fix: correct mechanism and stoichiometry of duplicate transport reactions#1041
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fix: correct mechanism and stoichiometry of duplicate transport reactions#1041edkerk wants to merge 1 commit into
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…ions (#347) Resolves the remaining similar-reaction pairs from #347, which split into distinct mechanistic groups rather than a single "2 vs 1 ATP" problem. Vesicular secretion (SLC18A1/A2/A3, SLC32A1): these transporters are H+ antiporters, but their gradient is across the secretory-vesicle membrane, which the model does not represent, so the ATP acts as a proxy for the V-ATPase loading cost. Standardised to 1 ATP per molecule (Recon3D form), removed the inconsistent HMR 2-ATP-per-3-molecule duplicates, and added a rxnNotes comment. Kept MAR01442,00052,00065,00334,01555,00058,00087,01396, 01314,01518; removed MAR07633-37,07681,07736-38,08922. Na+-multivitamin symport (SLC5A6/SMVT, biotin, pantothenate): removed the spurious ATP and modelled as Na+ symport, 2 Na+ : 1 substrate (PMID:25809983). Kept MAR00094, MAR01636; removed MAR07667, MAR08930. Na+/Cl- symport (SLC6A12/BGT1, betaine, GABA): set coupling to 3 Na+ : 1 Cl- : 1 substrate. Kept MAR09873, MAR09886; removed MAR09603, MAR09604. The GAT reaction MAR09613 (2 Na+ : 1 Cl-) is a distinct transporter and is unchanged. Bile acid / bile-acid-CoA transport (ABC transporters, 2 ATP): kept the HMR 2-ATP form, removed the Recon3D 1-ATP duplicate. Kept MAR01702, MAR01857, MAR01861; removed MAR02283, MAR02290, MAR02298. Sterol 4-methyl oxidation (MSMO1): kept MAR00116 (3 NADPH/3 O2, the correct 3-step monooxygenation), removed MAR02300 (1 NADPH/2 O2). Removed reactions moved to deprecatedReactions.tsv. The sulfate pair (MAR01913/MAR02304) is left for a closer look, as its mechanism is not clearly ABC. All modified reactions remain mass and charge balanced; no genes are orphaned.
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Main improvements in this PR:
Resolves the remaining similar-reaction-with-different-stoichiometry pairs from #347. They split into five mechanistically distinct groups rather than a single 2-vs-1-ATP problem:
rxnNotesnote. Removed MAR07633-37, MAR07681, MAR07736-38, MAR08922.Removed reactions are in
deprecatedReactions.tsv. All modified reactions remain mass and charge balanced; no genes are orphaned. The sulfate pair (MAR01913/MAR02304) is deliberately left for a closer look, as it is not obviously ABC.I hereby confirm that I have:
developas a target branch