Fix Various Issues with Lipoic Acid Biosynthesis

[Devlin-Moyer]

Main improvements in this PR:

As proposed in #685:

• Creates MAM02643m to represent mitochondrial octanoyl-ACP
• Creates MAM02042m to represent mitochondrial HS^-
• Creates MAM01098m to represent mitochondrial 5’-deoxyadenosine
• Creates MAM20084m to represent a mitochondrial 4Fe4S iron-sulfur cluster
• Creates MAM20085m to represent a mitochondrial 2Fe2S iron-sulfur cluster
• Creates MAM20086m to represent mitochondrial GSSH
• Adds all of these genes to Human-GEM:
  • ENSG00000100209, HSCB
  • ENSG00000105755, ETHE1
  • ENSG00000109519, GRPEL1
  • ENSG00000113013, HSPA9
  • ENSG00000135070, ISCA1
  • ENSG00000136003, ISCU2
  • ENSG00000137714, FDX1
  • ENSG00000137767, SQOR
  • ENSG00000165898, ISCA2
  • ENSG00000169599, NFU1
  • ENSG00000181873, IBA57
  • ENSG00000182512, GLRX5
  • ENSG00000214113, LRYM4
  • ENSG00000244005, NFS1
  • ENSG00000267673, FDX2
• Replaces MAM00210c with MAM00210m, MAM00209c with MAM00209m, and MAM00208c with MAM00208m in all of the reactions they participate in
• Replaces all cytosolic metabolites in MAR06404 with their mitochondrial equivalents
• Adds ENSG00000137767 to the GPR of MAR06911
• Changes MAR06402 to MAM02643m -> MAM00210m + MAM02484m, GPR: ENSG00000004779 and ENSG00000140905 and ENSG00000175536, references: PMID:24777537;PMID:28757203
• Changes MAR06403 to MAM00210m + 3 MAM02039m + MAM02555m + 2 MAM02877m + MAM20084m --> MAM00208m + 2 MAM01098m + 4 MAM01821m + 2 MAM02042m + 2 MAM02471m + MAM02554m
  • GPR: (ENSG00000121897 and ENSG00000137714 and ENSG00000140905 and ENSG00000161513 and ENSG00000135070 ) or (ENSG00000121897 and ENSG00000137714 and ENSG00000140905 and ENSG00000161513 and ENSG00000165898) or (ENSG00000121897 and ENSG00000137714 and ENSG00000140905 and ENSG00000161513 and ENSG00000169599)
  • references: PMID:24777537;PMID:31493409;PMID:36281303;PMID:37453661
• Creates MAR20184 to represent synthesis of 4Fe4S iron-sulfur clusters in mitochondria:
  • 2 MAM01371m + 2 MAM02040m + MAM02555m + 2 MAM20085m -> 2 MAM01285m + 3 MAM02039m + MAM02554m + 2 MAM02751m + MAM20084m
  • GPR: ENSG00000100209 and ENSG00000109519 and ENSG00000113013 and ENSG00000135070 and ENSG00000161513 and ENSG00000165898 and ENSG00000181873 and ENSG00000182512 and ENSG00000267673
  • references: PMID:31918395;PMID:31935115
• Creates MAR20185 to represent synthesis of 2Fe2S iron-sulfur clusters in mitochondria:
  • 2 MAM01628m + 2 MAM01821m + MAM02555m -> 2 MAM01307m + MAM02039m + MAM02554m + MAM20085m
  • GPR: ENSG00000004779 and ENSG00000136003 and ENSG00000161513 and ENSG00000165060 and ENSG00000214113 and ENSG00000244005 and ENSG00000267673
  • references: PMID:31918395;PMID:31935115
• Creates MAR20186 to represent the formation of GSSH from GSH and HS^- by SQOR:
  • MAM01802m + MAM02026m + MAM02042m -> MAM01803m + MAM20086m
  • GPR: ENSG00000137767
  • references: PMID:25225291
  • E.C.: 1.8.5.8, KEGG: R11929, RHEA:62608
• Creates MAR20187 to represent the conversion of GSSH into GSH and sulfite by ETHE1:
  • MAM02040m + MAM02630m + MAM20086m -> MAM02026m + 2 MAM02039m + MAM02949m
  • GPR: ENSG00000105755
  • references: PMID:25225291
  • E.C.: 1.13.11.18, KEGG: R08678, RHEA:12981
• Creates MAR20188: MAM01098m -> MAM01098c, references: PMID:34126623 (no GPR)

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]

hmm I'm not seeing whatever YAML formatting issue the tests are apparently finding (although it's weird that the "YAML validation" tests passed but the "Test YAML conversion" ones failed; I feel like they usually either both work or both fail, but I'm not sure what the differences between them are)

[feiranl]

Thanks! will start to review when the new release is published.

[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.