From c71afcdace723c2f5b1388f05c6c6a3b321e6789 Mon Sep 17 00:00:00 2001 From: Riley Juenemann Date: Fri, 19 Jul 2024 09:44:38 -0700 Subject: [PATCH] correct peroxisome compartment --- reconstruction/ecoli/dataclasses/getter_functions.py | 1 - reconstruction/ecoli/flat/complexation_reactions.tsv | 2 +- reconstruction/ecoli/flat/dna_sites.tsv | 2 +- reconstruction/ecoli/flat/equilibrium_reactions.tsv | 2 +- reconstruction/ecoli/flat/genes.tsv | 2 +- reconstruction/ecoli/flat/metabolic_reactions.tsv | 2 +- reconstruction/ecoli/flat/metabolites.tsv | 2 +- reconstruction/ecoli/flat/proteins.tsv | 10 +++++----- reconstruction/ecoli/flat/rnas.tsv | 2 +- reconstruction/ecoli/flat/transcription_units.tsv | 2 +- reconstruction/ecoli/flat/trna_charging_reactions.tsv | 2 +- 11 files changed, 14 insertions(+), 15 deletions(-) diff --git a/reconstruction/ecoli/dataclasses/getter_functions.py b/reconstruction/ecoli/dataclasses/getter_functions.py index 929ca09ae..f1a596b1c 100755 --- a/reconstruction/ecoli/dataclasses/getter_functions.py +++ b/reconstruction/ecoli/dataclasses/getter_functions.py @@ -27,7 +27,6 @@ 'CCO-CE-BAC': 'm', 'CCO-BAC-NUCLEOID': 'c', 'CCO-RIBOSOME': 'c', - 'CCO-PEROXISOME': 'c', ### TODO: DELETE AFTER 'CCO-PEROXISOME': 'c', is removed from "G7439-MONOMER" } IGNORED_DNA_SITE_TYPES = { diff --git a/reconstruction/ecoli/flat/complexation_reactions.tsv b/reconstruction/ecoli/flat/complexation_reactions.tsv index 42dd9ef1a..ba756b02b 100644 --- a/reconstruction/ecoli/flat/complexation_reactions.tsv +++ b/reconstruction/ecoli/flat/complexation_reactions.tsv @@ -1,7 +1,7 @@ # Organism: Escherichia coli K-12 substr. MG1655 # Database: EcoCyc # Version: 28.5 -# Date and time generated: July 18, 2024, 11:02:13 +# Date and time generated: July 19, 2024, 9:40:33 "id" "stoichiometry" "common_name" "cofactors" "1-PFK_RXN" {"1-PFK": 1, "1-PFK-MONOMER": -2} null {"MG+2": 1} "2OXOGLUTARATEDEH-CPLX_RXN" {"2OXOGLUTARATEDEH-CPLX": 1, "E1O": -1, "E2O": -1, "E3-CPLX": -1} "2-oxoglutarate dehydrogenase complex" {"LIPOIC-ACID": 1, "THIAMINE-PYROPHOSPHATE": 2, "FAD": 3, "MG+2": 2} diff --git a/reconstruction/ecoli/flat/dna_sites.tsv b/reconstruction/ecoli/flat/dna_sites.tsv index 5ccf12cfc..fcf38cf6c 100644 --- a/reconstruction/ecoli/flat/dna_sites.tsv +++ b/reconstruction/ecoli/flat/dna_sites.tsv @@ -1,7 +1,7 @@ # Organism: Escherichia coli K-12 substr. MG1655 # Database: EcoCyc # Version: 28.5 -# Date and time generated: July 18, 2024, 11:02:15 +# Date and time generated: July 19, 2024, 9:40:35 "id" "common_name" "synonyms" "type" "left_end_pos" "right_end_pos" "direction" "BS-7046" null [] "dna-binding-site" 1825765 1825784 null "BS-7048" null [] "dna-binding-site" 3169748 3169760 null diff --git a/reconstruction/ecoli/flat/equilibrium_reactions.tsv b/reconstruction/ecoli/flat/equilibrium_reactions.tsv index eaedc765b..992afc0f1 100644 --- a/reconstruction/ecoli/flat/equilibrium_reactions.tsv +++ b/reconstruction/ecoli/flat/equilibrium_reactions.tsv @@ -1,7 +1,7 @@ # Organism: Escherichia coli K-12 substr. MG1655 # Database: EcoCyc # Version: 28.5 -# Date and time generated: July 18, 2024, 11:02:16 +# Date and time generated: July 19, 2024, 9:40:36 "id" "stoichiometry" "common_name" "CPLX-123_RXN" {"CPLX-123": 1, "PC00033": null, "HYPOXANTHINE": null} "DNA-binding transcriptional repressor PurR-hypoxanthine" "CPLX-124_CPD0-1112_RXN" {"CPLX-124": 1, "CPD0-1112": null, "PC00086": null} "RhaS-L-rhamnose DNA-binding transcriptional activator" diff --git a/reconstruction/ecoli/flat/genes.tsv b/reconstruction/ecoli/flat/genes.tsv index e6612d7c1..6c3cfd2db 100644 --- a/reconstruction/ecoli/flat/genes.tsv +++ b/reconstruction/ecoli/flat/genes.tsv @@ -1,7 +1,7 @@ # Organism: Escherichia coli K-12 substr. MG1655 # Database: EcoCyc # Version: 28.5 -# Date and time generated: July 18, 2024, 11:02:22 +# Date and time generated: July 19, 2024, 9:40:40 "id" "symbol" "synonyms" "left_end_pos" "right_end_pos" "direction" "rna_ids" "EG10001" "alr" ["alr", "alr5", "b4053", "ECK4045"] 4265782 4266861 "+" ["EG10001_RNA"] "EG10002" "modB" ["modB", "chlJ", "tslJ", "b0764", "ECK0753"] 795862 796551 "+" ["EG10002_RNA"] diff --git a/reconstruction/ecoli/flat/metabolic_reactions.tsv b/reconstruction/ecoli/flat/metabolic_reactions.tsv index 710bc36ee..9f6af4d58 100644 --- a/reconstruction/ecoli/flat/metabolic_reactions.tsv +++ b/reconstruction/ecoli/flat/metabolic_reactions.tsv @@ -1,7 +1,7 @@ # Organism: Escherichia coli K-12 substr. MG1655 # Database: EcoCyc # Version: 28.5 -# Date and time generated: July 18, 2024, 11:02:52 +# Date and time generated: July 19, 2024, 9:41:02 "id" "stoichiometry" "direction" "catalyzed_by" "1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN" {"ACYL-SN-GLYCEROL-3P[CCO-CYTOSOL]": -1, "ACYL-ACP[CCO-CYTOSOL]": -1, "L-PHOSPHATIDATE[CCO-CYTOSOL]": 1, "ACP[CCO-CYTOSOL]": 1} "L2R" ["1-ACYLGLYCEROL-3-P-ACYLTRANSFER-MONOMER"] "1.1.1.127-RXN" {"2-DEHYDRO-3-DEOXY-D-GLUCONATE[CCO-CYTOSOL]": -1, "NAD[CCO-CYTOSOL]": -1, "CPD-343[CCO-CYTOSOL]": 1, "NADH[CCO-CYTOSOL]": 1, "PROTON[CCO-CYTOSOL]": 1} "BOTH" ["KDUD-MONOMER"] diff --git a/reconstruction/ecoli/flat/metabolites.tsv b/reconstruction/ecoli/flat/metabolites.tsv index b4b6dafb6..4c06e1dfc 100644 --- a/reconstruction/ecoli/flat/metabolites.tsv +++ b/reconstruction/ecoli/flat/metabolites.tsv @@ -1,7 +1,7 @@ # Organism: Escherichia coli K-12 substr. MG1655 # Database: EcoCyc # Version: 28.5 -# Date and time generated: July 18, 2024, 11:03:09 +# Date and time generated: July 19, 2024, 9:41:18 "id" "common_name" "synonyms" "chemical_formula" "mw" "molecular_charge" "_smiles" "--TRANS-ACENAPHTHENE-12-DIOL" "(+/-)-trans-acenaphthene-1,2-diol" ["trans-1,2-acenaphthylene glycol"] "C12H10O2" 186.21 0 "c2(cc1(cccc3(c1c(c2)[C@@H]([C@H]3O)O)))" "1-2-Beta-D-Glucans" "a 1,2-β-D-glucan" [] null null 0 "C(O)[C@H]7(O[C@@H](O)[C@H](O[C@@H]6(O[C@H](CO)[C@@H](O)[C@H](O)[C@@H](O[C@H]5([C@H](O[C@@H]4(O[C@H](CO)[C@@H](O)[C@H](O)[C@@H](O[C@H]3([C@H](O[C@@H]2(O[C@H](CO)[C@@H](O)[C@H](O)[C@@H](O[C@H]1([C@H](O[R])[C@@H](O)[C@H](O)[C@@H](CO)O1))2))[C@@H](O)[C@H](O)[C@@H](CO)O3))4))[C@@H](O)[C@H](O)[C@@H](CO)O5))6))[C@@H](O)[C@H](O)7)" diff --git a/reconstruction/ecoli/flat/proteins.tsv b/reconstruction/ecoli/flat/proteins.tsv index 4aaee1c01..742847469 100644 --- a/reconstruction/ecoli/flat/proteins.tsv +++ b/reconstruction/ecoli/flat/proteins.tsv @@ -1,7 +1,7 @@ # Organism: Escherichia coli K-12 substr. MG1655 # Database: EcoCyc # Version: 28.5 -# Date and time generated: July 18, 2024, 11:03:28 +# Date and time generated: July 19, 2024, 9:41:37 "id" "common_name" "synonyms" "seq" "experimental_compartment" "computational_compartment" "cleavage_of_initial_methionine" "selenocysteine_at_opal" "protein_feature_cofactors" "in_complex" "1-ACYLGLYCEROL-3-P-ACYLTRANSFER-MONOMER" "1-acylglycerol-3-phosphate O-acyltransferase PlsC" ["ParF", "PlsC"] "MLYIFRLIITVIYSILVCVFGSIYCLFSPRNPKHVATFGHMFGRLAPLFGLKVECRKPTDAESYGNAIYIANHQNNYDMVTASNIVQPPTVTVGKKSLLWIPFFGQLYWLTGNLLIDRNNRTKAHGTIAEVVNHFKKRRISIWMFPEGTRSRGRGLLPFKTGAFHAAIAAGVPIIPVCVSTTSNKINLNRLHNGLVIVEMLPPIDVSQYGKDQVRELAAHCRSIMEQKIAELDKEVAEREAAGKV" ["CCO-PM-BAC-NEG"] ["CCO-MEMBRANE", "CCO-PM-BAC-NEG"] 0 [] {} 0 "1-PFK-MONOMER" "1-phosphofructokinase" ["Fpk", "FruK"] "MSRRVATITLNPAYDLVGFCPEIERGEVNLVKTTGLHAAGKGINVAKVLKDLGIDVTVGGFLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTPADWERFVTDSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAAPWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGAEGALWVNASGEWIAKPPSVDVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRPQLAAMMARVDLQPFN" [] ["CCO-CYTOSOL"] 0 [] {} 1 @@ -2270,9 +2270,9 @@ "G6700-MONOMER" "outer membrane porin N" ["YnaG", "OmpN"] "MKSKVLALLIPALLAAGAAHAAEVYNKDGNKLDLYGKVDGLHYFSDNSAKDGDQSYARLGFKGETQINDQLTGYGQWEYNIQANNTESSKNQSWTRLAFAGLKFADYGSFDYGRNYGVMYDIEGWTDMLPEFGGDSYTNADNFMTGRANGVATYRNTDFFGLVNGLNFAVQYQGNNEGASNGQEGTNNGRDVRHENGDGWGLSTTYDLGMGFSAGAAYTSSDRTNDQVNHTAAGGDKADAWTAGLKYDANNIYLATMYSETRNMTPFGDSDYAVANKTQNFEVTAQYQFDFGLRPAVSFLMSKGRDLHAAGGADNPAGVDDKDLVKYADIGATYYFNKNMSTYVDYKINLLDEDDSFYAANGISTDDIVALGLVYQF" ["CCO-MEMBRANE"] ["CCO-OUTER-MEM"] 0 [] {} 0 "G6701-MONOMER" "putative pyruvate-flavodoxin oxidoreductase" ["Pfo", "YdbK"] "MITIDGNGAVASVAFRTSEVIAIYPITPSSTMAEQADAWAGNGLKNVWGDTPRVVEMQSEAGAIATVHGALQTGALSTSFTSSQGLLLMIPTLYKLAGELTPFVLHVAARTVATHALSIFGDHSDVMAVRQTGCAMLCAANVQEAQDFALISQIATLKSRVPFIHFFDGFRTSHEINKIVPLADDTILDLMPQVEIDAHRARALNPEHPVIRGTSANPDTYFQSREATNPWYNAVYDHVEQAMNDFSAATGRQYQPFEYYGHPQAERVIILMGSAIGTCEEVVDELLTRGEKVGVLKVRLYRPFSAKHLLQALPGSVRSVAVLDRTKEPGAQAEPLYLDVMTALAEAFNNGERETLPRVIGGRYGLSSKEFGPDCVLAVFAELNAAKPKARFTVGIYDDVTNLSLPLPENTLPNSAKLEALFYGLGSDGSVSATKNNIKIIGNSTPWYAQGYFVYDSKKAGGLTVSHLRVSEQPIRSAYLISQADFVGCHQLQFIDKYQMAERLKPGGIFLLNTPYSADEVWSRLPQEVQAVLNQKKARFYVINAAKIARECGLAARINTVMQMAFFHLTQILPGDSALAELQGAIAKSYSSKGQDLVERNWQALALARESVEEVPLQPVNPHSANRPPVVSDAAPDFVKTVTAAMLAGLGDALPVSALPPDGTWPMGTTRWEKRNIAEEIPIWKEELCTQCNHCVAACPHSAIRAKVVPPEAMENAPASLHSLDVKSRDMRGQKYVLQVAPEDCTGCNLCVEVCPAKDRQNPEIKAINMMSRLEHVEEEKINYDFFLNLPEIDRSKLERIDIRTSQLITPLFEYSGACSGCGETPYIKLLTQLYGDRMLIANATGCSSIYGGNLPSTPYTTDANGRGPAWANSLFEDNAEFGLGFRLTVDQHRVRVLRLLDQFADKIPAELLTALKSDATPEVRREQVAALRQQLNDVAEAHELLRDADALVEKSIWLIGGDGWAYDIGFGGLDHVLSLTENVNILVLDTQCYSNTGGQASKATPLGAVTKFGEHGKRKARKDLGVSMMMYGHVYVAQISLGAQLNQTVKAIQEAEAYPGPSLIIAYSPCEEHGYDLALSHDQMRQLTATGFWPLYRFDPRRADEGKLPLALDSRPPSEAPEETLLHEQRFRRLNSQQPEVAEQLWKDAAADLQKRYDFLAQMAGKAEKSNTD" [] ["CCO-PM-BAC-NEG"] 0 [] {"CPD-7": 3} 0 "G6702-MONOMER" "lipoprotein implicated in Novobiocin resistance" ["YdbI", "HslJ"] "MKKVAAFVALSLLMAGCVSNDKIAVTPEQLQHHRFVLESVNGKPVTSDKNPPEISFGEKMMISGSMCNRFSGEGKLSNGELTAKGLAMTRMMCANPQLNELDNTISEMLKEGAQVDLTANQLTLATAKQTLTYKLADLMN" [] ["CCO-MEMBRANE"] 0 [] {} 0 -"G6703-MONOMER" "putative phospholipid transport factor YdbH" ["YdbH"] "MLGKYKAVLALLLLIILVPLTLLMTLGLWVPTLAGIWLPLGTRIALDESPRITRKGLIIPDLRYLVGDCQLAHITNASLSHPSRWLLNVGTVELDSACLAKLPQTEQSPAAPKTLAQWQAMLPNTWINIDKLIFSPWQEWQGKLSLALTSDIQQLRYQGEKVKFQGQLKGQQLTVSELDVVAFENQPPVKLVGEFAMPLVPDGLPVSGHATATLNLPQEPSLVDAELDWQENSGQLIVLARDNGDPLLDLPWQITRQQLTVSDGRWSWPYAGFPLSGRLGVKVDNWQAGLENALVSGRLSVLTQGQAGKGNAVLNFGPGKLSMDNSQLPLQLTGEAKQADLILYARLPAQLSGSLSDPTLTFEPGALLRSKGRVIDSLDIDEIRWPLAGVKVTQRGVDGRLQAILQAHENELGDFVLHMDGLANDFLPDAGRWQWRYWGKGSFTPMNATWDVAGKGEWHDSTITLTDLSTGFDQLQYGTMTVEKPRLILDKPIVWVRDAQHPSFSGALSLDAGQTLFTGGSVLPPSTLKFSVDGRDPTYFLFKGDLHAGEIGPVRVNGRWDGIRLRGNAWWPKQSLTVFQPLVPPDWKMNLRDGELYAQVAFSAAPEQGFRAGGHGVLKGGSAWMPDNQVNGVDFVLPFRFADGAWHLGTRGPVTLRIAEVINLVTAKNITADLQGRYPWTEEEPLLLTDVSVDVLGGNVLMKQLRMPQHDPALLRLNNLSSSELVSAVNPKQFAMSGAFSGALPLWLNNEKWIVKDGWLANSGPMTLRLDKDTADAVVKDNMTAGSAINWLRYMEISRSSTKINLDNLGLLTMQANITGTSRVDGKSGTVNLNYHHEENIFTLWRSLRFGDNLQAWLEQNARLPGNDCPQGKECEEKQ" ["CCO-PM-BAC-NEG"] ["CCO-PM-BAC-NEG"] 0 [] {} 0 -"G6704-MONOMER" "lipoprotein YnbE" ["YnbE"] "MKILLAALTSSFMLVGCTPRIEVAAPKEPITINMNVKIEHEIIIKADKDVEELLETRSDLF" [] ["CCO-CYTOSOL"] 0 [] {} 0 -"G6705-MONOMER" "DUF1318 domain-containing protein YdbL" ["YdbL"] "MKKTLLLCAFLVGLVSSNVMALTLDEARTQGRVGETFYGYLVALKTDAETEKLVADINAERKASYQQLAKQNNVSVDDIAKLAGQKLVARAKPGEYVQGINGKWVRKF" [] [] 0 [] {} 0 +"G6703-MONOMER" "putative intermembrane phospholipid transport protein YdbH" ["YdbH"] "MLGKYKAVLALLLLIILVPLTLLMTLGLWVPTLAGIWLPLGTRIALDESPRITRKGLIIPDLRYLVGDCQLAHITNASLSHPSRWLLNVGTVELDSACLAKLPQTEQSPAAPKTLAQWQAMLPNTWINIDKLIFSPWQEWQGKLSLALTSDIQQLRYQGEKVKFQGQLKGQQLTVSELDVVAFENQPPVKLVGEFAMPLVPDGLPVSGHATATLNLPQEPSLVDAELDWQENSGQLIVLARDNGDPLLDLPWQITRQQLTVSDGRWSWPYAGFPLSGRLGVKVDNWQAGLENALVSGRLSVLTQGQAGKGNAVLNFGPGKLSMDNSQLPLQLTGEAKQADLILYARLPAQLSGSLSDPTLTFEPGALLRSKGRVIDSLDIDEIRWPLAGVKVTQRGVDGRLQAILQAHENELGDFVLHMDGLANDFLPDAGRWQWRYWGKGSFTPMNATWDVAGKGEWHDSTITLTDLSTGFDQLQYGTMTVEKPRLILDKPIVWVRDAQHPSFSGALSLDAGQTLFTGGSVLPPSTLKFSVDGRDPTYFLFKGDLHAGEIGPVRVNGRWDGIRLRGNAWWPKQSLTVFQPLVPPDWKMNLRDGELYAQVAFSAAPEQGFRAGGHGVLKGGSAWMPDNQVNGVDFVLPFRFADGAWHLGTRGPVTLRIAEVINLVTAKNITADLQGRYPWTEEEPLLLTDVSVDVLGGNVLMKQLRMPQHDPALLRLNNLSSSELVSAVNPKQFAMSGAFSGALPLWLNNEKWIVKDGWLANSGPMTLRLDKDTADAVVKDNMTAGSAINWLRYMEISRSSTKINLDNLGLLTMQANITGTSRVDGKSGTVNLNYHHEENIFTLWRSLRFGDNLQAWLEQNARLPGNDCPQGKECEEKQ" ["CCO-PM-BAC-NEG"] ["CCO-PM-BAC-NEG"] 0 [] {} 0 +"G6704-MONOMER" "putative intermembrane phospholipid transport lipoprotein YnbE" ["YnbE"] "MKILLAALTSSFMLVGCTPRIEVAAPKEPITINMNVKIEHEIIIKADKDVEELLETRSDLF" [] ["CCO-CYTOSOL"] 0 [] {} 0 +"G6705-MONOMER" "DUF1318 domain-containing protein YdbL" ["YdbL"] "MKKTLLLCAFLVGLVSSNVMALTLDEARTQGRVGETFYGYLVALKTDAETEKLVADINAERKASYQQLAKQNNVSVDDIAKLAGQKLVARAKPGEYVQGINGKWVRKF" [] ["CCO-PERI-BAC"] 0 [] {} 0 "G6706-MONOMER" "DNA-binding transcriptional activator FeaR" ["MaoX", "YdbM", "MaoB", "FeaR"] "MNPAVDNEFQQWLSQINQVCGNFTGRLLTERYTGVLDTHFAKGLKLSTVTTSGVNLSRTWQEVKGSDDAWFYTVFQLSGQAIMEQDERQVQIGAGDITLLDASRPCSLYWQESSKQISLLLPRTLLEQYFPHQKPICAERLDADLPMVQLSHRLLQESMNNPALSETESEAALQAMVCLLRPVLHQRESVQPRRERQFQKVVTLIDDNIREEILRPEWIAGETGMSVRSLYRMFADKGLVVAQYIRNRRLDFCADAIRHAADDEKLAGIGFHWGFSDQSHFSTVFKQRFGMTPGEYRRKFR" [] ["CCO-CYTOSOL"] 0 [] {} 0 "G6708-MONOMER" "fused 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase and oxepin-CoA hydrolase" ["YdbN", "PaaZ", "MaoC", "oxepin-CoA hydrolase/3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase"] "MQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFNQHQTPVALYSILTLVARQHGDFVD" [] ["CCO-CYTOSOL"] 0 [] {} 1 "G6709-MONOMER" "phenylacetyl-CoA 1,2-epoxidase, monooxygenase subunit" ["YdbO", "PaaA"] "MTQEERFEQRIAQETAIEPQDWMPDAYRKTLIRQIGQHAHSEIVGMLPEGNWITRAPTLRRKAILLAKVQDEAGHGLYLYSAAETLGCAREDIYQKMLDGRMKYSSIFNYPTLSWADIGVIGWLVDGAAIVNQVALCRTSYGPYARAMVKICKEESFHQRQGFEACMALAQGSEAQKQMLQDAINRFWWPALMMFGPNDDNSPNSARSLTWKIKRFTNDELRQRFVDNTVPQVEMLGMTVPDPDLHFDTESGHYRFGEIDWQEFNEVINGRGICNQERLDAKRKAWEEGTWVREAALAHAQKQHARKVA" [] ["CCO-CYTOSOL"] 0 [] {} 1 @@ -2852,7 +2852,7 @@ "G7434-MONOMER" "putative anti-terminator regulatory protein" ["YgcP"] "MPLLHLLRQNPVIAAVKDNASLQLAIDSECQFISVLYGNICTISNIVKKIKNAGKYAFIHVDLLEGASNKEVVIQFLKLVTEADGIISTKASMLKAARAEGFFCIHRLFIVDSISFHNIDKQVAQSNPDCIEILPGCMPKVLGWVTEKIRQPLIAGGLVCDEEDARNAINAGVVALSTTNTGVWTLAKKLL" [] ["CCO-CYTOSOL"] 0 [] {} 0 "G7435-MONOMER" "putative flavoprotein" ["YgcQ"] "MNIAIVTINQENAAIASWLAAQDFSGCTLAHWQIEPQPVVAEQVLDALVEQWQRTPADVVLFPPGTFGDELSTRLAWRLHGASICQVTSLDIPTVSVRKSHWGNALTATLQTEKRPLCLSLARQAGAAKNATLPSGMQQLNIVPGALPDWLVSTEDLKNVTRDPLAEARRVLVVGQGGEADNQEIAMLAEKLGAEVGYSRARVMNGGVDAEKVIGISGHLLAPEVCIVVGASGAAALMAGVRNSKFVVAINHDASAAVFSQADVGVVDDWKVVLEALVTNIHADCQ" [] ["CCO-MEMBRANE"] 0 [] {} 0 "G7436-MONOMER" "putative flavoprotein" ["YgcR"] "MNILLAFKAEPDAGMLAEKEWQAAAQGKSGPDISLLRSLLGADEQAAAALLLAQRKNGTPMSLTALSMGDERALHWLRYLMALGFEEAVLLETAADLRFAPEFVARHIAEWQHQNPLDLIITGCQSSEGQNGQTPFLLAEMLGWPCFTQVERFTLDALFITLEQRTEHGLRCCRVRLPAVIAVRQCGEVALPVPGMRQRMAAGKAEIIRKTVAAEMPAMQCLQLARAEQRRGATLIDGQTVAEKAQKLWQDYLRQRMQP" [] ["CCO-PM-BAC-NEG", "CCO-CYTOSOL"] 0 [] {} 0 -"G7439-MONOMER" "putative FAD-containing dehydrogenase" ["YgcV", "YgcU", "YgcT"] "MSLSRAAIVDQLKEIVGADRVITDETVLKKNSIDRFRKFPDIHGIYTLPIPAAVVKLGSTEQVSRVLNFMNAHKINGVPRTGASATEGGLETVVENSVVLDGSAMNQIINIDIENMQATAQCGVPLEVLENALREKGYTTGHSPQSKPLAQMGGLVATRSIGQFSTLYGAIEDMVVGLEAVLADGTVTRIKNVPRRAAGPDIRHIIIGNEGALCYITEVTVKIFKFTPENNLFYGYILEDMKTGFNILREIMVEGYRPSIARLYDAEDGTQHFTHFADGKCVLIFMAEGNPRIAKVTGEGIAEIVARYPQCQRVDSKLIETWFNNLNWGPDKVAAERVQILKTGNMGFTTEVSGCWSCIHEIYESVINRIRTEFPHADDITMLGGHSSHSYQNGTNMYFVYDYNVVDCKPEEEIDKYHNPLNKIICEETIRLGGSMVHHHGIGKHRVHWSKLEHGSAWALLEGLKKQFDPNGIMNTGTIYPIEK" [] ["CCO-PEROXISOME", "CCO-CYTOSOL"] 0 [] {} 0 +"G7439-MONOMER" "putative FAD-containing dehydrogenase" ["YgcV", "YgcU", "YgcT"] "MSLSRAAIVDQLKEIVGADRVITDETVLKKNSIDRFRKFPDIHGIYTLPIPAAVVKLGSTEQVSRVLNFMNAHKINGVPRTGASATEGGLETVVENSVVLDGSAMNQIINIDIENMQATAQCGVPLEVLENALREKGYTTGHSPQSKPLAQMGGLVATRSIGQFSTLYGAIEDMVVGLEAVLADGTVTRIKNVPRRAAGPDIRHIIIGNEGALCYITEVTVKIFKFTPENNLFYGYILEDMKTGFNILREIMVEGYRPSIARLYDAEDGTQHFTHFADGKCVLIFMAEGNPRIAKVTGEGIAEIVARYPQCQRVDSKLIETWFNNLNWGPDKVAAERVQILKTGNMGFTTEVSGCWSCIHEIYESVINRIRTEFPHADDITMLGGHSSHSYQNGTNMYFVYDYNVVDCKPEEEIDKYHNPLNKIICEETIRLGGSMVHHHGIGKHRVHWSKLEHGSAWALLEGLKKQFDPNGIMNTGTIYPIEK" [] ["CCO-CYTOSOL"] 0 [] {} 0 "G7440-MONOMER" "putative deoxygluconate dehydrogenase" ["YgcW"] "MSIESLNAFSMDFFSLKGKTAIVTGGNSGLGQAFAMALAKAGANIFIPSFVKDNGETKEMIEKQGVEVDFMQVGITAEGAPQKIIAACCERFGTVDILVNNAGICKLNKVLDFGRADWDPMIDVNLTAAFELSYEAAKIMIPQKSGKIINICSLFSYLGGQWSPAYSATKHALAGFTKAYCDELGQYNIQVNGIAPGYYATDITLATRSNPETNQRVLDHIPANRWGDTQDLMGAAVFLASPASNYVNGHLLVVDGGYLVR" [] ["CCO-CYTOSOL"] 0 [] {} 0 "G7442-MONOMER" "putative sugar kinase YgcE" ["YgcE"] "MSKKYIIGIDGGSQSTKVVMYDLEGNVVCEGKGLLQPMHTPDADTAEHPDDDLWASLCFAGHDLMSQFAGNKEDIVGIGLGSIRCCRALLKADGTPAAPLISWQDARVTRPYEHTNPDVAYVTSFSGYLTHRLTGEFKDNIANYFGQWPVDYKSWAWSEDAAVMDKFNIPRHMLFDVQMPGTVLGHITPQAALATHFPAGLPVVCTTSDKPVEALGAGLLDDETAVISLGTYIALMMNGKALPKDPVAYWPIMSSIPQTLLYEGYGIRKGMWTVSWLRDMLGESLIQDARAQDLSPEDLLNKKASCVPPGCNGLMTVLDWLTNPWEPYKRGIMIGFDSSMDYAWIYRSILESVALTLKNNYDNMCNEMNHFAKHVIITGGGSNSDLFMQIFADVFNLPARRNAINGCASLGAAINTAVGLGLYPDYATAVDNMVRVKDIFIPIESNAKRYDAMNKGIFKDLTKHTDVILKKSYEVMHGELGNVDSIQSWSNA" [] ["CCO-CYTOSOL"] 0 [] {} 0 "G7443-MONOMER" "putative 7-carboxy-7-deazaguanine synthase QueE" ["QueE", "YgcF", "putative CDG synthase"] "MQYPINEMFQTLQGEGYFTGVPAIFIRLQGCPVGCAWCDTKHTWEKLEDREVSLFSILAKTKESDKWGAASSEDLLAVIGRQGYTARHVVITGGEPCIHDLLPLTDLLEKNGFSCQIETSGTHEVRCTPNTWVTVSPKLNMRGGYEVLSQALERANEIKHPVGRVRDIEALDELLATLTDDKPRVIALQPISQKDDATRLCIETCIARNWRLSMQTHKYLNIA" ["CCO-CYTOSOL"] ["CCO-CYTOSOL"] 0 [] {"CPD-7": 1, "MG+2": 1} 0 diff --git a/reconstruction/ecoli/flat/rnas.tsv b/reconstruction/ecoli/flat/rnas.tsv index 7e505352c..9da8c3b6b 100644 --- a/reconstruction/ecoli/flat/rnas.tsv +++ b/reconstruction/ecoli/flat/rnas.tsv @@ -1,7 +1,7 @@ # Organism: Escherichia coli K-12 substr. MG1655 # Database: EcoCyc # Version: 28.5 -# Date and time generated: July 18, 2024, 11:03:33 +# Date and time generated: July 19, 2024, 9:41:42 "id" "common_name" "synonyms" "type" "modified_forms" "gene_id" "monomer_ids" "anticodon" "coding_segments" "EG10001_RNA" "alr" ["alr", "alr5", "b4053", "ECK4045"] "mRNA" [] "EG10001" ["ALARACEBIOSYN-MONOMER"] null [] "EG10002_RNA" "modB" ["modB", "chlJ", "tslJ", "b0764", "ECK0753"] "mRNA" [] "EG10002" ["MODB-MONOMER"] null [] diff --git a/reconstruction/ecoli/flat/transcription_units.tsv b/reconstruction/ecoli/flat/transcription_units.tsv index 0d4db8e82..fd3b1771e 100644 --- a/reconstruction/ecoli/flat/transcription_units.tsv +++ b/reconstruction/ecoli/flat/transcription_units.tsv @@ -1,7 +1,7 @@ # Organism: Escherichia coli K-12 substr. MG1655 # Database: EcoCyc # Version: 28.5 -# Date and time generated: July 18, 2024, 11:03:37 +# Date and time generated: July 19, 2024, 9:41:46 "id" "common_name" "genes" "left_end_pos" "right_end_pos" "direction" "evidence" "TU-8381" "spy" ["G6939"] 1825057 1825688 "-" ["EV-EXP-IDA-TRANSCRIPT-LEN-DETERMINATION", "EV-EXP-IDA-BOUNDARIES-DEFINED"] "TU-8382" "ycaC" ["EG11241"] 944931 945557 "-" ["EV-COMP-AINF-SINGLE-DIRECTON"] diff --git a/reconstruction/ecoli/flat/trna_charging_reactions.tsv b/reconstruction/ecoli/flat/trna_charging_reactions.tsv index 9c73d563e..7ce177f6b 100644 --- a/reconstruction/ecoli/flat/trna_charging_reactions.tsv +++ b/reconstruction/ecoli/flat/trna_charging_reactions.tsv @@ -1,7 +1,7 @@ # Organism: Escherichia coli K-12 substr. MG1655 # Database: EcoCyc # Version: 28.5 -# Date and time generated: July 18, 2024, 11:03:38 +# Date and time generated: July 19, 2024, 9:41:47 "id" "stoichiometry" "catalyzed_by" "common_name" "ALANINE--TRNA-LIGASE-RXN_alaT-tRNA" {"L-ALPHA-ALANINE": -1, "ATP": -1, "alaT-tRNA": -1, "PPI": 1, "AMP": 1, "charged-alaT-tRNA": 1} ["ALAS-CPLX"] "ALANYL-TRNA SYNTHETASE" "ALANINE--TRNA-LIGASE-RXN_alaU-tRNA" {"L-ALPHA-ALANINE": -1, "ATP": -1, "alaU-tRNA": -1, "PPI": 1, "AMP": 1, "charged-alaU-tRNA": 1} ["ALAS-CPLX"] "ALANYL-TRNA SYNTHETASE"