argA (PA5204, P22567) review notes

Literature summary

ArgA is the classical NAGS, the first enzyme of arginine biosynthesis PMID:22447897, using acetyl-CoA as the acetyl donor PMID:22447897.
The activity assays in this paper use glutamate plus acetyl-CoA PMID:22447897.
Domain dissection: PMID:22447897; PMID:22447897.
The UniProt record gives the acetyl-CoA reaction (RHEA:24292) and the HAMAP rule MF_01105 (N_acetyl_glu_synth).

Literature search (2026-11-05): PubMed MCP and NCBI E-utilities failed all session; Europe PMC search was
intermittent. The review rests on PMID:22447897 (full text cached, read), the UniProt record, and live QuickGO
queries for the E. coli seed P0A6C5 and for the GO:0004042/GO:0004358 definitions and synonyms.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN004744913	GO:0006526 L-arginine biosynthetic process	2	95 (48 taxa)	GO:0006526, IMP, PMID:22447897	SOUND	ArgA catalyses the first step of the pathway. The evidence is biochemical (IDA would be the better code), but the claim is right.	E. coli ArgA P0A6C5 (EcoCyc IMP PMID:1102931, IDA PMID:17651682)	Yes; E. coli ArgA IMP/IDA
PTN004744913	GO:0004358 L-glutamate N-acetyltransferase activity, acting on acetyl-L-ornithine as donor	2	95 (48 taxa)	GO:0004358, IMP, PMID:22447897	WRONG	Full text read: all assays use acetyl-CoA plus glutamate (GO:0004042). GO:0004358 is the ArgJ ornithine-acetyltransferase reaction. The two terms share the synonyms "N-acetylglutamate synthase activity" and "L-glutamate N-acetyltransferase activity" (checked in QuickGO), the likely cause.	E. coli ArgA P0A6C5 (EcoCyc IDA PMID:16890, PMID:17651682), same error: E. coli ArgA is also the acetyl-CoA NAGS (UniProt P0A6C5 reaction; PMID:16890 is titled "N-acetylglutamate synthase of Escherichia coli")	No. The only other seed has the same error, so the node term is wrong for the ArgA clade. GO_CENTRAL defect filed (CONFIRMED), repoint to GO:0004042

Defects filed on this gene:

PSEUDOCAP WRONG_TERM on the GO:0004358 IMP row, CONFIRMED (full text read), repoint to GO:0004042.
GO_CENTRAL WRONG_TERM on the GO:0004358 IBA row (node PTN004744913), CONFIRMED, repoint to GO:0004042.
UNIPROT WRONG_TERM on the ARBA00086662 GO:0004358 IEA row, PROBABLE.
Not filed here (another resource's record on another gene): the EcoCyc GO:0004358 IDA rows on E. coli ArgA P0A6C5
have the same error and should be repointed to GO:0004042.

Action summary

10 rows. MODIFY 4 (GO:0004358 IBA, IEA and IMP to GO:0004042; GO:0016747 IEA to GO:0004042); ACCEPT 5
(GO:0006526 x3, GO:0004042 IEA, GO:0005737 IEA); KEEP_AS_NON_CORE 1 (GO:0042802 IPI).