feat: apply curations from mitoYeast-GEM paper

[BenjaSanchez]

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@CarlMalina made significant curation in the mitochondrial compartment for his project. @CarlMalina would you mind sharing your changes so they can be integrated to the full model? You can make a pull request or just internally provide me with a list of changes, however you prefer

[edkerk]

This is now published with it's repository available here. Probably most of the changes can be directly applied to yeast-GEM.

Scripts can be found here and here.

• [ ] Change the lipid pseudoreaction to include additional lipid species (changeLipidPseudoRxns)
• [ ] Add new mitochondrial reactions (addMitochondrialRxns)
• [ ] Add biotin and ubiquinol to cofactor pseudoreaction (addCofactorsToBiomass)
• [ ] Add mitochondrial aa-tRNAs and prosthetic groups to protein pseudoreaction (changeProteinPseudoReaction)
• [ ] Correct GPR for mitochondrial reactions (updateMitoGPR)
• [ ] Add mitochondrial intermembrane space (IMS) compartment (addIMScomp)
• [ ] Update compartment of metabolites in IMS reactions (correctMetLocalization)
• [ ] Remove incorrect reactions (removeIncorrectRxns)
• [ ] Move reactions to correct compartment, this includes adding the mitochondrial outer membrane compartment (moveReactions)
• [ ] Represent the proton motive force (PMF) in model (addPMFcostToRxns)

More significant changes that might requires some additional discussion before inclusion: the additional compartments (mitochondrial intermembrane space and mitochondrial outer membrane) and representing the PMF