fix: GPR curation for transport reactions (7)

[JHL-452b]

Main improvements in this PR:

As proposed in #902 #918 #920 #925

• Remove ENSG00000165349, ENSG00000139514, ENSG00000003989 from MAR05092;
• Remove ENSG00000165349, ENSG00000139514, ENSG00000003989 from MAR05315;
• Remove ENSG00000174358, ENSG00000178537 from MAR05330;
• Remove ENSG00000148942 from MAR05450;
• Remove ENSG00000165029 from MAR05528;
• Remove ENSG00000165029 from MAR05529;
• Remove ENSG00000165029 from MAR05530;
• Remove ENSG00000165029 from MAR05531;
• Remove ENSG00000165029 from MAR05532;
• Remove ENSG00000165029 from MAR05534;
• Remove ENSG00000165029 from MAR05535;
• Remove ENSG00000165029 from MAR05536;
• Remove ENSG00000165029 from MAR05537;
• Remove ENSG00000165029 from MAR05538;
• Remove ENSG00000165029 from MAR05539;
• Remove ENSG00000165029 from MAR05541;
• Remove ENSG00000188687 from MAR05547;
• Remove ENSG00000103257 from MAR05565;
• Remove ENSG00000103257 from MAR05566;
• Remove ENSG00000103064 from MAR05600;
• Remove ENSG00000103064 from MAR05604;
• Remove ENSG00000103064 from MAR05605;
• Remove ENSG00000103064 from MAR05607;
• Remove ENSG00000103064 from MAR05609;
• Remove ENSG00000103064 from MAR05610;
• Remove ENSG00000103064, ENSG00000103257 from MAR05597;
• Remove ENSG00000103257, ENSG00000103064 from MAR05599;
• Remove ENSG00000165349, ENSG00000139514, ENSG00000003989, ENSG00000111371 from MAR05319;
• Remove ENSG00000139514, ENSG00000003989, ENSG00000165349 from MAR05305;
• Remove ENSG00000103064, ENSG00000103257 from MAR05613;
• Remove ENSG00000148942 from the model as it's connected 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.

[hhl-24]

Remove ENSG00000103064, ENSG00000103257 from MAR05613;

ENSG00000103257 was proposed in 904

[JHL-452b]

Reaction ID	issues
MAR05092, MAR05315, MAR05330, MAR05450, MAR05528, MAR05529, MAR05530, MAR05531, MAR05532, MAR05534, MAR05535, MAR05536, MAR05537, MAR05538, MAR05539, MAR05541, MAR05547, MAR05565, MAR05566, MAR05600, MAR05604, MAR05605, MAR05607, MAR05609, MAR05610	902
MAR05597, MAR05599	902, 918
MAR05319	902, 920
MAR05305	902, 925
MAR05613	902, 903

In this PR, the main focus is on the reactions related to 902. Among these reactions, some have also been mentioned in other issues. To avoid conflicts, duplicate reactions mentioned in other issues are also being addressed and curated here together. For specific details, refer to the content in the table above.