fix: GPR curation for transport reactions (6)

[JHL-452b]

Main improvements in this PR:

As proposed in #921 #922 #925 #901 #918

• Remove ENSG00000108932, ENSG00000141526 from MAR06004;
• Remove ENSG00000123643 from MAR05057;
• Remove ENSG00000123643 from MAR05066;
• Remove ENSG00000108932 from MAR06020;
• Remove ENSG00000125454 from MAR06338;
• Remove ENSG00000160190 from MAR06389;
• Remove ENSG00000174669 from MAR07499;
• Remove ENSG00000197818 from MAR07694;
• Remove ENSG00000115902 from MAR07811;
• Remove ENSG00000125454 from MAR07831;
• Remove ENSG00000125454 from MAR07848;
• Remove ENSG00000196517 from MAR09596;
• Remove ENSG00000168065 from MAR09884;
• Remove ENSG00000121270 from MAR10155;
• Remove ENSG00000021488 from MAR01899;
• Remove ENSG00000021488 from MAR01909;
• Remove ENSG00000169710 from MAR04844;
• Remove ENSG00000103064 from MAR05622;
• Remove ENSG00000103064 from MAR05634;
• Remove ENSG00000103064 from MAR05669;
• Remove ENSG00000103064 from MAR05677;
• Remove ENSG00000103064 from MAR05773;
• Remove ENSG00000103064 from MAR05807;
• Remove ENSG00000125454 from MAR07806;
• Remove ENSG00000165349, ENSG00000167703, ENSG00000139514, ENSG00000003989 from MAR05079;
• Remove ENSG00000165349, ENSG00000139514, ENSG00000003989 from MAR05080;
• Remove ENSG00000165349, ENSG00000123643, ENSG00000139514, ENSG00000003989 from MAR05082;
• Remove ENSG00000165349, ENSG00000139514, ENSG00000003989 from MAR05089;
• Remove ENSG00000165349, ENSG00000167703, ENSG00000139514, ENSG00000003989, ENSG00000149150 from MAR05077;
• Remove ENSG00000003989, ENSG00000165349, ENSG00000139514 from MAR05085;
• Remove ENSG00000165349, ENSG00000167703, ENSG00000139514, ENSG00000003989, ENSG00000103257 from MAR05087;
• Remove ENSG00000167703, ENSG00000139514, ENSG00000003989, ENSG00000155465, ENSG00000165349 from MAR05076;
• Remove ENSG00000167703, ENSG00000139514, ENSG00000165349, ENSG00000003989 from MAR05078;
• Remove ENSG00000167703, ENSG00000139514, ENSG00000003989, ENSG00000165349 from MAR05088;
• Remove ENSG00000123643, ENSG00000167703, ENSG00000003989, ENSG00000139514 from MAR05084;
• Remove ENSG00000167703, ENSG00000139514, ENSG00000003989 from MAR05091;
• Remove ENSG00000160190 from the model as it's connected with no 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 1523 dead-end metabolites.
 - Found 1328 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
 - Found 1975 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.

[JHL-452b]

ENSG00000160190 (SLC37A1) encode a protein which play a role as the antiporter for Inorganic phosphate and glucose-6-phosphate. MAR06386 matches the function of SLC37A1. So I think SLC37A1 can be added to the GPR of MAR06386.

[hhl-24]

As proposed in #921 #922 #925 #901 #918
Remove ENSG00000167703, ENSG00000139514, ENSG00000003989, ENSG00000155465, ENSG00000165349 from MAR05076;

ENSG00000165349 was proposed in 920

Remove ENSG00000167703, ENSG00000139514, ENSG00000003989 from MAR05091;

ENSG00000003989 was proposed in 902