astB (aruB, PA0899, O50175) review notes

Review session 2026-11-05 (PseudoCAP IBA-seed protocol, tier 2)

Fetched with just fetch-gene PSEAE O50175 --alias astB; accession matches the worklist. No
deep-research provider used. PMID:16593724 and PMID:9393691 are abstract-only (PubMed MCP returned
no body for PMC323859 or PMC179677).

Literature

AST pathway defined in P. aeruginosa from aru mutants and crude-extract enzyme assays
PMID:16593724
Some aru mutants accumulated N2-succinylarginine, the expected phenotype of a dihydrolase block.
Genes assigned later PMID:9393691.
Family: Pfam AstB (PF04996), HAMAP MF_01172, NCBIfam TIGR03241. PANTHER puts AstB in
PTHR30420:SF2, but the same PANTHER family also holds the unrelated AstA/AruG
succinyltransferases (SF1, Pfam AstA, GNAT-like acyl-CoA N-acyltransferase fold).

Annotation decisions

ACCEPT: GO:0009015 (IBA, IEA), GO:0006527 (IDA, IBA, IEA).
TOO_GENERAL: GO:0006525 arginine metabolic process (IEA); GO:0006527 is_a GO:0006525.
Pathway-specific children of GO:0006527 (GO:0019544, GO:0019545) are obsolete, so GO:0006527 is
as precise as GO allows.
Action counts: ACCEPT 5, TOO_GENERAL 1. No source defects on this gene.

PseudoCAP IBA-seed assessment

PTN000764516 is shared with astA (PA0896) and aruG (PA0897); verdicts are kept consistent. The
node-level GO_CENTRAL defect for the GO:0009015 IBD (dihydrolase placed at a node that also covers
the AstA succinyltransferase subfamily) is recorded once, on astA. On astB itself the GO:0009015
IBA is correct.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000764516	GO:0006527 L-arginine catabolic process	4	12 (6 taxa)	GO:0006527, IDA, PMID:16593724 (PseudoCAP)	SOUND	The term is right for AstB (step 2 of the AST pathway). The 1986 paper defines the pathway by extract assays and aru mutants; gene identity came in PMID:9393691, so the paper supports the pathway rather than naming this locus. Abstract only.	E. coli AstB P76216 (IMP PMID:9696779), astA P80357, aruG P80358 (same PseudoCAP paper)	Yes (E. coli AstB)
PTN000764516	GO:0009015 N-succinylarginine dihydrolase activity	1	12	not seeded by astB (sole seed E. coli AstB P76216, IDA PMID:15703173)	n/a	Correct for the AstB subfamily; wrongly inherited by AstA/AruG leaves.	—	Stands for SF2; defect recorded on astA