)" metaid="R_GSNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08672"/>
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+        <listOfProducts>
+          <speciesReference species="M_gsn_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_SBTtex" fast="false" reversible="true" name="D-sorbitol transport via diffusion (extracellular to periplasm)" metaid="R_SBTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09243"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09662"/>
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+        <listOfProducts>
+          <speciesReference species="M_sbt__D_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29679"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09682"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08526"/>
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+          <speciesReference species="M_for_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_for_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32810"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32807"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32809"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28923"/>
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+          <speciesReference species="M_phe__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+          <speciesReference species="M_phe__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0112"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01504"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97369"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20231"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20229"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20230"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/20232"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01093"/>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_23dhba_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0594"/>
+        </fbc:geneProductAssociation>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-267"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/11213"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09296"/>
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+          <speciesReference species="M_trdrd_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3781"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2480"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1710"/>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2582"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2480"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08967"/>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+          <speciesReference species="M_fum_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_pppg9_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+          <speciesReference species="M_ppp9_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="3" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3850"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16109"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16110"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16112"/>
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+          <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+          <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1723"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pdx5p_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_pydx5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1638"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102437"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_pdx5p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pydx5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_MDDCP1pp" fast="false" reversible="false" name="Murein D,D-carboxypeptidase (murein5px4p) (periplasm)" metaid="R_MDDCP1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_murein5px4p_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein4px4p_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3182"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0839"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2010"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0376"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2430"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100469"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01457"/>
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+        <listOfProducts>
+          <speciesReference species="M_tagur_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3092"/>
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+      <reaction id="R_OMBZLM" fast="false" reversible="false" name="2-Octaprenyl-6-methoxy-benzoquinol methylase" metaid="R_OMBZLM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_OMBZLM">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27777"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27776"/>
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+          <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2ommbl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3833"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_pa181_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2odec11eg3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3612"/>
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+        </fbc:geneProductAssociation>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hg2_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hg2_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3915"/>
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+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0431"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0429"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0430"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_malthx_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_t3c11vaceACP_c" stoichiometry="1" constant="true"/>
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+        </listOfProducts>
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+          <speciesReference species="M_octeACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <speciesReference species="M_tdeACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1tdec7eg3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2293"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0446"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22985"/>
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+          <speciesReference species="M_cbp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oxam_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+      <reaction id="R_UDCPPtppi" fast="false" reversible="false" name="Undecaprenyl phosphate transport (cytoplasm to periplasm)" metaid="R_UDCPPtppi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_udcpp_c" stoichiometry="1" constant="true"/>
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+      <reaction id="R_AGMH" fast="false" reversible="false" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl beta -1,4-N-acetylglucosaminidase" metaid="R_AGMH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08080"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_acgam_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anhm_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1107"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_G3PAT181" fast="false" reversible="false" name="Glycerol-3-phosphate acyltransferase (C18:1)" metaid="R_G3PAT181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_octeACP_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_1odec11eg3p_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4041"/>
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+        </fbc:geneProductAssociation>
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+        <listOfProducts>
+          <speciesReference species="M_cdpdtdecg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0175"/>
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+          <speciesReference species="M_murein5p5p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_c" stoichiometry="2" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0089"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3208"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3396"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0089"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2519"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0089"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa180_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_cdpdodecg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0175"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_MPTG2" fast="false" reversible="false" name="Murein polymerizing transglycosylase 2 (three linked units)" metaid="R_MPTG2" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_MPTG2">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143250"/>
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+              </bqbiol:is>
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+        </sbml:annotation>
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+          <speciesReference species="M_murein5p5p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uaagmda_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein5p5p5p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+              <fbc:geneProductRef fbc:geneProduct="G_b1069"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0089"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0089"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3208"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3396"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0089"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0089"/>
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+          </fbc:or>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pa141_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_cdpdtdec7eg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0175"/>
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+      <reaction id="R_MCTP1App" fast="false" reversible="false" name="Murein crosslinking transpeptidase 1A:(A2pm-&gt;D-ala) (periplasm)" metaid="R_MCTP1App" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein5px4p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0635"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0084"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3396"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0635"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0084"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0149"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MCTP2App" fast="false" reversible="false" name="Murein crosslinking transpeptidase 1A:(A2pm-&gt;D-ala) (periplasm)" metaid="R_MCTP2App" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MCTP2App">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MCTP2App"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143205"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08889"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_murein5p5p5p_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala__D_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_murein5px4px4p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0635"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0084"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3396"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0635"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0084"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0149"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CDAPPA160" fast="false" reversible="false" name="CDP-Diacylglycerol pyrophostatase (n-C16:0)" metaid="R_CDAPPA160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CDAPPA160">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDAPPA160"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.26"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96503"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08202"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cdpdhdecg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pa160_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3918"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CDAPPA141" fast="false" reversible="false" name="CDP-Diacylglycerol pyrophostatase (n-C14:1)" metaid="R_CDAPPA141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CDAPPA141">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDAPPA141"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.1.26"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96502"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08201"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cdpdtdec7eg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pa141_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3918"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MCTP1Bpp" fast="false" reversible="false" name="Murein crosslinking transpeptidase 1B:(A2pm-&gt;A2pm) (periplasm)" metaid="R_MCTP1Bpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MCTP1Bpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MCTP1Bpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143204"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08888"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_murein5p5p_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_alaala_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein5px3p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1678"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0925"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PERD" fast="false" reversible="true" name="Erythronate 4-phosphate (4per) dehydrogenase" metaid="R_PERD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PERD">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PERD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:ERYTHRON4PDEHYDROG-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.290"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04210"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102495"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18831"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18830"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18832"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18829"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02939"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_4per_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ohpb_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2320"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MELIBt3ipp" fast="false" reversible="false" name="Melibiose transport in via antiport (periplasm)" metaid="R_MELIBt3ipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MELIBt3ipp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MELIBt3ipp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138588"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_melib_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_melib_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1528"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PGSA141" fast="false" reversible="false" name="Phosphatidylglycerol synthase (n-C14:1)" metaid="R_PGSA141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PGSA141">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PGSA141"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102591"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cdpdtdec7eg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pgp141_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1912"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_alaala_e" fast="false" reversible="false" name="D-Alanyl-D-alanine exchange" metaid="R_EX_alaala_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_alaala_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_alaala_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95679"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08099"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_alaala_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_dtmp_e" fast="false" reversible="false" name="DTMP exchange" metaid="R_EX_dtmp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_dtmp_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_dtmp_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97806"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08374"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dtmp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_5DOAN" fast="false" reversible="false" name="5'-deoxyadenosine nuclosidase" metaid="R_5DOAN" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_5DOAN">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/5DOAN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-6550"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95069"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29862"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29860"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29859"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29861"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13649"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08013"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dad_5_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_5drib_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0159"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DM_5drib_c" fast="false" reversible="false" name="Sink needed to allow 5'-deoxyribose to leave system" metaid="R_DM_5drib_c" sboTerm="SBO:0000628" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DM_5drib_c">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DM_5drib_c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142736"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_5drib_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_lipoate_e" fast="false" reversible="false" name="Lipoate exchange" metaid="R_EX_lipoate_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_lipoate_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_lipoate_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-278"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101092"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29755"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29758"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29756"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29757"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_lipoate_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_pydx_e" fast="false" reversible="false" name="Pyridoxal exchange" metaid="R_EX_pydx_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_pydx_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_pydx_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-214"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103370"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28462"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28465"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28463"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28464"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12666"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pydx_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_g1p_e" fast="false" reversible="false" name="D-Glucose 1-phosphate exchange" metaid="R_EX_g1p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_g1p_e">
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+        </sbml:annotation>
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+          <speciesReference species="M_pydam_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyam5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2418"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_DHORDfum" fast="false" reversible="false" name="Fumarate dependent DHORD" metaid="R_DHORDfum" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30060"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30061"/>
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+          <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_orot_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35247#1"/>
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+          <speciesReference species="M_kdo2lipid4_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_kdo2lipid4_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0914"/>
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+        <listOfProducts>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ddca_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0452"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3hddecACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1093"/>
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+          <speciesReference species="M_toct2eACP_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0954"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0180"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_tddec2eACP_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0954"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_gthox_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2893"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_DSBGGT" fast="false" reversible="false" name="DsbG:glutathione thiotransferase" metaid="R_DSBGGT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_DSBGGT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_gthox_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0604"/>
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+          <speciesReference species="M_toctd2eACP_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcaACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1288"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4160"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0914"/>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
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+          <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
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+        <listOfProducts>
+          <speciesReference species="M_acon_C_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22144"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22146"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22147"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1276"/>
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+          <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3428"/>
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+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3666"/>
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+          <speciesReference species="M_pa140_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1tdecg3p_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+          <speciesReference species="M_mthgxl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_lald__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3945"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07919"/>
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+          <speciesReference species="M_12ppd__R_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/40893"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/40894"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/40892"/>
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+          <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
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+      <reaction id="R_ASNS1" fast="false" reversible="false" name="Asparagine synthase (glutamine-hydrolysing)" metaid="R_ASNS1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_asn__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0674"/>
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+          <speciesReference species="M_toct2eACP_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ocACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1288"/>
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+          <speciesReference species="M_tddec2eACP_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_3hcvac11eACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1093"/>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+          <speciesReference species="M_t3c5ddeceACP_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0180"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
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+      </reaction>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          </rdf:RDF>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LPLIPAL1G161pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C16:1) (periplasm)" metaid="R_LPLIPAL1G161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_1agpg161_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GTHRDHpp" fast="false" reversible="false" name="Glutathione hydralase (periplasmic)" metaid="R_GTHRDHpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.19.13"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00494"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-8943279"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-8943279"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-8943279"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-8943279"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-8943279"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28808"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28807"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28810"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/926"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00350"/>
+                </rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cgly_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3447"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_o2_e" fast="false" reversible="true" name="O2 exchange" metaid="R_EX_o2_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-474"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102090"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09641"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05468"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09031"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09032"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09734"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_PROGLYtex" fast="false" reversible="true" name="L-Prolinylglycine transport via diffusion (extracellular to periplasm)" metaid="R_PROGLYtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PROGLYtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103191"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09190"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_progly_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_progly_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_progly_e" fast="false" reversible="false" name="L-Prolinylglycine exchange" metaid="R_EX_progly_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_progly_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_progly_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103191"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09190"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_progly_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_MDDCP2pp" fast="false" reversible="false" name="Murein D,D-carboxypeptidase (murein5px4px4p) (periplasm)" metaid="R_MDDCP2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_MDDCP2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MDDCP2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.4.16.4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143207"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08891"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein5px4px4p_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein4px4px4p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0632"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3182"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0839"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2010"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2430"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0376"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LPLIPAL1G120pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C12:0) (periplasm)" metaid="R_LPLIPAL1G120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_LPLIPAL1G120pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101155"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_1agpg120_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_g3pg_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PLIPA2E140pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylethanolamine, n-C14:0) (periplasm)" metaid="R_PLIPA2E140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PLIPA2E140pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102997"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pe140_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1agpe140_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PLIPA2E160pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylethanolamine, n-C16:0) (periplasm)" metaid="R_PLIPA2E160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102999"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pe160_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1agpe160_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PLIPA2A161pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidate, n-C16:1) (periplasm)" metaid="R_PLIPA2A161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PLIPA2A161pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102993"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa161_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1hdec9eg3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PLIPA2A181pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidate, n-C18:1) (periplasm)" metaid="R_PLIPA2A181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102995"/>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa181_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1odec11eg3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_F6Ptex" fast="false" reversible="true" name="Fructose 6-phosphate transport via diffusion (extracellular to periplasm)" metaid="R_F6Ptex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </listOfReactants>
+        <listOfProducts>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08892"/>
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+          <speciesReference species="M_murein5p5p_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein5p4p_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3182"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0839"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2010"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2430"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0376"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tmrs2eACP_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1288"/>
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_butACP_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1288"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08591"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05568"/>
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+          <speciesReference species="M_gam6p_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3ocvac11eACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1095"/>
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+          <speciesReference species="M_t3c9palmeACP_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1288"/>
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+          <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1tdecg3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4041"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1hdecg3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4041"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1hdec9eg3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4041"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AGPAT160" fast="false" reversible="false" name="1-hexadecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C16:0)" metaid="R_AGPAT160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa160_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3018"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pa140_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3018"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0925"/>
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+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0925"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1990"/>
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+          <speciesReference species="M_LalaDgluMdapDala_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pa120_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0914"/>
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+          <speciesReference species="M_12dgr181_p" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1278"/>
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+      <reaction id="R_PA140abcpp" fast="false" reversible="false" name="Phosphatidate transport via ABC system (n-C14:0, periplasm)" metaid="R_PA140abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09054"/>
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+          <speciesReference species="M_pa140_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa140_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0914"/>
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+      <reaction id="R_CLPNH140pp" fast="false" reversible="false" name="Cardiolipin hydrolase (periplasm, n-C14:0)" metaid="R_CLPNH140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa140_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg140_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+      <reaction id="R_EX_12ppd__R_e" fast="false" reversible="false" name="(R)-Propane-1,2-diol exchange" metaid="R_EX_12ppd__R_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07920"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07919"/>
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+          <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pgp181_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1912"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1278"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pgp141_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_pg141_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1278"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MDDCP5pp" fast="false" reversible="false" name="Murein D,D-carboxypeptidase (murein5p3p) (periplasm)" metaid="R_MDDCP5pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08894"/>
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+          <speciesReference species="M_murein5p3p_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein4p3p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0632"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3182"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0839"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2010"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2430"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0376"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MLTGY3pp" fast="false" reversible="false" name="Murein lytic transglycosylase (murein3p3p) (periplasm)" metaid="R_MLTGY3pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143247"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08939"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_murein3p3p_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_anhgm3p_p" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4392"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2813"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2701"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1193"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2963"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2558"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0211"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1097"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_12DGR120tipp" fast="false" reversible="false" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C12:0)" metaid="R_12DGR120tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94675"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_12dgr120_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_12dgr120_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_MDDCP4pp" fast="false" reversible="false" name="Murein D,D-carboxypeptidase (murein5p4p) (periplasm)" metaid="R_MDDCP4pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_murein5p4p_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein4p4p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3182"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2010"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2430"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0376"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_CLPNS140pp" fast="false" reversible="true" name="Cardiolipin synthase (periplasmic, n-C14:0)" metaid="R_CLPNS140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_clpn140_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1249"/>
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+          <speciesReference species="M_glyc_p" stoichiometry="1" constant="true"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_ocdcaACP_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4041"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pg160_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2agpg160_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+      <reaction id="R_PG120abcpp" fast="false" reversible="false" name="Phosphatidylglycerol transport via ABC system (n-C12:0, periplasm)" metaid="R_PG120abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg120_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0914"/>
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+      <reaction id="R_EX_gal1p_e" fast="false" reversible="false" name="Alpha-D-Galactose 1-phosphate exchange" metaid="R_EX_gal1p_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pe140_p" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0914"/>
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+        <listOfProducts>
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+          <speciesReference species="M_cpe160_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1661"/>
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+          <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+          <speciesReference species="M_g3pe_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+          <speciesReference species="M_cpe180_c" stoichiometry="1" constant="true"/>
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+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1661"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2328"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2134"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0376"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2175"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1655"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1856"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pe180_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_12dgr140_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1278"/>
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+      <reaction id="R_MLTGY1pp" fast="false" reversible="false" name="Murein lytic transglycosylase (murein4p4p) (periplasm)" metaid="R_MLTGY1pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
+          <speciesReference species="M_anhgm4p_p" stoichiometry="2" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4392"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2813"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2701"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1193"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2558"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0211"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1097"/>
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+        </fbc:geneProductAssociation>
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+        <listOfProducts>
+          <speciesReference species="M_cgly_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+          <speciesReference species="M_but2eACP_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0180"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pe141_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2agpe141_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3ohexACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2323"/>
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+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_myrsACP_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_3opalmACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1095"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_pa141_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+          <speciesReference species="M_12dgr141_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1278"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1278"/>
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+      </reaction>
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+          <speciesReference species="M_gthox_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+        </sbml:annotation>
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+          <speciesReference species="M_dsbard_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dsbaox_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3860"/>
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+        </fbc:geneProductAssociation>
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+        </sbml:annotation>
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+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_dsbaox_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3860"/>
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+        </fbc:geneProductAssociation>
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+        </sbml:annotation>
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+          <speciesReference species="M_trdox_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b4136"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3781"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4136"/>
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+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TDSR1" fast="false" reversible="false" name="Thiol:disulfide reductase (DsbC)" metaid="R_TDSR1" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_dsbdrd_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_dsbcrd_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dsbdox_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4136"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_CGLYabcpp" fast="false" reversible="false" name="L-Cysteinylglycine (Cys-Gly) transport via ABC system (periplasm)" metaid="R_CGLYabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05539"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08210"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_cgly_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cgly_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3542"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3543"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3540"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3541"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PLIPA2A120pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidate, n-C12:0) (periplasm)" metaid="R_PLIPA2A120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_pa120_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_1ddecg3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+        <listOfProducts>
+          <speciesReference species="M_1hdecg3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa180_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg180_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3hhexACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1093"/>
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_3hoctACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1093"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_murein5px3p_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_alaala_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein3px3p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1990"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1113"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1678"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08927"/>
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+          <speciesReference species="M_murein4p4p_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala__D_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein4p3p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1990"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1678"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0819"/>
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+        </fbc:geneProductAssociation>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3odecACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2323"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1095"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_3OAS120" fast="false" reversible="false" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:0)" metaid="R_3OAS120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3oddecACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1095"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2323"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21599"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/21598"/>
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+          <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2amsa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1539"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_3OAR40" fast="false" reversible="true" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C4:0)" metaid="R_3OAR40" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3haACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1093"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3hdecACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1093"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30109"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30110"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30108"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08371"/>
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+          <speciesReference species="M_ser__D_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2amsa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1539"/>
+        </fbc:geneProductAssociation>
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+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thex2eACP_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0954"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0180"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05333"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tdec2eACP_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0180"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_3hmrsACP_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tmrs2eACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0954"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0180"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tpalm2eACP_c" stoichiometry="1" constant="true"/>
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+        </fbc:geneProductAssociation>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3018"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1278"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1655"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1856"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2175"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0376"/>
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_thex2eACP_c" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97098"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_12dgr180_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa180_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4042"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DAGK181" fast="false" reversible="false" name="Diacylglycerol kinase (n-C18:1)" metaid="R_DAGK181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DAGK181">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97100"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_12dgr181_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pa181_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4042"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MLDEP2pp" fast="false" reversible="false" name="Murein L,D-endopeptidase (murein5px3p) (periplasm)" metaid="R_MLDEP2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MLDEP2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143243"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08932"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein5px3p_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_murein5p3p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2328"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_ag_e" fast="false" reversible="false" name="Silver exchange" metaid="R_EX_ag_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_ag_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ag_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR142917"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ag_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_MLTGY2pp" fast="false" reversible="false" name="Murein lytic transglycosylase (murein4p3p) (periplasm)" metaid="R_MLTGY2pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MLTGY2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTGY2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143246"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08938"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_murein4p3p_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_anhgm3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_anhgm4p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2963"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4392"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2813"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2701"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1193"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2558"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0211"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1097"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PLIPA2E120pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylethanolamine, n-C12:0) (periplasm)" metaid="R_PLIPA2E120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PLIPA2E120pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2E120pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102996"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pe120_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1agpe120_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PLIPA2G141pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylglycerol, n-C14:1) (periplasm)" metaid="R_PLIPA2G141pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PLIPA2G141pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103005"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg141_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1agpg141_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MLTGY4pp" fast="false" reversible="false" name="Murein lytic transglycosylase (murein4px4p4p) (periplasm)" metaid="R_MLTGY4pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MLTGY4pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MLTGY4pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143248"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08940"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_murein4px4p4p_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_anhgm4p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_murein4px4p_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4392"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2813"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2701"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1193"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2963"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2558"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0211"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1097"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EAR60x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C6:0)" metaid="R_EAR60x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EAR60x">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97865"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thex2eACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_hexACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1288"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PLIPA2G161pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylglycerol, n-C16:1) (periplasm)" metaid="R_PLIPA2G161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PLIPA2G161pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PLIPA2G161pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103007"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg161_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1agpg161_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_cys__D_e" fast="false" reversible="false" name="D-Cysteine exchange" metaid="R_EX_cys__D_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_cys__D_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_cys__D_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96997"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08283"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cys__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_LPLIPAL1A120pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C12:0) (periplasm)" metaid="R_LPLIPAL1A120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_LPLIPAL1A120pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LPLIPAL1A120pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101141"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_1ddecg3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LPLIPAL1A140pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C14:0) (periplasm)" metaid="R_LPLIPAL1A140pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.1.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101142"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_1tdecg3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EAR80x" fast="false" reversible="false" name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C8:0)" metaid="R_EAR80x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_EAR80x">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97867"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_toct2eACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1288"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0914"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_12DGR161tipp" fast="false" reversible="false" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:1)" metaid="R_12DGR161tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
+          <speciesReference species="M_12dgr181_c" stoichiometry="1" constant="true"/>
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+      <reaction id="R_NTP11" fast="false" reversible="false" name="Nucleoside-triphosphatase (dITP)" metaid="R_NTP11" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30860"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30859"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30861"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09011"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_didp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4394"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_LPLIPAL1A181pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C18:1) (periplasm)" metaid="R_LPLIPAL1A181pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
+          <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
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+      <reaction id="R_LPLIPAL1E120pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C12:0) (periplasm)" metaid="R_LPLIPAL1E120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_g3pe_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3hoctaACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1093"/>
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+          <speciesReference species="M_glyc3p_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_1ddecg3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4041"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <listOfProducts>
+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pgp120_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1912"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3ooctdACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1095"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2323"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_3HAD180" fast="false" reversible="false" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:0)" metaid="R_3HAD180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07764"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07979"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_toctd2eACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0954"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0180"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_cmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pa120_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3918"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                <rdf:Bag>
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+          <speciesReference species="M_dsbgox_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_dsbdox_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dsbgrd_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4136"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_acser_e" fast="false" reversible="false" name="O-Acetyl-L-serine exchange" metaid="R_EX_acser_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0221"/>
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+          <speciesReference species="M_tdcoa_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_td2coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0221"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2279"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2277"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2284"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2282"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2278"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2288"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2276"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2287"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2283"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2281"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2286"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2280"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2285"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_h_c" stoichiometry="4" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2dmmql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2277"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2284"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2282"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2278"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2288"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2276"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2287"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2283"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2281"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2286"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2280"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2285"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35200"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35202"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08638"/>
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+          <speciesReference species="M_glyb_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4111"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_5dglcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4265"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GALCTNt2pp" fast="false" reversible="false" name="D-galactonate transport via proton symport (periplasm)" metaid="R_GALCTNt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10160"/>
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+          <speciesReference species="M_galctn__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3691"/>
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+      <reaction id="R_GALCTNLtex" fast="false" reversible="true" name="L-galactonate transport via diffusion (extracellular to periplasm)" metaid="R_GALCTNLtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_galctn__L_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+      <reaction id="R_EX_galctn__L_e" fast="false" reversible="false" name="L-Galactonate exchange" metaid="R_EX_galctn__L_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5130"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08372"/>
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+          <speciesReference species="M_ser__D_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ser__D_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b4208"/>
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+      <reaction id="R_ALAt4pp" fast="false" reversible="false" name="L-alanine transport in via sodium symport (periplasm)" metaid="R_ALAt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <fbc:geneProductRef fbc:geneProduct="G_b0007"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08855"/>
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+          <speciesReference species="M_lys__L_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0874"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_KDUI" fast="false" reversible="false" name="5-keto-4-deoxyuronate isomerase" metaid="R_KDUI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
+          <speciesReference species="M_dkdglcn_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2843"/>
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+      <reaction id="R_EX_tungs_e" fast="false" reversible="true" name="Tungstate exchange" metaid="R_EX_tungs_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32839"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1216"/>
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+      <reaction id="R_CTBTCAL2" fast="false" reversible="false" name="Crotonobetaine-CoA Ligase" metaid="R_CTBTCAL2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_ctbt_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ctbtcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0037"/>
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+          <speciesReference species="M_ppcoa_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3114"/>
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_mql8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2278"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2288"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2276"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2287"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2283"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2286"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2280"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2285"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_ppa_p" stoichiometry="1" constant="true"/>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1015"/>
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+          <speciesReference species="M_orot_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3528"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28717"/>
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+          <speciesReference species="M_mal__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3528"/>
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+      <reaction id="R_FA100ACPHi" fast="false" reversible="false" name="Fatty-acyl-ACP hydrolase" metaid="R_FA100ACPHi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_dca_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+      <reaction id="R_CRNDCAL2" fast="false" reversible="false" name="D-Carnitine-CoA Ligase" metaid="R_CRNDCAL2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_crn__D_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_crnDcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0037"/>
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+      <reaction id="R_5DGLCNtex" fast="false" reversible="true" name="5-Dehydro-D-gluconate transport via diffusion (extracellular to periplasm)" metaid="R_5DGLCNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        <listOfProducts>
+          <speciesReference species="M_5dglcn_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18292"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/820"/>
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+          <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4122"/>
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+          <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_crncoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0037"/>
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+          <speciesReference species="M_chol_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1801"/>
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+      <reaction id="R_PLIPA2E161pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylethanolamine, n-C16:1) (periplasm)" metaid="R_PLIPA2E161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
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+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pe180_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_1agpe180_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FRULYSE" fast="false" reversible="true" name="Fructoselysine 3-epimerase" metaid="R_FRULYSE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28390"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28392"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28393"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08531"/>
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+          </rdf:RDF>
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+        <listOfReactants>
+          <speciesReference species="M_psclys_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_frulys_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4474"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FRULYSt2pp" fast="false" reversible="false" name="Fructoselysine transport via proton symport (periplasm)" metaid="R_FRULYSt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99656"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08533"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_frulys_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_frulys_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3370"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_LalaDgluMdap_e" fast="false" reversible="false" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate exchange" metaid="R_EX_LalaDgluMdap_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_LalaDgluMdap_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94971"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08004"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_LalaDgluMdap_e" stoichiometry="1" constant="true"/>
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+      </reaction>
+      <reaction id="R_EX_psclys_e" fast="false" reversible="false" name="Psicoselysine exchange" metaid="R_EX_psclys_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-418"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103228"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28453"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28451"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28452"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09196"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_psclys_e" stoichiometry="1" constant="true"/>
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+      </reaction>
+      <reaction id="R_TUNGStex" fast="false" reversible="true" name="Tungstate transport via diffusion (extracellular to periplasm)" metaid="R_TUNGStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104979"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32842"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32841"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32840"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/32839"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09334"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_tungs_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_tungs_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PLIPA2G120pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylglycerol, n-C12:0) (periplasm)" metaid="R_PLIPA2G120pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103003"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg120_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_1agpg120_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ddca_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_PLIPA2G180pp" fast="false" reversible="false" name="Phospholipase A2 (phosphatidylglycerol, n-C18:0) (periplasm)" metaid="R_PLIPA2G180pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103008"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pg180_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_1agpg180_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3821"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LPLIPAL1A161pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C16:1) (periplasm)" metaid="R_LPLIPAL1A161pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_LPLIPAL1A161pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101145"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdcea_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LPLIPAL1A160pp" fast="false" reversible="false" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C16:0) (periplasm)" metaid="R_LPLIPAL1A160pp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_LPLIPAL1A160pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101144"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08799"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc3p_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdca_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0494"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PSCLYSt2pp" fast="false" reversible="false" name="Psicoselysine transport via proton symport (periplasm)" metaid="R_PSCLYSt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PSCLYSt2pp">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103227"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_psclys_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_psclys_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3370"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LYSt2pp" fast="false" reversible="false" name="L-lysine transport in via proton symport (periplasm)" metaid="R_LYSt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28914"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28911"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28912"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09740"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08854"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09674"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lys__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2156"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_COBALT2tpp" fast="false" reversible="false" name="Cobalt transport in via permease (no H+)" metaid="R_COBALT2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96821"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28580"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28581"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28578"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12148"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08241"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08242"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10474"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cobalt2_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cobalt2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3040"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3816"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_OXCDC" fast="false" reversible="false" name="Oxalyl-CoA decarboxylase" metaid="R_OXCDC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_oxalcoa_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_forcoa_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+          <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+      <reaction id="R_GLYt2pp" fast="false" reversible="false" name="Glycine transport in via proton symport (periplasm)" metaid="R_GLYt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4208"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4130"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala_B_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4208"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_ala__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4208"/>
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+          <speciesReference species="M_fe2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3040"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
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+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3825"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tagur_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4358"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_THYMt3pp" fast="false" reversible="false" name="Thymine transport out via proton antiport (periplasm)" metaid="R_THYMt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_THYMt3pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104854"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09308"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09656"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thym_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thym_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_CLt3_2pp" fast="false" reversible="false" name="Chloride transport out via proton antiport (2:1) (periplasm)" metaid="R_CLt3_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2501"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96796"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29569"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29567"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29568"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29570"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08233"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_cl_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cl_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0155"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_ppal_e" fast="false" reversible="false" name="Propanal exchange" metaid="R_EX_ppal_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103071"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09169"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09170"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ppal_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_POR5" fast="false" reversible="true" name="Pyruvate synthase" metaid="R_POR5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_POR5">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/POR5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103064"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_flxr_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1378"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0684"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1378"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2895"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HACD8" fast="false" reversible="true" name="3-hydroxyacyl-CoA dehydrogenase (3-oxooctadecanoyl-CoA), peroxisomal" metaid="R_HACD8" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HACD8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.35"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100549"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08700"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3ohodcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3hodcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3846"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2341"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CTECOAI8" fast="false" reversible="true" name="3-cis-2-trans-enoyl-CoA isomerase" metaid="R_CTECOAI8" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CTECOAI8">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.3.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96942"/>
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+              </bqbiol:is>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_odecoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_od2coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3846"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CTECOAI6" fast="false" reversible="true" name="3-cis-2-trans-enoyl-CoA isomerase" metaid="R_CTECOAI6" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CTECOAI6">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.3.8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96940"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tdecoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_td2coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3846"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MTHTHFSs" fast="false" reversible="false" name="(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran synthesis (spontaneous)" metaid="R_MTHTHFSs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_MTHTHFSs">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-10017"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101756"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35161"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35162"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35159"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35160"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mdhdhf_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_mththf_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SELGTHR" fast="false" reversible="false" name="Selenate glutathione reductase" metaid="R_SELGTHR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-12864"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09367"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104318"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-2408556"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-2408553"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34906"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34903"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34904"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34905"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gthrd_c" stoichiometry="4" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_slnt_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dgslnt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="3" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_SELGTHR3" fast="false" reversible="false" name="Selenate glutathione reductase III" metaid="R_SELGTHR3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_SELGTHR3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SELGTHR3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104320"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_gslnt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_seln_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_EX_slnt_e" fast="false" reversible="true" name="Selenite exchange" metaid="R_EX_slnt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104325"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34891"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34893"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34892"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+          <speciesReference species="M_slnt_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_MALCOAMT" fast="false" reversible="false" name="Malonyl-CoA methyltransferase" metaid="R_MALCOAMT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MALCOAMT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101337"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34900"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34899"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34902"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34901"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malcoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malcoame_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0777"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PSCLYStex" fast="false" reversible="true" name="Psicoselysine transporter via diffusion (extracellular)" metaid="R_PSCLYStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-418"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103228"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28453"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28451"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28452"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09196"/>
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+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_psclys_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_psclys_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_THYMtex" fast="false" reversible="true" name="Thymine transport via diffusion (extracellular to periplasm)" metaid="R_THYMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09309"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_thym_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_thym_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CU2tpp" fast="false" reversible="false" name="Copper transport in via permease (no H+)" metaid="R_CU2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-437300"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-437300"/>
+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-437300"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28704"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28703"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08274"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05212"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08273"/>
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+        <listOfProducts>
+          <speciesReference species="M_cu2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3040"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FE2t3pp" fast="false" reversible="false" name="Iron (Fe+2) transport out via proton antiport (periplasm)" metaid="R_FE2t3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99506"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29441"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29442"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29440"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08474"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fe2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fe2_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3915"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MN2t3pp" fast="false" reversible="false" name="Manganese (Mn+2) transport out via proton antiport (periplasm)" metaid="R_MN2t3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MN2t3pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101669"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08946"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mn2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mn2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3915"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0752"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MG2t3_2pp" fast="false" reversible="true" name="Magnesium (Mg+2) transport in/out via proton antiport (periplasm)" metaid="R_MG2t3_2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MG2t3_2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101508"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08921"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mg2_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mg2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_CD2tpp" fast="false" reversible="false" name="Cadmium (+2) transport in via permease (no H+)" metaid="R_CD2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CD2tpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96499"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28709"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28708"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28707"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28710"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/13041"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08198"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08197"/>
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+            </rdf:Description>
+          </rdf:RDF>
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+        <listOfReactants>
+          <speciesReference species="M_cd2_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cd2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3040"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ETHAt2pp" fast="false" reversible="false" name="Ethanolamine transport in via proton symport" metaid="R_ETHAt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ETHAt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ETHAt2pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97975"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08423"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05551"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_etha_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_etha_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_FE3abcpp" fast="false" reversible="false" name="Iron (III) transport via ABC system (periplasm to cytoplasm)" metaid="R_FE3abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_FE3abcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:3.6.3.30-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.6.3.30"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99525"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12335#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12332#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12334#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12333#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05195"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08477"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe3_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_THRA" fast="false" reversible="false" name="Threonine aldolase" metaid="R_THRA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:THREONINE-ALDOLASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.48"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00751"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104833"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19625"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19626"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19627"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19628"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00541"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_thr__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2551"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0870"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_OGMEACPS" fast="false" reversible="false" name="3-Oxo-glutaryl-[ACP] methyl ester synthase" metaid="R_OGMEACPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malcoame_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ogmeACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1091"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_OGMEACPR" fast="false" reversible="false" name="3-Oxo-glutaryl-[ACP] methyl ester reductase" metaid="R_OGMEACPR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102160"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ogmeACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_hgmeACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1093"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_OPMEACPS" fast="false" reversible="false" name="3-Oxo-pimeloyl-[ACP] methyl ester synthase" metaid="R_OPMEACPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102208"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_gmeACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_opmeACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2323"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LIPAabctex" fast="false" reversible="false" name="Lipid A transport via ABC system (periplasm to extracellular)" metaid="R_LIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4262"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4261"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3199"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3201"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3200"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0054"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0641"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DGUNC" fast="false" reversible="false" name="Diguanylate cyclase" metaid="R_DGUNC" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_gtp_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cdigmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1341"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1794"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1535"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1025"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1490"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_XYLK2" fast="false" reversible="false" name="L-xylulokinase" metaid="R_XYLK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:LYXK-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.53"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01901"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138925"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18869"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/18870"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01389"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xylu__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xu5p__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0063"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3580"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLDBRAN2" fast="false" reversible="false" name="Glycogen debranching enzyme (bglycogen -&gt; glycogen)" metaid="R_GLDBRAN2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_GLDBRAN2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.18"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100155"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08605"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glycogen_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3431"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LALADGLUtex" fast="false" reversible="true" name="L-alanyl-D-glutamate transport via diffusion (extracellular to periplasm)" metaid="R_LALADGLUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_LALADGLUtex">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101003"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35127"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35128"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35129"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35130"/>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_LalaDglu_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_LalaDglu_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_S2FE2SR" fast="false" reversible="false" name="SUF [2Fe-2S] regeneration" metaid="R_S2FE2SR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104149"/>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2fe1s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufbcd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufsesh_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="5" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufbcd_2fe2s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufse_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1680"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1679"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1682"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1681"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1683"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CDGUNPD" fast="false" reversible="false" name="3,5-cyclic-nucleotide phosphodiesterase" metaid="R_CDGUNPD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CDGUNPD"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96524"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cdigmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_5pg35pg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2503"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1489"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3525"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1285"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0315"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACACT8r" fast="false" reversible="true" name="Acetyl-CoA acyltransferase (hexadecanoyl-CoA), (r)" metaid="R_ACACT8r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35280"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35279"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35281"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08767"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_3ohodcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pmtcoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3845"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35132"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35133"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35134"/>
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+          <speciesReference species="M_LalaLglu_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_LalaLglu_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1634"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3496"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4130"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0709"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CTECOAI7" fast="false" reversible="true" name="3-cis-2-trans-enoyl-CoA isomerase" metaid="R_CTECOAI7" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        <listOfProducts>
+          <speciesReference species="M_hdd2coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3846"/>
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+      <reaction id="R_CLIPAabctex" fast="false" reversible="false" name="Cold lipid A transport via ABC system (periplasm to extracellular)" metaid="R_CLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_cold_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipa_cold_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4262"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4261"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3199"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3200"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0054"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0641"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_3AMACHYD" fast="false" reversible="false" name="3-aminoacrylate hydrolase" metaid="R_3AMACHYD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <fbc:geneProductRef fbc:geneProduct="G_b4261"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3200"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0054"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0641"/>
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+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b1476"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1475"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_FDH5pp" fast="false" reversible="false" name="Formate Dehydrogenase (menaquinone-8) (periplasm)" metaid="R_FDH5pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <fbc:geneProductRef fbc:geneProduct="G_b3892"/>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1285"/>
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+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0009"/>
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+          <speciesReference species="M_ttdceap_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b3059"/>
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+          <speciesReference species="M_moadamp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_iscs_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_moadcosh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0462"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FUSAtpp" fast="false" reversible="false" name="Fusidic acid transport via TolC system" metaid="R_FUSAtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2470"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_APG3PAT181" fast="false" reversible="false" name="Acyl-phosphate:glycerol-3-phosphate acyltransferase (C18:1)" metaid="R_APG3PAT181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_ocdceap_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_1odec11eg3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3059"/>
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+      <reaction id="R_APH140" fast="false" reversible="false" name="Acylphosphatase (C14:0)" metaid="R_APH140" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_ttdcap_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdca_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0968"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_APH160" fast="false" reversible="false" name="Acylphosphatase (C16:0)" metaid="R_APH160" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdcap_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0968"/>
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+      <reaction id="R_OPMEACPD" fast="false" reversible="false" name="3-Oxo-pimeloyl-[ACP] methyl ester dehydratase" metaid="R_OPMEACPD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102206"/>
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+        <listOfProducts>
+          <speciesReference species="M_epmeACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0180"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_EPMEACPR" fast="false" reversible="false" name="Enoylpimeloyl-[ACP] methyl ester reductase" metaid="R_EPMEACPR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_pmeACP_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1288"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35232"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35233"/>
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+        <listOfProducts>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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+      <reaction id="R_MINCYCtex" fast="false" reversible="true" name="Minocycline transport via diffusion (extracellular to periplasm)" metaid="R_MINCYCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35169"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35170"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95855"/>
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+          <speciesReference species="M_pimACP_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_8aonn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0776"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_mincyc_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+          <speciesReference species="M_mincyc_e" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2470"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0463"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0462"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34874"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10570"/>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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+          <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufse_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufsesh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1679"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DOXRBCNtex" fast="false" reversible="true" name="Doxorubicin transport via diffusion (extracellular to periplasm)" metaid="R_DOXRBCNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0462"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2470"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufbcd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufsesh_c" stoichiometry="2" constant="true"/>
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+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="7" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufbcd_2fe2s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufse_c" stoichiometry="2" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1680"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1683"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1681"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1682"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1679"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_S4FE4SR" fast="false" reversible="false" name="SUF [4Fe-4S] Reduction" metaid="R_S4FE4SR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_sufbcd_2fe2s2_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_sufbcd_4fe4s_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1682"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1681"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1683"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_preq0_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0444"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34941"/>
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+          <speciesReference species="M_mqn8_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_slnt_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1590"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1587"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_egmeACP_c" stoichiometry="1" constant="true"/>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0180"/>
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1288"/>
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+      <reaction id="R_OPMEACPR" fast="false" reversible="false" name="3-Oxo-pimeloyl-[ACP] methyl ester reductase" metaid="R_OPMEACPR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <fbc:geneProductRef fbc:geneProduct="G_b3412"/>
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+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_etoh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_REPHACCOAI" fast="false" reversible="true" name="Ring 1,2-epoxyphenylacetyl-CoA isomerase (oxepin-CoA forming)" metaid="R_REPHACCOAI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        <listOfProducts>
+          <speciesReference species="M_2oxpaccoa_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1394"/>
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+      <reaction id="R_ACPPAT141" fast="false" reversible="false" name="Acyl-(acyl carrier protein):phosphate acyltransferase (C14:1)" metaid="R_ACPPAT141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tdeACP_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdceap_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1090"/>
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+        </fbc:geneProductAssociation>
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+        </sbml:annotation>
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+          <speciesReference species="M_hdeACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdceap_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1090"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_ocdcaACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcap_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1090"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_hdcap_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_1hdecg3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3059"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_APG3PAT161" fast="false" reversible="false" name="Acyl-phosphate:glycerol-3-phosphate acyltransferase (C16:1)" metaid="R_APG3PAT161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_hdceap_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_1hdec9eg3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3059"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_MEOHtex" fast="false" reversible="true" name="Methanol transport via diffusion (extracellular to periplasm)" metaid="R_MEOHtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34874"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10570"/>
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+        <listOfProducts>
+          <speciesReference species="M_meoh_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_5mtr_e" fast="false" reversible="false" name="5-Methylthio-D-ribose exchange" metaid="R_EX_5mtr_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95091"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34955"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34958"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34956"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34957"/>
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+          <speciesReference species="M_5mtr_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_ocdcap_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_1odecg3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3059"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ICYSDS" fast="false" reversible="false" name="ISC Cysteine desulfuration" metaid="R_ICYSDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100790"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iscs_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iscssh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2530"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MECDPDH5" fast="false" reversible="false" name="2C-methyl-D-erythritol 2,4 cyclodiphosphate dehydratase" metaid="R_MECDPDH5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101450"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_2mecdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_flxr_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h2mb4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2515"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2895"/>
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+            <fbc:and>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0684"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_nadph_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_preq0_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_preq1_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2794"/>
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+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
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+          <speciesReference species="M_datp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3924"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0684"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4237"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3924"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2895"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4237"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0684"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2895"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_RNTR2c2" fast="false" reversible="false" name="Ribonucleoside-triphosphate reductase (GTP) (flavodoxin)" metaid="R_RNTR2c2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+        </sbml:annotation>
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+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dgtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3924"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2895"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4237"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2895"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3924"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0684"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4237"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0684"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_I4FE4SR" fast="false" reversible="false" name="ISC [4Fe-4S] Reduction" metaid="R_I4FE4SR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100770"/>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_iscu_2fe2s2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iscu_4fe4s_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2529"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_S2FE2ST" fast="false" reversible="false" name="SUF [2Fe-2S] Transfer" metaid="R_S2FE2ST" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_S2FE2ST">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104152"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="4" constant="true"/>
+          <speciesReference species="M_sufbcd_2fe2s_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2fe2s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufbcd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1682"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1681"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1684"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1683"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BMOCOS" fast="false" reversible="false" name="Bis-molybdenum cofactor synthase" metaid="R_BMOCOS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_BMOCOS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BMOCOS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138144"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_moco_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mptamp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_bmoco_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cu2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0827"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BWCOS" fast="false" reversible="false" name="Tungsten bispterin cofactor synthase" metaid="R_BWCOS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_BWCOS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BWCOS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138151"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mptamp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_wco_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_bwco_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cu2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0827"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_RNTR3c2" fast="false" reversible="false" name="Ribonucleoside-triphosphate reductase (CTP) (flavodoxin)" metaid="R_RNTR3c2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_RNTR3c2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104078"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_flxr_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dctp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3924"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0684"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4237"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3924"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2895"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4237"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2895"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0684"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_RNTR4c2" fast="false" reversible="false" name="Ribonucleoside-triphosphate reductase (UTP) (flavodoxin)" metaid="R_RNTR4c2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_RNTR4c2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNTR4c2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104081"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_flxr_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dutp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3924"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0684"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4237"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3924"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2895"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4237"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0684"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2895"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b4238"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BWCOGDS1" fast="false" reversible="false" name="Tungsten bispterin guanine dinucleotide synthase (single GDP)" metaid="R_BWCOGDS1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_BWCOGDS1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BWCOGDS1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96356"/>
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+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_bwco_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_bwco1gdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3856"/>
+            </fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BWCOGDS2" fast="false" reversible="false" name="Tungsten bispterin guanine dinucleotide synthase" metaid="R_BWCOGDS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96357"/>
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+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_bwco1gdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_bwcogdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FLDR2" fast="false" reversible="false" name="Flavodoxin reductase (NADPH)" metaid="R_FLDR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99599"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_flxso_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_flxr_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3924"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2895"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0684"/>
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+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CDGS" fast="false" reversible="false" name="7-deaza-7-carboxyguanine synthase" metaid="R_CDGS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27974"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27977"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27975"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cph4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cdg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_5MTRtpp" fast="false" reversible="false" name="5-Methylthio-D-ribose transport via proton symport (periplasm)" metaid="R_5MTRtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95090"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05481"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_5mtr_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_TTRCYCtex" fast="false" reversible="true" name="Tetracycline transport via diffusion (extracellular to periplasm)" metaid="R_TTRCYCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104976"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35240"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35241"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35239"/>
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+        <listOfProducts>
+          <speciesReference species="M_ttrcyc_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHNPTE" fast="false" reversible="true" name="Dihydroneopterin epimerase" metaid="R_DHNPTE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138236"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dhnpt_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhmpt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3058"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHMPTR" fast="false" reversible="false" name="Dihydromonapterin reductase" metaid="R_DHMPTR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97405"/>
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+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dhmpt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thmnp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1606"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NOVBCNtpp" fast="false" reversible="false" name="Novobiocin transport via TolC system" metaid="R_NOVBCNtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NOVBCNtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NOVBCNtpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102009"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_novbcn_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_novbcn_e" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0463"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2470"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0463"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0462"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CMtex" fast="false" reversible="true" name="Chloramphenicol transport via diffusion (extracellular to periplasm)" metaid="R_CMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96808"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35290"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35287"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35289"/>
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+        <listOfProducts>
+          <speciesReference species="M_cm_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TTRCYCtpp" fast="false" reversible="false" name="Tetracycline transport via TolC system" metaid="R_TTRCYCtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttrcyc_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttrcyc_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0463"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2470"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b0463"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0462"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LALALGLUtex" fast="false" reversible="true" name="L-alanyl-L-glutamate transport via diffusion (extracellular to periplasm)" metaid="R_LALALGLUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101005"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35137"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35138"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35135"/>
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+          <speciesReference species="M_LalaLglu_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_LalaLglu_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96481"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15649"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/15650"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05064"/>
+                </rdf:Bag>
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+          </rdf:RDF>
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+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LALADGLUtpp" fast="false" reversible="false" name="L-alanyl-D-glutamate transport in via proton symport (periplasm)" metaid="R_LALADGLUtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101004"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35126"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35125"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35124"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_LalaDglu_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0709"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1634"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3496"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4130"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_I2FE2SS" fast="false" reversible="false" name="ISC [2Fe-2S] Synthesis" metaid="R_I2FE2SS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_iscssh_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_iscu_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="6" constant="true"/>
+          <speciesReference species="M_iscs_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_iscu_2fe2s_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2529"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_I2FE2ST" fast="false" reversible="false" name="ISC [2Fe-2S] Transfer" metaid="R_I2FE2ST" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_iscu_2fe2s_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
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+          <speciesReference species="M_2fe2s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iscu_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2528"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FESR" fast="false" reversible="false" name="Iron-sulfur cluster repair" metaid="R_FESR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_3fe4s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_4fe4s_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4209"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_OXCOAHDH" fast="false" reversible="false" name="Oxepin-CoA hydrolase/ 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (NADP+)" metaid="R_OXCOAHDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34875"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34876"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34877"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34878"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3oxdhscoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1387"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHACOAH" fast="false" reversible="true" name="2,3-dehydroadipyl-CoA hydratase" metaid="R_DHACOAH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.2.1.17"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97357"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34866"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34863"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34865"/>
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+          <speciesReference species="M_23dhacoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3hadpcoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1393"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_I2FE2SS2" fast="false" reversible="false" name="ISC [2Fe-2S] Synthesis II" metaid="R_I2FE2SS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100768"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_iscssh_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_iscu_2fe2s_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="6" constant="true"/>
+          <speciesReference species="M_iscs_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_iscu_2fe2s2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2530"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2529"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MSAR" fast="false" reversible="false" name="Malonic semialdehyde reductase" metaid="R_MSAR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MSAR"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-8974"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09289"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101737"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/26439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/26438"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/26441"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/26440"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/12224"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_msa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3hpp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1008"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1539"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_I4FE4ST" fast="false" reversible="false" name="ISC [4Fe-4S] Transfer" metaid="R_I4FE4ST" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/I4FE4ST"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100771"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="4" constant="true"/>
+          <speciesReference species="M_iscu_4fe4s_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_4fe4s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iscu_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2529"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2528"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_S4FE4ST" fast="false" reversible="false" name="SUF [4Fe-4S] Transfer" metaid="R_S4FE4ST" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_S4FE4ST">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/S4FE4ST"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104172"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="4" constant="true"/>
+          <speciesReference species="M_sufbcd_4fe4s_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4fe4s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufbcd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1682"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1681"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1684"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1683"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_THFAT" fast="false" reversible="false" name="Tetrahydrofolate aminomethyltransferase" metaid="R_THFAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_THFAT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THFAT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.1.2.10"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02300"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34770"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34769"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34767"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2262"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01652"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_5fthf_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2551"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FOMETRi" fast="false" reversible="false" name="Aminomethyltransferase" metaid="R_FOMETRi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FOMETRi">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99614"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34770"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34767"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2262"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01652"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_5fthf_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2912"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SLNTtex" fast="false" reversible="true" name="Selenite transport via diffusion (extracellular to periplasm)" metaid="R_SLNTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_SLNTtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SLNTtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104325"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34894"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34891"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34893"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34892"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_slnt_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_slnt_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_S2FE2SS2" fast="false" reversible="false" name="SUF [2Fe-2S] Synthesis II" metaid="R_S2FE2SS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_S2FE2SS2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/S2FE2SS2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104151"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufbcd_2fe2s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufsesh_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="7" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufbcd_2fe2s2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sufse_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1680"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1683"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1681"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1682"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1679"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BTS5" fast="false" reversible="false" name="Biotin synthase" metaid="R_BTS5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_BTS5">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BTS5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96344"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dtbt_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2fe1s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_btn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dad_5_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0775"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SELGTHR2" fast="false" reversible="false" name="Selenate glutathione reductase II" metaid="R_SELGTHR2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gslnt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_EX_LalaLglu_e" fast="false" reversible="false" name="L-alanine-L-glutamate exchange" metaid="R_EX_LalaLglu_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35137"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35138"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35135"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33057"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33056"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/33055"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3650"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LIPOS" fast="false" reversible="false" name="Lipoate synthase" metaid="R_LIPOS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101090"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_4fe4s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_amet_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_octapb_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2fe2s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dad_5_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_lipopb_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0628"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_COLIPAKpp" fast="false" reversible="false" name="Lipid A core kinase (periplasm)" metaid="R_COLIPAKpp" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96842"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_colipa_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpdp_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_colipap_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udcpp_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2174"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_ACPPAT120" fast="false" reversible="false" name="Acyl-(acyl carrier protein):phosphate acyltransferase (C12:0)" metaid="R_ACPPAT120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95395"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_ddcaACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ddcap_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1094"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1090"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_3HPPtpp" fast="false" reversible="false" name="3-hydroxypropionate transport via proton symport (periplasm)" metaid="R_3HPPtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_3HPPtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94905"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3hpp_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+      <reaction id="R_MPTSS" fast="false" reversible="false" name="Molybdopterin synthase sulfurylase" metaid="R_MPTSS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101736"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_moadcoo_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_moadamp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0826"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CPMPS" fast="false" reversible="false" name="Cyclic pyranopterin monophosphate synthase" metaid="R_CPMPS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.99.18"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cpmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0783"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0781"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LIPOCT" fast="false" reversible="false" name="Lipoyl(octanoyl) transferase" metaid="R_LIPOCT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocACP_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_octapb_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0630"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LIPATPT" fast="false" reversible="false" name="Lipoate-ATP adenylate transferase" metaid="R_LIPATPT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07770"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12916"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/12913"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn07584"/>
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+          <speciesReference species="M_lipoate_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_lipoamp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4386"/>
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+      <reaction id="R_LIPAMPL" fast="false" reversible="false" name="Lipoyl-adenylate protein ligase" metaid="R_LIPAMPL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lipopb_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4386"/>
+        </fbc:geneProductAssociation>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/2456"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01840"/>
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+          <speciesReference species="M_pacald_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pac_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1385"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MMM" fast="false" reversible="false" name="Methylmalonyl-CoA mutase" metaid="R_MMM" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2917"/>
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+      <reaction id="R_MOGDS" fast="false" reversible="false" name="Molybdopterin guanine dinucleotide synthase" metaid="R_MOGDS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_moco_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_mocogdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_CPH4S" fast="false" reversible="false" name="6-carboxy-5,6,7,8-tetrahydropterin synthase" metaid="R_CPH4S" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/27968"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_acald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cph4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2765"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_WCOS" fast="false" reversible="false" name="Tungsten pterin cofactor synthase" metaid="R_WCOS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_mptamp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tungs_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cu2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_wco_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0827"/>
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+      <reaction id="R_RFAMPtpp" fast="false" reversible="false" name="Rifampin transport via TolC system" metaid="R_RFAMPtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104015"/>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rfamp_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rfamp_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0463"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0462"/>
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+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b0463"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3035"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2470"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SHCHCS3" fast="false" reversible="false" name="2-succinyl-6-hydroxy-2,4-cyclohexadiene 1-carboxylate synthase" metaid="R_SHCHCS3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25600"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25599"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/25597"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11703"/>
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+          <speciesReference species="M_2sephchc_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2shchc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2263"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.6.1.66"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22912"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/22913"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00904"/>
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+          <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3572"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACOLIPAabctex" fast="false" reversible="false" name="Arabinose modified core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" metaid="R_ACOLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acolipa_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4261"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3199"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3201"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3200"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0054"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0641"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PYK4" fast="false" reversible="false" name="Pyruvate kinase(4)" metaid="R_PYK4" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00411"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1854"/>
+        </fbc:geneProductAssociation>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_nadphx__S_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4167"/>
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+        <listOfProducts>
+          <speciesReference species="M_nadhx__R_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1779"/>
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+      <reaction id="R_ECA4COLIPAabctex" fast="false" reversible="false" name="Enterobacterial common antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" metaid="R_ECA4COLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_eca4colipa_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4261"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3199"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3201"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3200"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0054"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0641"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_ttrcyc_e" fast="false" reversible="false" name="Tetracycline exchange" metaid="R_EX_ttrcyc_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_ttrcyc_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_ttrcyc_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104976"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35242"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35240"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35241"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35239"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ttrcyc_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_COLIPAPabctex" fast="false" reversible="false" name="Core oligosaccharide lipid A diphosphate transport via ABC system (periplasm to extracellular)" metaid="R_COLIPAPabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_COLIPAPabctex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/COLIPAPabctex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96843"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_colipap_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_colipap_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4262"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4261"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3199"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3201"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3200"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0054"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0641"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NADPHXE" fast="false" reversible="true" name="NADPHX epimerase" metaid="R_NADPHXE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_NADPHXE">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADPHXE"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_nadphx__R_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadphx__S_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4167"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ALAtpp" fast="false" reversible="false" name="L-alanine export via facilited diffusion" metaid="R_ALAtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ALAtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ALAtpp"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ala__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2670"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CH4tex" fast="false" reversible="true" name="Methane Transport(extracellular via diffusion)" metaid="R_CH4tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CH4tex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CH4tex"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ch4_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ch4_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_EX_mincyc_e" fast="false" reversible="false" name="Minocycline exchange" metaid="R_EX_mincyc_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_mincyc_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mincyc_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101582"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35168"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35167"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35169"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35170"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mincyc_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_TARTRDtex" fast="false" reversible="true" name="D-tartrate transport via diffusion (extracellular to periplasm)" metaid="R_TARTRDtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_TARTRDtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/TARTRDtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104722"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35199"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35200"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35202"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35201"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_tartr__D_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_tartr__D_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DM_4crsol_c" fast="false" reversible="false" name="Sink needed to allow p-Cresol to leave system" metaid="R_DM_4crsol_c" sboTerm="SBO:0000628" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DM_4crsol_c">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DM_4crsol_c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-500"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96888"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35071"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35072"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35074"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35073"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_4crsol_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_3OXCOAT" fast="false" reversible="false" name="3-oxoadipyl-CoA thiolase" metaid="R_3OXCOAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_3OXCOAT">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3OXCOAT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-3641"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.16"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.174"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00829"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94967"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19482"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19483"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19481"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/19484"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1170"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00598"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oxadpcoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1397"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BTNt2ipp" fast="false" reversible="false" name="Biotin transport via proton symport (periplasm)" metaid="R_BTNt2ipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_BTNt2ipp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BTNt2ipp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96334"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09693"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_btn_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_btn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_URACPAH" fast="false" reversible="false" name="Peroxyureidoacrylate hydrolase" metaid="R_URACPAH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_URACPAH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URACPAH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-6460"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/3.5.1.110"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R09947"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105143"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31592"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31594"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31593"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/31591"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uracp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cbm_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_poaac_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1011"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BTNtex" fast="false" reversible="true" name="Biotin transport via diffusion (extracellular to periplasm)" metaid="R_BTNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_BTNtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BTNtex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-240"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28459"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28461"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28460"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28458"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_btn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_btn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHBSZ3FEabcpp" fast="false" reversible="false" name="23dhbsz3 Fe III transport via ABC system periplasm" metaid="R_DHBSZ3FEabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DHBSZ3FEabcpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHBSZ3FEabcpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97371"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe3dhbzs3_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fe3dhbzs3_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0588"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0589"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0590"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0592"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FE3DHBZS3R" fast="false" reversible="false" name="Fe(III)-(2,3-dihydroxybenzoylserine)3 reductase via NADPH" metaid="R_FE3DHBZS3R" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_23dhbzs3_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3070"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DXYLONtpp" fast="false" reversible="true" name="D-xylonate reversible tranposrt (periplasm)" metaid="R_DXYLONtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        <listOfProducts>
+          <speciesReference species="M_dxylnt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+      <reaction id="R_DXYLTD" fast="false" reversible="true" name="D-xylonate dehydratase" metaid="R_DXYLTD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+          <speciesReference species="M_2ddara_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0269"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4297"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_2DDARAA" fast="false" reversible="true" name="2-dehydro-3-deoxy-D-arabinonate Aldolase" metaid="R_2DDARAA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfProducts>
+          <speciesReference species="M_gcald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0268"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_2DGLCptspp" fast="false" reversible="false" name="2-Deoxy-D-glucose transport via PEP:Pyr PTS (periplasm)" metaid="R_2DGLCptspp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2doxg6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1817"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1819"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1818"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_2DGULRGx" fast="false" reversible="false" name="2-Dehydro-L-gulonate reductase to gluconate (NADH)" metaid="R_2DGULRGx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_2dhguln_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3553"/>
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+      <reaction id="R_2DGULRGy" fast="false" reversible="false" name="2-Dehydro-L-gulonate reductase to gluconate (NADPH)" metaid="R_2DGULRGy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_2dhguln_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3553"/>
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+      </reaction>
+      <reaction id="R_AP4AS" fast="false" reversible="false" name="Ap4A synthetase" metaid="R_AP4AS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5208"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34935"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34938"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34937"/>
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+          <speciesReference species="M_atp_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ap4a_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4129"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34943"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05501"/>
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+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_arbt6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b3722"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2715"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
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+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ARBTtex" fast="false" reversible="false" name="Arbutin transport via diffusion (extracellular to periplasm)" metaid="R_ARBTtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95933"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35023"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35026"/>
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+          <speciesReference species="M_arbt_e" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_arbt_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_arbt_e" fast="false" reversible="false" name="Arbutin exchange" metaid="R_EX_arbt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35023"/>
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+          <speciesReference species="M_arbt_e" stoichiometry="1" constant="true"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_6pgc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3715"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2690"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_ALLTAMH2" fast="false" reversible="false" name="Allantoate amidinohydrolase" metaid="R_ALLTAMH2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_alltt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_urdgci_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0516"/>
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+      </reaction>
+      <reaction id="R_UGCIAMH" fast="false" reversible="false" name="Ureidoglycine aminohydrolase" metaid="R_UGCIAMH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_urdgci_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_urdglyc_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0515"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DMSOtpp" fast="false" reversible="true" name="Dimethyl sulfoxide transport via diffusion (periplasm)" metaid="R_DMSOtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29701"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29699"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08358"/>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dmso_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_POAACR" fast="false" reversible="false" name="Peroxyaminoacrylate reductase" metaid="R_POAACR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_poaac_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3amac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1010"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PYDXtex" fast="false" reversible="true" name="Pyridoxal transport via diffusion (extracellular)" metaid="R_PYDXtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28465"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28463"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28464"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12666"/>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pydx_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pydx_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PYDXtpp" fast="false" reversible="false" name="Pyridoxal import" metaid="R_PYDXtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28463"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28464"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12666"/>
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+        </sbml:annotation>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pydx_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+      <reaction id="R_SUCASPtpp" fast="false" reversible="true" name="Succinate:aspartate antiporter (periplasm)" metaid="R_SUCASPtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-106A"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104611"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29343"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29345"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29344"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29346"/>
+                </rdf:Bag>
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+          <speciesReference species="M_asp__L_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4138"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4123"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0621"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_METGLCUR" fast="false" reversible="false" name="1-O-Methyl-Beta-D-glucuronidase" metaid="R_METGLCUR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
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+          <speciesReference species="M_metglcur_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glcur_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_meoh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1617"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACOAD1fr" fast="false" reversible="false" name="Acyl-CoA dehydrogenase (butanoyl-CoA)" metaid="R_ACOAD1fr" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_b2coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1695"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_23DOGULNt4pp" fast="false" reversible="false" name="Na+/ 2,3-Dioxo-L-gulonate symport (periplasm)" metaid="R_23DOGULNt4pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_23doguln_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_na1_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_23doguln_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_na1_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3579"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3578"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FE3DCITexs" fast="false" reversible="false" name="Dicitrate Fe(III) binding (spontaneous)" metaid="R_FE3DCITexs" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_FE3DCITexs">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cit_e" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe3_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fe3dcit_e" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SUCMALtpp" fast="false" reversible="true" name="Succinate:malate antiporter (periplasm)" metaid="R_SUCMALtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-106B"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97456"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29327"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29328"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29330"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09767"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_mal__L_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b4138"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4123"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0621"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PYDXNtex" fast="false" reversible="true" name="Pyridoxine transport via diffusion (extracellular)" metaid="R_PYDXNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-205"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103364"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28470"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28473"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28471"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13097"/>
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+          <speciesReference species="M_pydxn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pydxn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FEENTERES" fast="false" reversible="false" name="Enterochelin Esterase (Fe containing)" metaid="R_FEENTERES" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_FEENTERES">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fe3dhbzs3_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0585"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PYDXNtpp" fast="false" reversible="false" name="Pyridoxine import" metaid="R_PYDXNtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103364"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28470"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28473"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28471"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13097"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pydxn_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pydxn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
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+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
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+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <speciesReference species="M_palmACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_hdcap_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1090"/>
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+      <reaction id="R_PYDAMtex" fast="false" reversible="true" name="Pyridoxamine transport via diffusion (extracellular)" metaid="R_PYDAMtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+        <listOfProducts>
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+      <reaction id="R_PSURItex" fast="false" reversible="true" name="Pseudouridine transport via diffusion (extracellular to periplasm)" metaid="R_PSURItex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        <listOfProducts>
+          <speciesReference species="M_psuri_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_ALR2x" fast="false" reversible="false" name="Aldose reductase (methylglyoxal) (nadh)" metaid="R_ALR2x" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1771"/>
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+      <reaction id="R_OMPHHXy" fast="false" reversible="false" name="2-octaprenyl-6-methoxyphenol hydroxylase (NADPH)" metaid="R_OMPHHXy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0543"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_tartr__D_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_tartr__D_c" stoichiometry="1" constant="true"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/14104"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12049"/>
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+          <speciesReference species="M_ametam_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_na15dap_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_chtbs6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1738"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1737"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b1736"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLYBt3pp" fast="false" reversible="false" name="Glycine betaine transport via proton antiport (periplasm)" metaid="R_GLYBt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
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+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0543"/>
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+      <reaction id="R_AI2tpp" fast="false" reversible="false" name="Quorum signal AI-2 exporter" metaid="R_AI2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_mththf_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_mththf_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1601"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACPPAT181" fast="false" reversible="false" name="Acyl-(acyl carrier protein):phosphate acyltransferase (C18:1)" metaid="R_ACPPAT181" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_octeACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdceap_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1094"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1090"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_Ftpp" fast="false" reversible="false" name="F- efflux transport" metaid="R_Ftpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_f_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_f_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0624"/>
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+      </reaction>
+      <reaction id="R_SQVOSI" fast="false" reversible="false" name="Sulfoquinovose isomerase" metaid="R_SQVOSI" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfProducts>
+          <speciesReference species="M_sf_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3880"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_6D6SPA" fast="false" reversible="false" name="6-deoxy-6-sulfofructose-1-phosphate aldolase" metaid="R_6D6SPA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfProducts>
+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sla_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3881"/>
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+      </reaction>
+      <reaction id="R_CHTBStex" fast="false" reversible="true" name="Chitobiose transport via diffusion (extracellular to periplasm)" metaid="R_CHTBStex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfProducts>
+          <speciesReference species="M_chtbs_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0681"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_TRPtipp" fast="false" reversible="false" name="L-tryptophan transport out (periplasm)" metaid="R_TRPtipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_trp__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1473"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_TYRtipp" fast="false" reversible="false" name="L-tyrosine transport out (periplasm)" metaid="R_TYRtipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_tyr__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1473"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ThDPAT" fast="false" reversible="false" name="ThDP adenylyl transferase" metaid="R_ThDPAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-5291"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35244"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35243"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35245"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thmpp_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_athtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23949"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1781"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn01201"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sucsal_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ghb_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3882"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHPStr" fast="false" reversible="false" name="2,3-dihydroxypropane 1-sulfonate transporter" metaid="R_DHPStr" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
+          <speciesReference species="M_dhps_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3877"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_SQtr" fast="false" reversible="false" name="Sulfoquinovose transporter" metaid="R_SQtr" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
+          <speciesReference species="M_sq_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3876"/>
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+        <listOfProducts>
+          <speciesReference species="M_dhps_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3875"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16518"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02667"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_aact_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_appl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3945"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SPMDt3pp" fast="false" reversible="false" name="Spermidine transport out via proton antiport (periplasm)" metaid="R_SPMDt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28738"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28736"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28735"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05652"/>
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+          <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_spmd_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1600"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1599"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FMNtex" fast="false" reversible="true" name="FMN transport, outer membrane" metaid="R_FMNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fmn_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_fmn_e" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:or>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_APH141" fast="false" reversible="false" name="Acylphosphatase (C14:1)" metaid="R_APH141" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
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+          <speciesReference species="M_ttdceap_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ttdcea_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0968"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_dxylnt_e" fast="false" reversible="false" name="D-Xylonate exchange" metaid="R_EX_dxylnt_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dxylnt_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_AI2K" fast="false" reversible="false" name="Autoinducer-2 kinase" metaid="R_AI2K" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dhptd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dhptdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1511"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PHEtipp" fast="false" reversible="false" name="L-phenylalanine transport out (periplasm)" metaid="R_PHEtipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_phe__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1473"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_G2PP" fast="false" reversible="false" name="Glycerol-2-phosphate phosphatase" metaid="R_G2PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01043"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99852"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13106"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13108"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13107"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/13105"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1325"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00766"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2533"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MALt3pp" fast="false" reversible="false" name="L-malate transport out via proton antiport (periplasm)" metaid="R_MALt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mal__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CITt3pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CITt3pp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96747"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cit_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_APH161" fast="false" reversible="false" name="Acylphosphatase (C16:1)" metaid="R_APH161" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_APH161">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/APH161"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95880"/>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_hdceap_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_hdcea_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0968"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHNPA2r" fast="false" reversible="true" name="Dihydroneopterin aldolase reversible" metaid="R_DHNPA2r" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHNPA2r"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:H2NEOPTERINALDOL-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.25"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R03504"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR125603"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10541"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10540"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10542"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10543"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/3293"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn02504"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_dhnpt_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_6hmhpt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gcald_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3058"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_QUIN2tpp" fast="false" reversible="true" name="Quinate transport (periplasm)" metaid="R_QUIN2tpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_QUIN2tpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103397"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35195"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35196"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35198"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn12452"/>
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+            </rdf:Description>
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+          <speciesReference species="M_quin_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_quin_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_GLYC2Pabcpp" fast="false" reversible="false" name="Sn-Glycerol 2-phosphate transport via ABC system (periplasm)" metaid="R_GLYC2Pabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100318"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34761#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34759#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34760#1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34762#1"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glyc2p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3450"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3453"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3451"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3452"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35068"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35070"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SHGO" fast="false" reversible="false" name="S-2-hydroxyglutarate oxidase" metaid="R_SHGO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
+          <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2660"/>
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+      <reaction id="R_CLBtex" fast="false" reversible="true" name="Cellobiose transport transport via diffusion extracellular to periplasm " metaid="R_CLBtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        <listOfProducts>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACOXT" fast="false" reversible="true" name="Acetyl-CoA:oxalate CoA-transferase" metaid="R_ACOXT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        </sbml:annotation>
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+          <speciesReference species="M_oxa_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oxalcoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2371"/>
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+      <reaction id="R_EX_mththf_e" fast="false" reversible="false" name="(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran exchange" metaid="R_EX_mththf_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mththf_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_2HESR" fast="false" reversible="false" name="2-hydroxyethyldisulfide reductase" metaid="R_2HESR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
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+          <speciesReference species="M_dtgcl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gthrd_c" stoichiometry="2" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mercpeth_c" stoichiometry="2" constant="true"/>
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+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2989"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2302"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CHOLID" fast="false" reversible="false" name="7-?-hydroxysteroid dehydrogenase" metaid="R_CHOLID" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhcholn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1619"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CHOLATEtpp" fast="false" reversible="false" name="Cholate transport via proton antiport" metaid="R_CHOLATEtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_cholate_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cholate_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4337"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NADHXD" fast="false" reversible="false" name="NADHX dehydratase" metaid="R_NADHXD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+        </sbml:annotation>
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+          <speciesReference species="M_nadhx__S_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4167"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadphx__R_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1779"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_NADPHHS" fast="false" reversible="false" name="NADPH hydratase" metaid="R_NADPHHS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadphx__S_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1779"/>
+            <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_4ABZGLUH" fast="false" reversible="true" name="P-aminobenzoyl-glutamate hydrolase" metaid="R_4ABZGLUH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+          <speciesReference species="M_4abzglu_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_4abz_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1337"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1338"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_4ABZGLUtr" fast="false" reversible="true" name="P-aminobenzoyl glutamate:H+ symporter" metaid="R_4ABZGLUtr" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_4abzglu_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1336"/>
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+      </reaction>
+      <reaction id="R_NADHHS" fast="false" reversible="false" name="NADH hydratase" metaid="R_NADHHS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadhx__S_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1779"/>
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+        </fbc:geneProductAssociation>
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+      <reaction id="R_APH180" fast="false" reversible="false" name="Acylphosphatase (C18:0)" metaid="R_APH180" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95881"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ocdcap_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ocdca_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0968"/>
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+      </reaction>
+      <reaction id="R_NADHXE" fast="false" reversible="true" name="NADHX epimerase" metaid="R_NADHXE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_nadhx__S_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadhx__R_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4167"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SELabcpp" fast="false" reversible="false" name="Selenatenate transport via ABC system (periplasm)" metaid="R_SELabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sel_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sel_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2423"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2422"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2425"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2424"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2423"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2422"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3917"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2424"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PHDA" fast="false" reversible="false" name="Phenylhydantoinase" metaid="R_PHDA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_5phua_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2873"/>
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+      <reaction id="R_TEO2M" fast="false" reversible="false" name="Tellurite methyltransferase" metaid="R_TEO2M" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_teo2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mteo2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1430"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PACOAT" fast="false" reversible="false" name="Phenylacetyl-CoA thioesterase" metaid="R_PACOAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        <listOfReactants>
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+          <speciesReference species="M_phaccoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pac_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1396"/>
+        </fbc:geneProductAssociation>
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+        <listOfReactants>
+          <speciesReference species="M_cysi__L_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_cysi__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3943"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_PYK2" fast="false" reversible="false" name="Pyruvate kinase(2)" metaid="R_PYK2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00659"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/53"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00460"/>
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+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1854"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30296"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30298"/>
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+          <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1854"/>
+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_ocdceap_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_ocdcea_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0968"/>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17866"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17865"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17868"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05088"/>
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+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thptdn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0578"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17871"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17869"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17870"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17872"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05087"/>
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+          <speciesReference species="M_h_c" stoichiometry="3" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_thptdn_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0578"/>
+        </fbc:geneProductAssociation>
+      </reaction>
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+          <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/>
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+          <speciesReference species="M_ichor_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2262"/>
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+          <speciesReference species="M_puacgam_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1022"/>
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+          <speciesReference species="M_ac_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mchtbs6p_c" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b1733"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2987"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FADtex" fast="false" reversible="true" name="FAD transport, outer membrane" metaid="R_FADtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+          <speciesReference species="M_fad_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_fad_e" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AI2abcpp" fast="false" reversible="false" name="Autoinducer-2 ABC transporter" metaid="R_AI2abcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mththf_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mththf_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1516"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1513"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1515"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1514"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PAI2I" fast="false" reversible="false" name="Phospho-AI-2 isomerase" metaid="R_PAI2I" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        <listOfProducts>
+          <speciesReference species="M_dhptdd_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1518"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_4HBZt3pp" fast="false" reversible="false" name="4-hydroxybenzoate transport out via antiporter" metaid="R_4HBZt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_4hbz_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3241"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CURR" fast="false" reversible="false" name="NADPH-dependent curcumin reductase" metaid="R_CURR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_dhcur_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1449"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LKDRA" fast="false" reversible="true" name="2-keto-3-deoxy-L-rhamnonate aldolase" metaid="R_LKDRA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_lkdr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_lald__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2245"/>
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+      </reaction>
+      <reaction id="R_LEUt2rpp" fast="false" reversible="false" name="L-leucine reversible transport via proton symport (periplasm)" metaid="R_LEUt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05243"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08785"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11119"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13340"/>
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+          <speciesReference species="M_leu__L_p" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_leu__L_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0401"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_LCTStpp" fast="false" reversible="false" name="Lactose transport via proton symport (periplasm)" metaid="R_LCTStpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28868"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28870"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28867"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10169"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08781"/>
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+          <speciesReference species="M_lcts_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_lcts_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0343"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ILEt3pp" fast="false" reversible="false" name="L-isoleucine transport out via proton antiport (periplasm)" metaid="R_ILEt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ILEt3pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+          <speciesReference species="M_ile__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ile__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4141"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_METNA" fast="false" reversible="true" name="L-amino acid N-acyltransferase" metaid="R_METNA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_acmet_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1448"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_METt3pp" fast="false" reversible="false" name="L-methionine tranport out via proton antiport (periplasm)" metaid="R_METt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1798"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4141"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99585"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_4fe4s_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_3fe4s_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe3_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_GSNt3pp" fast="false" reversible="false" name="Guanosine transport out via proton antiport (periplasm)" metaid="R_GSNt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_gsn_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3662"/>
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+      <reaction id="R_CLtipp" fast="false" reversible="false" name="Chloride ion transport in via diffusion (periplasm)" metaid="R_CLtipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                <rdf:Bag>
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+        <listOfProducts>
+          <speciesReference species="M_cl_c" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1592"/>
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+      <reaction id="R_5DKGR" fast="false" reversible="true" name="5-keto-D-gluconate 5-reductase" metaid="R_5DKGR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        </sbml:annotation>
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+          <speciesReference species="M_glcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_5dglcn_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2842"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4266"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_XYHDL" fast="false" reversible="false" name="?-D-xyloside xylohydrolase" metaid="R_XYHDL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_XYHDL">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/XYHDL"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iprimv_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_xyl__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3656"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_2DGLCtex" fast="false" reversible="true" name="2-Deoxy-D-glucose transport via diffusion (extracellular)" metaid="R_2DGLCtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2dglc_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_2dglc_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_E4PP" fast="false" reversible="false" name="Erythrose-4-phosphate phosphatase" metaid="R_E4PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_erthrs_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0822"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2293"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2690"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3826"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1727"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PUACGAMS" fast="false" reversible="true" name="Poly-?-1,6-N-acetyl-D-glucosamine synthase" metaid="R_PUACGAMS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PUACGAMS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PUACGAMS"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_puacgam_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_uacgam_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1021"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1022"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PItpp" fast="false" reversible="false" name="Phosphate export via facillated diffusion (periplasm)" metaid="R_PItpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PItpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PItpp"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4020"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_RU5PP" fast="false" reversible="false" name="Ribulose-5-Phosphate Phosphatase" metaid="R_RU5PP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_RU5PP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RU5PP"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ru5p__D_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rbl__D_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2293"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_doxrbcn_e" fast="false" reversible="false" name="Doxorubicin exchange" metaid="R_EX_doxrbcn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_doxrbcn_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_doxrbcn_e"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97760"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35079"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35081"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35080"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35082"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_doxrbcn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_6D6SFK" fast="false" reversible="false" name="6-deoxy-6-sulfofructose kinase" metaid="R_6D6SFK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_6D6SFK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/6D6SFK"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sf_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sfp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3883"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_3SLAR" fast="false" reversible="false" name="3-sulfolactaldehyde reductase" metaid="R_3SLAR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_3SLAR">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/3SLAR"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sla_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_dhps_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3882"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_LEUt3pp" fast="false" reversible="false" name="L-leucine transport out via proton antiport (periplasm)" metaid="R_LEUt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_LEUt3pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/LEUt3pp"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_leu__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_leu__L_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1798"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4141"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_INSt3pp" fast="false" reversible="false" name="Inosine transport out via proton antiport (perisplasm)" metaid="R_INSt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_INSt3pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INSt3pp"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ins_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ins_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3662"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_INDOLEt2rpp" fast="false" reversible="false" name="Indole transport via proton symport, reversible (periplasm)" metaid="R_INDOLEt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_INDOLEt2rpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INDOLEt2rpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN-142"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100835"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29228"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29227"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29230"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/29229"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08750"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn10176"/>
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+              </bqbiol:is>
+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_indole_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_indole_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3161"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SQtex" fast="false" reversible="true" name="Sulphoquinovose transport via diffusion" metaid="R_SQtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+            <rdf:Description rdf:about="#R_SQtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SQtex"/>
+                </rdf:Bag>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_sq_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_sq_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3875"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ILEt2rpp" fast="false" reversible="false" name="L-isoleucine reversible transport via proton symport (periplasm)" metaid="R_ILEt2rpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ILEt2rpp"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100822"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13322"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05244"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08746"/>
+                </rdf:Bag>
+              </bqbiol:is>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ile__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ile__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0401"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GLYtpp" fast="false" reversible="true" name="Glycine transport via facillitated diffusion" metaid="R_GLYtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+            <rdf:Description rdf:about="#R_GLYtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/GLYtpp"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gly_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3927"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_dhps_e" fast="false" reversible="false" name="2,3-Dihydroxypropane-1-sulfonate exchange" metaid="R_EX_dhps_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+      <reaction id="R_MOX" fast="false" reversible="false" name="Malate oxidase" metaid="R_MOX" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10512"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10515"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/10514"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00264"/>
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+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_URATEtex" fast="false" reversible="true" name="Uric acid transport" metaid="R_URATEtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+          <speciesReference species="M_urate_e" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_urate_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_cs1_e" fast="false" reversible="false" name="Cesium ion exchange" metaid="R_EX_cs1_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cs1_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_fusa_e" fast="false" reversible="false" name="Fusidic acid exchange" metaid="R_EX_fusa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_EX_fusa_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99717"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35105"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35104"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35103"/>
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+          <speciesReference species="M_fusa_e" stoichiometry="1" constant="true"/>
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+      </reaction>
+      <reaction id="R_CBL1tonex" fast="false" reversible="false" name="Cob(1)alamin transport via ton system (extermal)" metaid="R_CBL1tonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CBL1tonex">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96472"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_cbl1_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cbl1_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1252"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3005"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3006"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b3966"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CBItonex" fast="false" reversible="false" name="Cobinamide transport via ton system (extermal)" metaid="R_CBItonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CBItonex">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96468"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_cbi_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_cbi_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b1252"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3005"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3006"/>
+            </fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3966"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ARHGDx" fast="false" reversible="true" name="(R)-alpha-hydroxyglutarate dehydrogenase" metaid="R_ARHGDx" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_r2hglut_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2913"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CPL" fast="false" reversible="false" name="Carbon-phosphorous lyase" metaid="R_CPL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_CPL">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CPL"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_prpmn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ch4_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_prcp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4098"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_EX_mepn_e" fast="false" reversible="false" name="Methylphosphonic acid exchange" metaid="R_EX_mepn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_EX_mepn_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_mepn_e"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mepn_e" stoichiometry="1" constant="true"/>
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+      <reaction id="R_PSURItpp" fast="false" reversible="false" name="Pseudouridine transport via permease" metaid="R_PSURItpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+        <listOfReactants>
+          <speciesReference species="M_psuri_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_psuri_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2164"/>
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+      <reaction id="R_CYSTA" fast="false" reversible="false" name="Cysteine transaminase" metaid="R_CYSTA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17442"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/17443"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00647"/>
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+          <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mercppyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0928"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FE3DCITR5" fast="false" reversible="false" name="Ferric-dicitrate reductase via nadph" metaid="R_FE3DCITR5" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
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+          <speciesReference species="M_fe3dcit_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cit_c" stoichiometry="4" constant="true"/>
+          <speciesReference species="M_fe2_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3070"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_CH4t2pp" fast="false" reversible="false" name="Methane Transport(periplasm)" metaid="R_CH4t2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+        <listOfProducts>
+          <speciesReference species="M_ch4_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+      <reaction id="R_EX_cm_e" fast="false" reversible="false" name="Chloramphenicol exchange" metaid="R_EX_cm_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96808"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35288"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35290"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35287"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35289"/>
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+          <speciesReference species="M_cm_e" stoichiometry="1" constant="true"/>
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+      </reaction>
+      <reaction id="R_4HTHRA" fast="false" reversible="true" name="4-hydroxy-L-threonine aldolase" metaid="R_4HTHRA" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_4HTHRA">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/4HTHRA"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_4hthr_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_gcald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0870"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_novbcn_e" fast="false" reversible="false" name="Novobiocin exchange" metaid="R_EX_novbcn_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102008"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35178"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35176"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35175"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35177"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_novbcn_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_I2FE2SR" fast="false" reversible="false" name="ISC [2Fe-2S] regeneration" metaid="R_I2FE2SR" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100766"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_2fe1s_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iscssh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iscu_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="4" constant="true"/>
+          <speciesReference species="M_iscs_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iscu_2fe2s_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b2529"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2530"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_GAPP" fast="false" reversible="false" name="Glyceraldehyde-3-phosphate phosphatase" metaid="R_GAPP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_GAPP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyald_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1727"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_TYRL" fast="false" reversible="false" name="Tyrosine lyase" metaid="R_TYRL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_TYRL">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-11319"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.99.19"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104993"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/26361"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/26363"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/26362"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/26364"/>
+                </rdf:Bag>
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+            </rdf:Description>
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+        </sbml:annotation>
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+          <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4crsol_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dad_5_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dhgly_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3991"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_METGLCURt2pp" fast="false" reversible="false" name="1-O-methyl-Beta-D-glucuronate transport via proton symport (periplasm)" metaid="R_METGLCURt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_METGLCURt2pp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_metglcur_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_metglcur_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1616"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_METGLCURtex" fast="false" reversible="true" name="1-O-methyl-Beta-D-glucuronate via diffusion (extracellular)" metaid="R_METGLCURtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_METGLCURtex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_metglcur_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_metglcur_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_INOSTO" fast="false" reversible="true" name="Myo-Inositol:oxygen oxidoreductase" metaid="R_INOSTO" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/INOSTO"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MYO-INOSITOL-OXYGENASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.13.99.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01184"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100839"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23697"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23696"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23699"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/23698"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00880"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_inost_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glcur_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3488"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_THZPSN3" fast="false" reversible="false" name="Thiazole phosphate synthesis" metaid="R_THZPSN3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_THZPSN3">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/THZPSN3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104861"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dhgly_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dxyl5p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_iscssh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_4mpetz_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_iscs_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0423"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3990"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2530"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3992"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4407"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HPYRP" fast="false" reversible="false" name="3-phosphohydroxypyruvate phosphatase" metaid="R_HPYRP" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_HPYRP">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HPYRP"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3php_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_hpyr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1813"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PSURIK" fast="false" reversible="false" name="Pseudouridine kinase" metaid="R_PSURIK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PSURIK">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PSURIK"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_psuri_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_psd5p_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2166"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FMNt" fast="false" reversible="false" name="FMN transporter, periplasm" metaid="R_FMNt" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FMNt">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FMNt"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fmn_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fmn_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1985"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AI2tex" fast="false" reversible="true" name="Ai2 transport, outer membrane" metaid="R_AI2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_AI2tex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/AI2tex"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mththf_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_mththf_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_PAI2T" fast="false" reversible="false" name="3-hydroxy-2,4-pentadione 5-phosphate thiolase" metaid="R_PAI2T" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PAI2T">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PAI2T"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dhptdd_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1517"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CUt2pp" fast="false" reversible="false" name="Copper transport out via permease (no H+)" metaid="R_CUt2pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <fbc:geneProductRef fbc:geneProduct="G_b0808"/>
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_phpyr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nalme_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1103"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_4HTHRK" fast="false" reversible="false" name="4-Hydroxy-L-threonine kinase" metaid="R_4HTHRK" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28788"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28790"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28789"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/28787"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_4hthr_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_phthr_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0003"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ACOAD1f" fast="false" reversible="false" name="Acyl-CoA dehydrogenase (butanoyl-CoA)" metaid="R_ACOAD1f" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-77319"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24007"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30734"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24005"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/24004"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30731"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/30732"/>
+                  <rdf:li rdf:resource="http://identifiers.org/sabiork/1412"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00872"/>
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+          <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_b2coa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0221"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_AMPNTAT" fast="false" reversible="false" name="Aminoalkylphosphonate N-acetyltransferase" metaid="R_AMPNTAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ampnt_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acampnt_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4093"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_sq_e" fast="false" reversible="false" name="Sulphoquinovose exchange" metaid="R_EX_sq_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_EX_sq_e">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_sq_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_APH120" fast="false" reversible="false" name="Acylphosphatase (C12:0)" metaid="R_APH120" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95876"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_ddcap_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ddca_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0968"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_URATEtpp" fast="false" reversible="false" name="Uric acid transporter" metaid="R_URATEtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_URATEtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URATEtpp"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_urate_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_urate_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2888"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_CS1tex" fast="false" reversible="true" name="Cesium transport via diffusion" metaid="R_CS1tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_CS1tex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/CS1tex"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cs1_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_cs1_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ADOCBLtonex" fast="false" reversible="false" name="Adenosylcobalimin transport via ton system (extermal)" metaid="R_ADOCBLtonex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ADOCBLtonex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ADOCBLtonex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR95472"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08071"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_adocbl_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adocbl_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b1252"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3005"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3006"/>
+            </fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3966"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SQGH" fast="false" reversible="false" name="Sulfoquinovosidase" metaid="R_SQGH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_SQGH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SQGH"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sqg_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_glyc_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_sq_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b3878"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_URAtpp" fast="false" reversible="false" name="Uracil export via facillitated diffusion (periplasm)" metaid="R_URAtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/URAtpp"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_ura_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_ura_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction id="R_ASPtpp" fast="false" reversible="true" name="L-aspartate uptake via facillitated diffusion" metaid="R_ASPtpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_ASPtpp">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ASPtpp"/>
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+            </rdf:Description>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_asp__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1206"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FUMt1pp" fast="false" reversible="true" name="Fumarate transport via diffusion in (periplasm)" metaid="R_FUMt1pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_fum_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1206"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SUCCt1pp" fast="false" reversible="true" name="Succinate transport via diffusion in (periplasm)" metaid="R_SUCCt1pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/SUCCt1pp"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_succ_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_succ_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1206"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_QUINDH" fast="false" reversible="false" name="Quinate dehydrogenase" metaid="R_QUINDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+            <rdf:Description rdf:about="#R_QUINDH">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/QUINDH"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:QUINATE-5-DEHYDROGENASE-RXN"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.24"/>
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+          <speciesReference species="M_sheme_c" stoichiometry="0.000223" constant="true"/>
+          <speciesReference species="M_so4_c" stoichiometry="0.004126" constant="true"/>
+          <speciesReference species="M_spmd_c" stoichiometry="0.006744" constant="true"/>
+          <speciesReference species="M_succoa_c" stoichiometry="9.8e-05" constant="true"/>
+          <speciesReference species="M_thf_c" stoichiometry="0.000223" constant="true"/>
+          <speciesReference species="M_thmpp_c" stoichiometry="0.000223" constant="true"/>
+          <speciesReference species="M_thr__L_c" stoichiometry="0.246506" constant="true"/>
+          <speciesReference species="M_trp__L_c" stoichiometry="0.055234" constant="true"/>
+          <speciesReference species="M_tyr__L_c" stoichiometry="0.133993" constant="true"/>
+          <speciesReference species="M_udcpdp_c" stoichiometry="5.5e-05" constant="true"/>
+          <speciesReference species="M_utp_c" stoichiometry="0.140101" constant="true"/>
+          <speciesReference species="M_val__L_c" stoichiometry="0.411184" constant="true"/>
+          <speciesReference species="M_zn2_c" stoichiometry="0.000324" constant="true"/>
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+          <speciesReference species="M_ppi_c" stoichiometry="0.749831" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
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+          <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_udcpgl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2047"/>
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+          <speciesReference species="M_mepn_p" stoichiometry="1" constant="true"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4105"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4106"/>
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+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0662"/>
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+      <reaction id="R_OPHHXy" fast="false" reversible="false" name="2-Octaprenylphenol hydroxylase (NADPH)" metaid="R_OPHHXy" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
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+          <fbc:geneProductRef fbc:geneProduct="G_b2906"/>
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+          <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/>
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+          <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1014"/>
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+      </reaction>
+      <reaction id="R_NOVBCNtex" fast="false" reversible="true" name="Novobiocin transport via diffusion (extracellular to periplasm)" metaid="R_NOVBCNtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b0822"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3697"/>
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+        </fbc:geneProductAssociation>
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+          <speciesReference species="M_ribflv_p" stoichiometry="1" constant="true"/>
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+          <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
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+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_rfamp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_3HPADHi" fast="false" reversible="false" name="3-Hydroxypropanal Dehydrogenase" metaid="R_3HPADHi" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3hpp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1300"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_4ABZGLUtex" fast="false" reversible="true" name="P-aminobenzoyl glutamate transport via diffusion (extracellular to periplasm)" metaid="R_4ABZGLUtex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+        </sbml:annotation>
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+        <listOfProducts>
+          <speciesReference species="M_4abzglu_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_QUIN2tex" fast="false" reversible="true" name="Quinate transport via diffusion (extracellular to periplasm)" metaid="R_QUIN2tex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35196"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35198"/>
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+        <listOfProducts>
+          <speciesReference species="M_quin_p" stoichiometry="1" constant="true"/>
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+        <fbc:geneProductAssociation>
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+            <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_2HPTCOAT" fast="false" reversible="false" name="2-hydroxycyclohepta-1,4,6-triene-1-carboxyl-CoA thioesterase" metaid="R_2HPTCOAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_2hptcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_2hptcl_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1400"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_EX_metglcur_e" fast="false" reversible="false" name="1-O-methyl-Beta-D-glucuronate exchange" metaid="R_EX_metglcur_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_metglcur_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_EX_quin_e" fast="false" reversible="false" name="Quinate exchange" metaid="R_EX_quin_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35195"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35198"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_quin_e" stoichiometry="1" constant="true"/>
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+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mchtbs6p_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_acgam6p_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gam_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1734"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FORCT" fast="false" reversible="true" name="Formyl-CoA Transferase" metaid="R_FORCT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R07290"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16546"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16545"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/16548"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05044"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
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+          <speciesReference species="M_forcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oxa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oxalcoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b2374"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_SLNTabcpp" fast="false" reversible="false" name="Selenite ABC transporter (periplasm)" metaid="R_SLNTabcpp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_slnt_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_slnt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2423"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2422"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2425"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2424"/>
+            </fbc:and>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2423"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2422"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3917"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2424"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
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+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09707"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn11190"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09374"/>
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+        </sbml:annotation>
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+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_val__L_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0401"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DHPTDCs2" fast="false" reversible="false" name="4,5-dihydroxy-2,3-pentanedione cyclization (spontaneous)" metaid="R_DHPTDCs2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DHPTDCs2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-10015"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97442"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35158"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35155"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35156"/>
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+          <speciesReference species="M_dhptd_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_mdhdhf_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
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+      <reaction id="R_VALt3pp" fast="false" reversible="false" name="L-valine transport out via proton antiport (periplasm)" metaid="R_VALt3pp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+        </sbml:annotation>
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+          <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_val__L_p" stoichiometry="1" constant="true"/>
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+              <fbc:geneProductRef fbc:geneProduct="G_b2683"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b2682"/>
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+            <fbc:geneProductRef fbc:geneProduct="G_b4141"/>
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+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MN2tipp" fast="false" reversible="false" name="Manganese transport in via permease (no H+)" metaid="R_MN2tipp" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+          <speciesReference species="M_mn2_c" stoichiometry="1" constant="true"/>
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+        <listOfProducts>
+          <speciesReference species="M_mn2_p" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1821"/>
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+      </reaction>
+      <reaction id="R_EX_3hpp_e" fast="false" reversible="false" name="3-Hydroxypropanoate exchange" metaid="R_EX_3hpp_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR94904"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34951"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34953"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34952"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34954"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3hpp_e" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_PACCOAE" fast="false" reversible="false" name="Ring 1,2-phenylacetyl-CoA epoxidase (NADPH)" metaid="R_PACCOAE" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+            <rdf:Description rdf:about="#R_PACCOAE">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
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+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102314"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_phaccoa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_rephaccoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1391"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1388"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1392"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1389"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1390"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_OXDHCOAT" fast="false" reversible="false" name="3-oxo-5,6-dehydrosuberyl-CoA thiolase" metaid="R_OXDHCOAT" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OXDHCOAT"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.223"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102241"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34441"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34440"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34439"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34442"/>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3oxdhscoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_23dhacoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1397"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1394"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_HADPCOADH3" fast="false" reversible="true" name="3-hydroxyadipyl-CoA dehydrogenase (NAD+)" metaid="R_HADPCOADH3" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
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+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/HADPCOADH3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN0-2044"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.35"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.157"/>
+                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R06941"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR100555"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34851"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34852"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34853"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/34854"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn04750"/>
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+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_3hadpcoa_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_oxadpcoa_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b1395"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_O16A4COLIPAabctex" fast="false" reversible="false" name="O16 antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" metaid="R_O16A4COLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_O16A4COLIPAabctex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O16A4COLIPAabctex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102075"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o16a4colipa_p" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o16a4colipa_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4262"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4261"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3199"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3201"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3200"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0054"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0641"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_COLIPAabctex" fast="false" reversible="false" name="Core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" metaid="R_COLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_COLIPAabctex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/COLIPAabctex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96845"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_colipa_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_colipa_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0641"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3200"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4262"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3201"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3199"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0054"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4261"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_ENLIPAabctex" fast="false" reversible="false" name="Phosphoethanolamine lipid A transport via ABC system (periplasm to extracellular)" metaid="R_ENLIPAabctex" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_ENLIPAabctex">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ENLIPAabctex"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR97922"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_enlipa_p" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_enlipa_e" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b4262"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4261"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3199"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3201"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3200"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0054"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0641"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_DM_mththf_c" fast="false" reversible="false" name="Sink needed to allow (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran to leave system" metaid="R_DM_mththf_c" sboTerm="SBO:0000628" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_DM_mththf_c">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DM_mththf_c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-453"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR124017"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35148"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35147"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35149"/>
+                  <rdf:li rdf:resource="http://identifiers.org/rhea/35150"/>
+                </rdf:Bag>
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+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_mththf_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+      </reaction>
+      <reaction id="R_PYROX" fast="false" reversible="false" name="Pyrimidine oxygenase" metaid="R_PYROX" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_PYROX">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PYROX"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR103383"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ura_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_uracp_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b1007"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b1012"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BMOGDS1" fast="false" reversible="false" name="Bis-molybdopterin guanine dinucleotide synthase (single GDP)" metaid="R_BMOGDS1" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_BMOGDS1">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BMOGDS1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96315"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_bmoco_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_bmoco1gdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3856"/>
+            </fbc:and>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MPTS" fast="false" reversible="false" name="Molybdopterin synthase" metaid="R_MPTS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MPTS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MPTS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR143253"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_cpmp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cu2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_moadcosh_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_h_c" stoichiometry="5" constant="true"/>
+          <speciesReference species="M_moadcoo_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mpt_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b0785"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0784"/>
+          </fbc:and>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_MOCOS" fast="false" reversible="false" name="Molybdenum cofactor synthase" metaid="R_MOCOS" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_MOCOS">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/MOCOS"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR138626"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_mobd_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_mptamp_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_cu2_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_moco_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b0827"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_BMOGDS2" fast="false" reversible="false" name="Bis-molybdopterin guanine dinucleotide synthase" metaid="R_BMOGDS2" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_BMOGDS2">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/BMOGDS2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96316"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_bmoco1gdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_bmocogdp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:or>
+            <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b3856"/>
+            </fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
+          </fbc:or>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_FESD2s" fast="false" reversible="false" name="Iron-sulfur cluster damage (nitrous oxide, spontaneous)" metaid="R_FESD2s" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_FESD2s">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FESD2s"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99586"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_4fe4s_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_no_c" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_3fe4s_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_fe3_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_n2o_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+      <reaction id="R_OCTNLL" fast="false" reversible="false" name="Octanoate non-lipoylated apo domain ligase" metaid="R_OCTNLL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
+        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+            <rdf:Description rdf:about="#R_OCTNLL">
+              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OCTNLL"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102155"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </sbml:annotation>
+        <listOfReactants>
+          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_octa_c" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_octapb_c" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <fbc:geneProductAssociation>
+          <fbc:geneProductRef fbc:geneProduct="G_b4386"/>
+        </fbc:geneProductAssociation>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>

From aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Tue, 26 Sep 2023 22:47:25 +0200
Subject: [PATCH 54/61] feat(tools): get_sbml_model, load file from history
 (#143)

Co-authored-by: Guillaume Gricourt <guipagui@gmail.com>
---
 tools/get_sbml_model/.gitignore         | 1 +
 tools/get_sbml_model/get_sbml_model.xml | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/tools/get_sbml_model/.gitignore b/tools/get_sbml_model/.gitignore
index e7e13ad6..e4b65458 100644
--- a/tools/get_sbml_model/.gitignore
+++ b/tools/get_sbml_model/.gitignore
@@ -2,3 +2,4 @@
 package.json
 package-lock.json
 node_modules
+planemo/
\ No newline at end of file
diff --git a/tools/get_sbml_model/get_sbml_model.xml b/tools/get_sbml_model/get_sbml_model.xml
index 005c836f..917b4b0e 100644
--- a/tools/get_sbml_model/get_sbml_model.xml
+++ b/tools/get_sbml_model/get_sbml_model.xml
@@ -15,6 +15,8 @@
             echo "#ID" > '$taxid' &&
             cat tmpfile >> '$taxid' &&
         #end if
+        echo "listdir:";
+        ls;
         python '$__tool_directory__/'get_infos.py
             #if str($cond_src.from_src) == 'from_bigg'
                 '$model'

From e3d02271d8fc1d37db81db5d2acfdb27ad6a3b5a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 29 Sep 2023 11:04:01 +0200
Subject: [PATCH 55/61] chore(deps): bump tj-actions/changed-files from 37 to
 39 (#142)

Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 37 to 39.
- [Release notes](https://github.com/tj-actions/changed-files/releases)
- [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md)
- [Commits](https://github.com/tj-actions/changed-files/compare/v37...v39)

---
updated-dependencies:
- dependency-name: tj-actions/changed-files
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/pr.yml          | 2 +-
 .github/workflows/prworkflows.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index 12f2e450..48b9c3a9 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -24,7 +24,7 @@ jobs:
       - name: 'Select modified files'
         id: files
         #uses: Ana06/get-changed-files@v2.2.0
-        uses: tj-actions/changed-files@v37
+        uses: tj-actions/changed-files@v39
         with:
           files: tools/**
           separator: ","
diff --git a/.github/workflows/prworkflows.yml b/.github/workflows/prworkflows.yml
index 521ba3f1..23077e42 100644
--- a/.github/workflows/prworkflows.yml
+++ b/.github/workflows/prworkflows.yml
@@ -24,7 +24,7 @@ jobs:
       - name: 'Select modified files'
         id: files
         #uses: Ana06/get-changed-files@v2.2.0
-        uses: tj-actions/changed-files@v37
+        uses: tj-actions/changed-files@v39
         with:
           files: workflows/**
           separator: ","

From 513db7f056db275f3f5d8d1337d39ff66012d89f Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Fri, 29 Sep 2023 11:31:38 +0200
Subject: [PATCH 56/61] Updating dnabot from version 3.1.0 to 4.1.0 (#141)

* Updating dnabot from version 3.1.0 to 4.1.0

* fix(tools): dnabot, update test

* fix(tools): dnabot, syntax
---
 tools/dnabot/dnabot.xml | 19 ++++---------------
 1 file changed, 4 insertions(+), 15 deletions(-)

diff --git a/tools/dnabot/dnabot.xml b/tools/dnabot/dnabot.xml
index 6db18f80..13f9c96f 100644
--- a/tools/dnabot/dnabot.xml
+++ b/tools/dnabot/dnabot.xml
@@ -1,7 +1,7 @@
-<tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="21.09">
+<tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="21.09" license="MIT">
     <description>DNA assembly using BASIC on OpenTrons</description>
     <macros>
-        <token name="@TOOL_VERSION@">3.1.0</token>
+        <token name="@TOOL_VERSION@">4.1.0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">dnabot</requirement>
@@ -63,7 +63,7 @@
             <param name="plate_files" value="user_parts_coords.csv,linker_parts_coords.csv"/>
             <output name="dnabot_scripts" ftype="tar">
                 <assert_contents>
-                    <has_size value="153600" delta="10000"/>
+                    <has_size value="165900" delta="10000"/>
                 </assert_contents>
             </output>
         </test>
@@ -99,23 +99,12 @@ Ouput
 
 * **Dnabot scripts**: DNA-Bot scripts in TAR format which implement the 4 assembly steps and metainformation to keep track of parameters.
 
-Version
--------
-
-3.1.0
-
 Authors
 -------
 
 * **Matthew C Haines**
 * Thomas Duigou
 
-License
--------
-
-`MIT <https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/blob/master/LICENSE>`_
-
-
 Acknowledgments
 ---------------
 
@@ -125,4 +114,4 @@ Acknowledgments
     <citations>
         <citation type="doi">10.1093/synbio/ysaa010</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>

From 9fe4f29ddc7f4a81ffe82551f34a3dbb606715bc Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 3 Oct 2023 00:53:51 +0000
Subject: [PATCH 57/61] doc(changelog): update

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bfd21c90..be6b97ae 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.12](https://github.com/brsynth/galaxytools/tree/0.2.12) (2023-09-19)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.11...0.2.12)
+
 ## [0.2.11](https://github.com/brsynth/galaxytools/tree/0.2.11) (2023-09-12)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.10...0.2.11)

From 14f6dc27a280e891c139f3100c6281bcbff3a167 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Mon, 9 Oct 2023 16:09:06 +0200
Subject: [PATCH 58/61] feat(tools): add `neo4jsbml` (#144)

* feat(tools): add `neo4jsbml`

* docs(tools): update
---
 tools/neo4jsbml/.shed.yml                     |   8 +
 tools/neo4jsbml/neo4jsbml.xml                 |  76 +++++
 .../test-data/PathwayModelisation-2.0.3.json  | 265 ++++++++++++++++++
 tools/neo4jsbml/test-data/e_coli_core.xml.gz  | Bin 0 -> 39399 bytes
 4 files changed, 349 insertions(+)
 create mode 100644 tools/neo4jsbml/.shed.yml
 create mode 100644 tools/neo4jsbml/neo4jsbml.xml
 create mode 100644 tools/neo4jsbml/test-data/PathwayModelisation-2.0.3.json
 create mode 100644 tools/neo4jsbml/test-data/e_coli_core.xml.gz

diff --git a/tools/neo4jsbml/.shed.yml b/tools/neo4jsbml/.shed.yml
new file mode 100644
index 00000000..ac5309e8
--- /dev/null
+++ b/tools/neo4jsbml/.shed.yml
@@ -0,0 +1,8 @@
+categories:
+  - Systems Biology
+description: Import SBML file into Neo4j
+long_description: Import SBML file into Neo4j
+name: neo4jsbml
+owner: tduigou
+homepage_url: https://github.com/brsynth/neo4jsbml
+remote_repository_url: https://github.com/brsynth/neo4jsbml
diff --git a/tools/neo4jsbml/neo4jsbml.xml b/tools/neo4jsbml/neo4jsbml.xml
new file mode 100644
index 00000000..3d79942e
--- /dev/null
+++ b/tools/neo4jsbml/neo4jsbml.xml
@@ -0,0 +1,76 @@
+<tool id="neo4jsbml" name="neo4jsbml" version="@TOOL_VERSION@" profile="21.09" license="MIT">
+    <description>Import SBML file into Neo4j</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.12.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">neo4jsbml</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m neo4jsbml
+            --input-auradb-file '$input_auradb_file'
+            --input-file-sbml '$input_file_sbml'
+            #if str($input_tag_str) != ""
+                --input-tag-str '$input_tag_str'
+            #end if
+            --input-modelisation-json '$input_modelisation_json' | tee '$output'
+    ]]></command>
+    <inputs>
+        <param name="input_auradb_file" type="data" format="txt" label="Config file provided by AuraDB"/>
+        <param name="input_file_sbml" type="data" format="sbml" label="SBML model"/>
+        <param name="input_tag_str" type="text" label="Identifier of the model">
+            <validator type="regex" message="No special characters allowed">^(?:[\w-]*)$</validator>
+        </param>
+        <param name="input_modelisation_json" type="data" format="json" label="Arrow's schema"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" label="${tool.name} - log" />
+    </outputs>
+    <help><![CDATA[
+Neo4jSbml
+=========
+
+Step 1
+------
+
+Create a schema with `Arrows <https://arrows.app>`_
+
+Rules:
+- Nodes are labelled based on SBML object name as defined in the `SBML specification <https://sbml.org>`_
+- Properties are labelled based on SBML object properties as defined the `SBML specification <https://sbml.org>`_
+
+Step 2
+------
+Export your schema at the JSON format.
+
+Step 3
+------
+
+Import your data with `neo4jsbml` into Neo4j.
+- Use either a configuration file `ini` or individual parameters
+- Password needs to be store in a file for safety security
+- If you have multiple model in the database, pass a `tag` to identify the model loaded into the database if you want to avoid collision
+
+Inputs
+------
+
+- **AuraDB config like**: a txt file with these variables NEO4J_URI, NEO4J_USERNAME, NEO4J_PASSWORD and AURA_INSTANCENAME. One per line like: NEO4J_USERNAME=neo4j
+- **SBML model**: SBML model
+- **Identifier of the model**: Associate an ID to the nodes (optional)
+- **Arrow's schema**: Schema created with Arrow
+
+Ouput
+-----
+
+- Traceback of the tool
+]]></help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{neo4jsbml
+                author = {Guillaume Gricourt, Thomas Duigou, Sandra Dérozier, Jean-Loup Faulon},
+                title = {{Neo4jSbml}},
+                url = {https://github.com/brsynth/neo4jsbml/},
+            }
+        </citation>
+    </citations>
+</tool>
diff --git a/tools/neo4jsbml/test-data/PathwayModelisation-2.0.3.json b/tools/neo4jsbml/test-data/PathwayModelisation-2.0.3.json
new file mode 100644
index 00000000..ceeb1797
--- /dev/null
+++ b/tools/neo4jsbml/test-data/PathwayModelisation-2.0.3.json
@@ -0,0 +1,265 @@
+{
+  "style": {
+    "font-family": "sans-serif",
+    "background-color": "#ffffff",
+    "background-image": "",
+    "background-size": "100%",
+    "node-color": "#ffffff",
+    "border-width": 4,
+    "border-color": "#000000",
+    "radius": 50,
+    "node-padding": 5,
+    "node-margin": 2,
+    "outside-position": "auto",
+    "node-icon-image": "",
+    "node-background-image": "",
+    "icon-position": "inside",
+    "icon-size": 64,
+    "caption-position": "inside",
+    "caption-max-width": 200,
+    "caption-color": "#000000",
+    "caption-font-size": 50,
+    "caption-font-weight": "normal",
+    "label-position": "inside",
+    "label-display": "pill",
+    "label-color": "#000000",
+    "label-background-color": "#ffffff",
+    "label-border-color": "#000000",
+    "label-border-width": 4,
+    "label-font-size": 40,
+    "label-padding": 5,
+    "label-margin": 4,
+    "directionality": "directed",
+    "detail-position": "inline",
+    "detail-orientation": "parallel",
+    "arrow-width": 5,
+    "arrow-color": "#000000",
+    "margin-start": 5,
+    "margin-end": 5,
+    "margin-peer": 20,
+    "attachment-start": "normal",
+    "attachment-end": "normal",
+    "relationship-icon-image": "",
+    "type-color": "#000000",
+    "type-background-color": "#ffffff",
+    "type-border-color": "#000000",
+    "type-border-width": 0,
+    "type-font-size": 16,
+    "type-padding": 5,
+    "property-position": "outside",
+    "property-alignment": "colon",
+    "property-color": "#000000",
+    "property-font-size": 16,
+    "property-font-weight": "normal"
+  },
+  "nodes": [
+    {
+      "id": "n0",
+      "position": {
+        "x": 0,
+        "y": 0
+      },
+      "caption": "",
+      "style": {},
+      "labels": [],
+      "properties": {}
+    },
+    {
+      "id": "n1",
+      "position": {
+        "x": 884.6635137872785,
+        "y": 380.3581544878789
+      },
+      "caption": "",
+      "labels": [
+        "Compartment"
+      ],
+      "properties": {
+        "id": "str (required)",
+        "name": "str (optional)",
+        "metaid": "str (optional)",
+        "sboTerm": "str (optional)",
+        "spatialDimensions": "int (optional)",
+        "size": "int (optional)",
+        "constant": "bool (optional)"
+      },
+      "style": {}
+    },
+    {
+      "id": "n2",
+      "position": {
+        "x": 560.2494455950304,
+        "y": 380.3581544878789
+      },
+      "caption": "",
+      "labels": [
+        "Species"
+      ],
+      "properties": {
+        "id": "str (required)",
+        "initialAmount": "float (optional)",
+        "hasOnlySubstanceUnits": "bool (optional)",
+        "boundaryCondition": "bool (optional)",
+        "constant": "bool (optional)"
+      },
+      "style": {}
+    },
+    {
+      "id": "n3",
+      "position": {
+        "x": 432.24944559503035,
+        "y": 204.94864525928773
+      },
+      "caption": "",
+      "labels": [
+        "Parameter"
+      ],
+      "properties": {
+        "id": "str (required)",
+        "name": "str (optional)",
+        "metaid": "str (optional)",
+        "sboTerm": "str (optional)",
+        "value": "float (optional)",
+        "constant": "bool"
+      },
+      "style": {}
+    },
+    {
+      "id": "n4",
+      "position": {
+        "x": 833.1523435518487,
+        "y": 204.94864525928796
+      },
+      "caption": "",
+      "labels": [
+        "Reaction"
+      ],
+      "properties": {
+        "id": "str (required)",
+        "name": "str (optional)",
+        "metaid": "str (optional)",
+        "sboTerm": "str (optional)",
+        "reversible": "bool"
+      },
+      "style": {}
+    },
+    {
+      "id": "n5",
+      "position": {
+        "x": 129,
+        "y": 204.94864525928773
+      },
+      "caption": "",
+      "labels": [
+        "model"
+      ],
+      "properties": {
+        "id": "str",
+        "name": "str",
+        "metaid": "str",
+        "sboTerm": "str"
+      },
+      "style": {}
+    },
+    {
+      "id": "n6",
+      "position": {
+        "x": 129,
+        "y": 380.3581544878789
+      },
+      "caption": "",
+      "labels": [
+        "UnitDefinition"
+      ],
+      "properties": {
+        "id": "str (optional)",
+        "name": "str (optional)",
+        "metaid": "str (optional)",
+        "sboTerm": "str (optional)"
+      },
+      "style": {}
+    },
+    {
+      "id": "n7",
+      "position": {
+        "x": 560.2494455950304,
+        "y": -4
+      },
+      "caption": "",
+      "labels": [
+        "GeneProduct"
+      ],
+      "properties": {
+        "id": "str",
+        "name": "str"
+      },
+      "style": {}
+    }
+  ],
+  "relationships": [
+    {
+      "id": "n0",
+      "fromId": "n2",
+      "toId": "n1",
+      "type": "IN_COMPARTMENT",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n1",
+      "fromId": "n4",
+      "toId": "n2",
+      "type": "HAS_PRODUCT",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n2",
+      "fromId": "n4",
+      "toId": "n3",
+      "type": "HAS_LOWERFLUXBOUND",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n3",
+      "fromId": "n5",
+      "toId": "n3",
+      "type": "HAS_PARAMETER",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n4",
+      "type": "HAS_UNITS",
+      "style": {},
+      "properties": {},
+      "fromId": "n3",
+      "toId": "n6"
+    },
+    {
+      "id": "n5",
+      "fromId": "n4",
+      "toId": "n3",
+      "type": "HAS_UPPERFLUXBOUND",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n6",
+      "fromId": "n4",
+      "toId": "n7",
+      "type": "IS_IMPLIED",
+      "properties": {},
+      "style": {}
+    },
+    {
+      "id": "n7",
+      "fromId": "n2",
+      "toId": "n4",
+      "type": "IS_REACTANT",
+      "properties": {},
+      "style": {}
+    }
+  ]
+}
\ No newline at end of file
diff --git a/tools/neo4jsbml/test-data/e_coli_core.xml.gz b/tools/neo4jsbml/test-data/e_coli_core.xml.gz
new file mode 100644
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HcmV?d00001


From f8bd74925ba212d7958340e1440bb6b0c0a4ab76 Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 10 Oct 2023 00:53:01 +0000
Subject: [PATCH 59/61] doc(changelog): update

---
 CHANGELOG.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index be6b97ae..fee2405d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,16 @@
 # Changelog
 
+## [0.3.0](https://github.com/brsynth/galaxytools/tree/0.3.0) (2023-09-29)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.12...0.3.0)
+
+**Merged pull requests:**
+
+- Get sbml model [\#143](https://github.com/brsynth/galaxytools/pull/143) ([breakthewall](https://github.com/breakthewall))
+- chore\(deps\): bump tj-actions/changed-files from 37 to 39 [\#142](https://github.com/brsynth/galaxytools/pull/142) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Updating dnabot from version 3.1.0 to 4.1.0 [\#141](https://github.com/brsynth/galaxytools/pull/141) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+- get\_sbml\_model, load file from history [\#139](https://github.com/brsynth/galaxytools/pull/139) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+
 ## [0.2.12](https://github.com/brsynth/galaxytools/tree/0.2.12) (2023-09-19)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.11...0.2.12)

From 1ce9c19b7ed1a5df6307f1eb64eed2539ea1fa0d Mon Sep 17 00:00:00 2001
From: guillaume-gricourt <guipagui@gmail.com>
Date: Tue, 17 Oct 2023 00:53:59 +0000
Subject: [PATCH 60/61] doc(changelog): update

---
 CHANGELOG.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fee2405d..3867b5b0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # Changelog
 
+## [0.4.0](https://github.com/brsynth/galaxytools/tree/0.4.0) (2023-10-09)
+
+[Full Changelog](https://github.com/brsynth/galaxytools/compare/0.3.0...0.4.0)
+
+**Merged pull requests:**
+
+- Add tool `neo4jsbml` [\#144](https://github.com/brsynth/galaxytools/pull/144) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+
 ## [0.3.0](https://github.com/brsynth/galaxytools/tree/0.3.0) (2023-09-29)
 
 [Full Changelog](https://github.com/brsynth/galaxytools/compare/0.2.12...0.3.0)

From 8963ffc51170ec079a8c5719d7d33d8f8d9d3dfb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Fri, 20 Oct 2023 21:35:49 +0200
Subject: [PATCH 61/61] Rptools (#146)

* feat(rpextractsink): add --standalone arg

* chore(rp2paths): update version

* chore(rptools): v 6.3.0
---
 tools/rp2paths/rp2paths.xml     | 2 +-
 tools/rptools/macros.xml        | 2 +-
 tools/rptools/rpextractsink.xml | 7 +++++--
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/tools/rp2paths/rp2paths.xml b/tools/rp2paths/rp2paths.xml
index 3b77642b..cc040bfa 100644
--- a/tools/rp2paths/rp2paths.xml
+++ b/tools/rp2paths/rp2paths.xml
@@ -1,7 +1,7 @@
 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT">
     <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.5.0</token>
+        <token name="@TOOL_VERSION@">1.5.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
diff --git a/tools/rptools/macros.xml b/tools/rptools/macros.xml
index d31cddda..8f7f5ef3 100644
--- a/tools/rptools/macros.xml
+++ b/tools/rptools/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">6.2.3</token>
+    <token name="@TOOL_VERSION@">6.3.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
diff --git a/tools/rptools/rpextractsink.xml b/tools/rptools/rpextractsink.xml
index 8ea09d69..2e27ce91 100644
--- a/tools/rptools/rpextractsink.xml
+++ b/tools/rptools/rpextractsink.xml
@@ -11,8 +11,9 @@
         python -m rptools.rpextractsink
             '$input'
             '$sink'
-            --compartment_id '$compartment_id'
+            --compartment-id '$compartment_id'
             $adv.remove_dead_end
+            $adv.standalone
             --cache-dir "\${TMPDIR:-.}"
     ]]></command>
     <inputs>
@@ -21,7 +22,8 @@
             <validator type="empty_field" message="SBML compartment ID is required"/>
         </param>
         <section name="adv" title="Advanced Options" expanded="false">
-            <param argument="--remove_dead_end" type="boolean" truevalue="--remove_dead_end" falsevalue="" checked="true" label="Remove dead-end metabolites using FVA evaluation?" help="Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites" />
+            <param argument="--remove_dead_end" type="boolean" truevalue="--remove-dead-end" falsevalue="" checked="true" label="Remove dead-end metabolites using FVA evaluation?" help="Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites" />
+            <param argument="--standalone" type="boolean" truevalue="--standalone" falsevalue="" checked="true" label="Do not connect to Internet" help="If True, do not retrieve InChI from Internet" />
         </section>
     </inputs>
     <outputs>
@@ -55,6 +57,7 @@ Required:
 Advanced options:
 
 * **Remove dead-end metabolites using FVA evaluation?**\ : (boolean, default: True) Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites.
+* **Do not connect to Internet**: (boolean, default: False) If True, do not retrieve InChI from Internet
 
 Output
 ------