fix-GPR_curation_for_Serotonin and melatonin biosynthesis and Keratan…

[JHL-452b]

… sulfate biosynthesis

Main improvements in this PR:

As proposed in #861 and #863

• Remove ENSG00000171004, ENSG00000166507, ENSG00000140835, ENSG00000164100, ENSG00000154252, ENSG00000136720, ENSG00000183196, ENSG00000185352, ENSG00000111962, ENSG00000175040, ENSG00000175229, ENSG00000198075, ENSG00000124302 from MAR04549;
• Remove ENSG00000175711 from MAR07336;
• Remove ENSG00000175711 from MAR07338;
• Remove ENSG00000135702 from MAR07339;
• Remove ENSG00000175711 from MAR07341;
• Remove ENSG00000135702 from MAR07345;
• Remove ENSG00000175711 from MAR07347;
• Remove ENSG00000135702 from MAR07351;
• Remove ENSG00000135702 from MAR07354;
• Remove ENSG00000135702 from MAR07357;
• Remove ENSG00000175711 from MAR07359;
• Remove ENSG00000135702 from MAR07360;
• Remove ENSG00000175711 from MAR07362;
• Remove ENSG00000135702 from MAR07363;
• Remove ENSG00000175711 from MAR07365;
• Remove ENSG00000135702 from MAR07366;
• Remove ENSG00000175711 from MAR07368;
• Remove ENSG00000175711 from MAR07444;
• Remove ENSG00000175711 from MAR07446;
• Remove ENSG00000175711 from MAR07449;
• Remove ENSG00000175711 from MAR07473;
• Remove ENSG00000175711 from MAR07475;
• Remove ENSG00000135702 from MAR07479;
• Remove ENSG00000175711 from MAR07353;
• Remove ENSG00000135702 from MAR07342;
• Remove ENSG00000175711 from MAR07344;
• Remove ENSG00000135702 from MAR07348;
• Remove ENSG00000175711 from MAR07350;
• Remove ENSG00000175711 from MAR07356;
• Remove ENSG00000135702 from MAR07447;
• Remove ENSG00000135702 from MAR07476;
• Remove ENSG00000175711 from MAR07478.

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

[github-actions]

This PR has been automatically tested with GH Actions. Here is the output of the MACAW test:

Starting dead-end test...
 - Found 1514 dead-end metabolites.
 - Found 1319 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
 - Found 1977 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
 - Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
 - Found 447 reactions that were some type of duplicate:
   - 0 were completely identical to at least one other reaction.
   - 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
   - 447 involve the same metabolites but with different coefficients as at least one other reaction.

This and a more detailed output from MACAW are also committed to data/macawResults/.

Note: In the case of multiple test runs, this post will be edited.