Fix Peroxisomal Cofactor Transport Reactions

[Devlin-Moyer]

Main improvements in this PR:

As proposed in #640:

• Removes MAR07785 for being a less accurate/complete duplicate of MAR04908
• Removes MAR07775 because there's no evidence that NADH is transported across the peroxisomal membrane
• Removes MAR07788 because there’s no evidence that FADH₂ is transported across the peroxisomal membrane
• Removes MAR04915, MAR07771, MAR07782, MAR07783, and MAR07790 because the only known peroxisomal transporters of those metabolites catalyze antiport, not uniport
• Changes MAR03473 to be ADP [c] + AMP [x] <-> ADP [x] + AMP [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20115: AMP [c] <-> AMP [x], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20116: ADP [c] <-> ADP [x], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new FMN [x] metabolite MAM01828x
• Adds new reaction MAR20117: FAD [x] + H₂O [x] -> FMN [x] + AMP [x], GPR: ENSG00000112874, reference: PMID:22185573
• Adds new reaction MAR20118: FMN [c] + CoA [x] <-> FMN [x] + CoA [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20119: FMN [c] + FAD [x] <-> FMN [x] + FAD [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20120: FMN [c] + NAD⁺ [x] <-> FMN [x] + NAD⁺ [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20121: FMN [c] + AMP [x] <-> FMN [x] + AMP [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20122: FMN [c] + ADP [x] <-> FMN [x] + ADP [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20123: FAD [c] + CoA [x] <-> FAD [x] + CoA [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20124: FAD [c] + NAD⁺ [x] <-> FAD [x] + NAD⁺ [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20125: FAD [c] + AMP [x] <-> FAD [x] + AMP [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20126: FAD [c] + ADP [x] <-> FAD [x] + ADP [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20127: NAD⁺ [c] + CoA [x] <-> NAD⁺ [x] + CoA [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20128: NAD⁺ [c] + AMP [x] <-> NAD⁺ [x] + AMP [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20129: NAD⁺ [c] + ADP [x] <-> NAD⁺ [x] + ADP [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20130: AMP [c] + CoA [x] <-> AMP [x] + CoA [c], GPR: ENSG00000100372, reference: PMID:22185573
• Adds new reaction MAR20131: ADP [c] + CoA [x] <-> ADP [x] + CoA [c], GPR: ENSG00000100372, reference: PMID:22185573

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

[Devlin-Moyer]

I can't figure out why the YAML conversion checks are failing; I feel like that's usually due to a formatting issue where like I didn't indent a particular line right or misspelled one of the field names, but I keep failing to see any of those kinds of typos.

[haowang-bioinfo]

yes there are formatting issues that should be due to the missing "eccodes" fields from MAR20117 onward

I wonder how did you output the yaml file, which function did you use? @Devlin-Moyer

[Devlin-Moyer]

aha thanks for spotting that; I'll fix it when I get back to my computer

also I've been editing it directly with a text editor cuz I don't know Matlab and found out the hard way that Cobrapy doesn't output YAML files in this exact format and it seemed easier (if more tedious) to just do it by hand than figure out what changes I'd need to make Cobrapy's yaml output

[haowang-bioinfo]

editing directly with a text editor is fine but not optimal way, which might end up with something mentioned in #558

[feiranl]

LGTM! Good job!

[haowang-bioinfo]

@Devlin-Moyer great job! a small thing: MAR20117 is not fully balanced - now fixed in 3eb0817

@feiranl probably at some point it's good to have a mass/charge balance check for new reactions?

[feiranl]

Yes, I totally agree. A new issue has been opened to address this.

[Devlin-Moyer]

ah thanks for catching that. and yea, incorporating that into the automated checks would be very useful, because it's easy to miss a few protons like I did here, and #670 would've been way easier to resolve if one of the automated checks had told us that one of those edits un-balanced a reaction