fix: update ferrochelatase (FECH) EC number to 4.98.1.1 - #1048
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EC 4.99.1.1 is a transferred entry pointing to EC 4.98.1.1 (protoporphyrin ferrochelatase), following the IUBMB creation of sub-class 4.98 for enzymes forming carbon-metal bonds. Update MAR01044 to the current EC 4.98.1.1. The old code is a deleted entry, so it is replaced rather than kept, to avoid a dead lookup for EC-based tools.
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* feat: fill in missing EC numbers for 236 reactions (#416) Curate EC numbers for metabolic reactions that have a GPR but no EC, keeping to the "fill only the empty fields" approach agreed in the issue. EC numbers were assigned from three sources, preferring reaction-level evidence and requiring gene corroboration: - KEGG reaction -> EC (via rxnKEGGID), which ties the EC to the reaction chemistry; - gene -> EC from UniProt and KEGG (via the geneUniProtID / geneEntrezID already in genes.tsv), used when the gene set gives one unambiguous EC; - MetaNetX reaction EC, used only to disambiguate multifunctional genes. Reactions were left untouched when gene- and reaction-level evidence disagreed, or when a multifunctional gene could not be disambiguated, so no low-confidence EC is introduced. Transport and exchange reactions were excluded, as transporters are classified by TC number rather than EC. All 236 assignments are complete four-part EC numbers, none overwrite an existing value, and a biochemical spot-check confirmed they match the reaction chemistry. EC codes are annotation only, so model structure and balance are unchanged. This leaves 531 metabolic GPR reactions without an EC (multifunctional or without database evidence), better suited to a dedicated GECKO getECfromDatabases run or manual curation. * fix: correct obsolete and erroneous EC numbers (#366) Systematic sweep of the existing EC numbers against the IUBMB/ExPASy ENZYME database (enzyme.dat), addressing the general checking question raised in #366. - 510 reactions updated where an EC had been transferred to a new number, e.g. the ABC-transporter ATPases 3.6.3.44 -> 7.6.2.2 and 3.6.3.1 -> 7.6.2.1 (moved into the translocase class EC 7), and many cytochrome P450 monooxygenases 1.14.13.x -> 1.14.14.x. Transfer chains were followed to the current entry; where one old EC was split into several, the successor was chosen from KEGG reaction and gene evidence, or all closely related successors were kept. - Corrected erroneous EC strings: 1.4.11.1 -> 1.14.11.1 (typo, gamma- butyrobetaine dioxygenase), 2.1.3.85 -> 2.3.1.85 (typo, fatty-acid synthase, matching six sibling reactions), removed the spurious 5.2.2.2 from phosphoglucomutase, and updated the deleted 3.1.2.15 -> 3.4.19.12 (ubiquitinyl hydrolase). Nine reactions with ambiguous deleted or divergent-split ECs are left unchanged for manual review. MAR01044 (FECH, 4.99.1.1 -> 4.98.1.1) is handled separately in #1048. EC codes are annotation only, so model structure and balance are unchanged. * fix: resolve the 9 flagged EC numbers (#366) Resolve the nine reactions left for manual review in the obsolete-EC sweep, by a per-reaction decision against the reaction chemistry, genes, and ExPASy. Reassigned: - MAR06916 -> 7.1.2.2 (proton-translocating ATP synthase; replaces a grab-bag of generic ATPase codes). - MAR07145 -> 4.1.99.22 and 4.6.1.17 (the reaction spans both MOCS1 domains, GTP to cyclic pyranopterin monophosphate). - MAR09473, MAR09482 -> 3.4.17.1 and 3.4.17.15 (carboxypeptidase A, from the CPA1/CPA2/CPA3 gene set). - MAR09491 -> 2.3.2.23, 2.3.2.27 and 6.2.1.45 (the lumped ubiquitin E1/E2/E3 cascade). Removed the obsolete EC where no valid current entry fits the reaction and there is no gene to support one: - MAR04372 (3.1.3.13 deleted; acylphosphatase 3.6.1.7 does not act on bisphosphoglycerate). - MAR08442 (1.2.7.2 deleted, a bacterial ferredoxin enzyme). - MAR04767 (2.4.1.95 deleted; the UDP-glucuronosyltransferase 2.4.1.17 uses a different donor). - MAR03911 (1.8.1.3 deleted, hypotaurine dehydrogenase not substantiated). EC codes are annotation only, so model structure and balance are unchanged. * fix: fill missing EC numbers by gene-consensus propagation (#416) Assign EC numbers to 94 metabolic reactions that had a GPR but no EC. For each, propagate the EC shared by its genes across the model's already-annotated reactions: a full EC where the genes agree exactly, a sub-subclass wildcard (a.b.c.-) where they agree only to that level. Transport/exchange reactions and SLC/ABC transporter genes are excluded as evidence. Every assignment was cross-checked against the gene's UniProt EC. The 94 applied here (35 full, 59 wildcard) are UniProt-confirmed; 13 candidates that UniProt contradicts or cannot support were left out. * fix: fill more EC numbers from UniProt gene annotations (#416) Add EC numbers to 32 further metabolic reactions that had a GPR but no EC, taking the code directly from the UniProt annotation of the reaction's genes: a full EC where the genes agree, a sub-subclass wildcard otherwise. Transport reactions and SLC/ABC genes are excluded; two reactions with a non-catalytic or spurious GPR were left out.
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Main improvements in this PR:
Resolves #366. Ferrochelatase (FECH) was reclassified in the IUBMB Enzyme nomenclature: EC 4.99.1.1 is now a transferred entry pointing to EC 4.98.1.1 (protoporphyrin ferrochelatase), part of the new sub-class 4.98 for enzymes that form carbon-metal bonds.
MAR01044(Ferrochelatase, Mitochondrial)eccodesfrom4.99.1.1to4.98.1.1.The old code is a deleted entry and is replaced rather than kept, to avoid a dead lookup for EC-based tools such as GECKO. Verified against the ExPASy ENZYME database.
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