arcB (PA5172, P08308) review notes

Literature

arcB defines the catabolic ornithine carbamoyltransferase of the arginine deiminase (ADI) pathway; arc mutants were isolated as unable to grow anaerobically on arginine PMID:6438064 and PMID:6438064.
UniProt (curated, with PubMed evidence): the enzyme catalyses citrulline phosphorolysis to ornithine and carbamoyl phosphate, feeding ATP generation, and does not perform the biosynthetic reaction [file:PSEAE/arcB/arcB-uniprot.txt "This catabolic OTCase does not carry out the biosynthetic reaction because of a poor affinity and a marked cooperativity for carbamoyl phosphate"]; it is allosterically regulated (activated by phosphate and nucleoside monophosphates, inhibited by polyamines) and dodecameric; disruption blocks the ADI pathway.
arcA (PA5171) is reviewed in genes/PSEAE/arcA/; that review uses GO:0006527 L-arginine catabolic process as the process term (GO has no ADI-pathway-specific term), and this review follows it.

Search: PubMed metadata for PMID:6438064 (abstract only; PMC215798 exists but was not retrieved). UniProt-cited primary papers (PMID:2118516, 4962140, 8102605, 3109911) are not in the publication cache; their content is used only via the curated UniProt statements. NCBI E-utilities and Europe PMC search were unavailable (HTTP 500/503) during this session.

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?
PTN000150424	GO:0004585 ornithine carbamoyltransferase activity	9	157 (119 taxa)	GO:0004585, IMP, PMID:6438064	SOUND	arcB mutants lack catabolic OTC activity and the locus was later shown to be the structural gene (purified enzyme, sequence). Loss of activity in mutants is weak evidence on its own, but the term is correct.	S. pombe Arg3 (SPAC4G9.10), rat Otc (RGD:3236), M. tuberculosis ArgF (P9WIT9), E. coli ArgI/ArgF (P04391, P06960), human OTC (P00480), yeast Arg3 (SGD:S000003624), Q9YHY9	Yes

Node term suits the clade (all members are OTCs). No GO_CENTRAL defect for the seed node term.

Separate propagation problem (not a PseudoCAP seed): the same node carries IBDs of GO:0006526 L-arginine biosynthetic process (seeds yeast Arg3, Q4WNW5, Mtb ArgF, S. pombe Arg3) and GO:0019240 citrulline biosynthetic process (rat, human, E. coli ArgI/ArgF). Both propagate to catabolic ArcB, which runs the reaction in the citrulline-consuming direction and cannot carry out the biosynthetic reaction. Both IBA rows are removed, and one GO_CENTRAL defect (requesting a NOT/withheld propagation for the catabolic OTC subclade) is recorded on the GO:0006526 IBA row; the GO:0019240 row cross-references it. The UniRule-derived IEA to GO:0006526 is likewise removed with a UNIPROT defect.