Fix: GPR curation for Carnitine shuttle

[JHL-452b]

Main improvements in this PR:

As proposed in #871 #872 #873 #874

• Remove ENSG00000197119 from MAR02592;
• Remove ENSG00000197119 from MAR02596;
• Remove ENSG00000149742, ENSG00000197119 from MAR02600;
• Remove ENSG00000149742, ENSG00000197119, ENSG00000175003 from MAR02603;
• Remove ENSG00000149742, ENSG00000197119, ENSG00000175003 from MAR02606;
• Remove ENSG00000149742, ENSG00000197119 from MAR02609;
• Remove ENSG00000149742, ENSG00000197119 from MAR02612;
• Remove ENSG00000149742, ENSG00000197119 from MAR02616;
• Remove ENSG00000149742, ENSG00000197119 from MAR02621;
• Remove ENSG00000149742, ENSG00000197119 from MAR02624;
• Remove ENSG00000149742, ENSG00000197119 from MAR02629;
• Remove ENSG00000149742, ENSG00000197119 from MAR02634;
• Remove ENSG00000149742, ENSG00000197119 from MAR02638;
• Remove ENSG00000149742, ENSG00000197119, ENSG00000175003 from MAR02644;
• Remove ENSG00000149742, ENSG00000197119 from MAR02649;
• Remove ENSG00000149742, ENSG00000197119 from MAR02652;
• Remove ENSG00000149742, ENSG00000197119, ENSG00000175003 from MAR02655;
• Remove ENSG00000149742, ENSG00000197119 from MAR02658;
• Remove ENSG00000149742, ENSG00000197119 from MAR02661;
• Remove ENSG00000149742, ENSG00000197119 from MAR02664;
• Remove ENSG00000149742, ENSG00000197119 from MAR02667;
• Remove ENSG00000149742, ENSG00000197119 from MAR02670;
• Remove ENSG00000149742, ENSG00000197119 from MAR02673;
• Remove ENSG00000149742, ENSG00000197119, ENSG00000175003 from MAR02676;
• Remove ENSG00000149742, ENSG00000197119 from MAR02679;
• Remove ENSG00000149742, ENSG00000197119 from MAR02682;
• Remove ENSG00000149742, ENSG00000197119 from MAR02685;
• Remove ENSG00000149742, ENSG00000197119 from MAR02688;
• Remove ENSG00000149742, ENSG00000197119 from MAR02691;
• Remove ENSG00000149742, ENSG00000197119 from MAR02695;
• Remove ENSG00000149742, ENSG00000197119 from MAR02700;
• Remove ENSG00000149742, ENSG00000197119 from MAR02703;
• Remove ENSG00000149742, ENSG00000197119 from MAR02706;
• Remove ENSG00000149742, ENSG00000197119 from MAR02709;
• Remove ENSG00000149742, ENSG00000197119 from MAR02712;
• Remove ENSG00000197119 from MAR02715;
• Remove ENSG00000149742, ENSG00000197119 from MAR02718;
• Remove ENSG00000149742, ENSG00000197119 from MAR02722;
• Remove ENSG00000149742, ENSG00000197119 from MAR02727;
• Remove ENSG00000149742, ENSG00000197119 from MAR02731;
• Remove ENSG00000149742, ENSG00000197119, ENSG00000175003 from MAR02734;
• Remove ENSG00000149742, ENSG00000197119 from MAR02737;
• Remove ENSG00000149742, ENSG00000197119 from MAR02740;
• Remove ENSG00000197119 from MAR02744;
• Remove ENSG00000149742, ENSG00000197119, ENSG00000175003 from MAR02748;
• Remove ENSG00000149742, ENSG00000197119 from MAR02753;
• Remove ENSG00000149742, ENSG00000197119 from MAR02757;
• Remove ENSG00000149742, ENSG00000197119, ENSG00000175003 from MAR02760;
• Remove ENSG00000149742, ENSG00000197119 from MAR02764;
• Remove ENSG00000169169 from MAR02768;
• Remove ENSG00000149742, ENSG00000197119 from MAR02769;
• Remove ENSG00000197119 from MAR02772;
• Remove ENSG00000197119 from MAR02775;
• Remove ENSG00000197119 from MAR02783;
• Remove ENSG00000169169 from MAR02924;
• Remove ENSG00000197119 from MAR03033;
• Remove ENSG00000197119 from MAR03035;
• Add PubMed:10215651, PubMed:15107849, PubMed:16729965 to the references of MAR02629;
• Add PubMed:10215651, PubMed:15107849, PubMed:16729965 to the references of MAR02734;
• Add PubMed:10215651, PubMed:15107849, PubMed:16729965 to the references of MAR02655;
• Remove ENSG00000197119 from model as it's not connected to any reactions after this curation.

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.

[feiranl]

LGTM!