PA1204 (Q9I4D4) review notes

Literature

Crystal structure (1.28 A) of Q9I4D4, an NAD(P)H-dependent FMN reductase; FMN binding confirmed and an unusual FMN-binding motif identified PMID:16552139; activity PMID:16552139.
P. aeruginosa orthologs of MdaB, ChrR, WrbA, NfsB and NQO1 reduce quinones in vitro by a two-electron route PMID:25085734; only WrbA and MdaB overexpression protected a katA mutant from H2O2 PMID:25085734.
Ryan et al. place PA1204 among putative azoreductases by structure and cite its quinone reductase activity PMID:24915188; PA1204 is in the BexR-repressed pa1202-pa1205 operon PMID:24915188.
PANTHER places PA1204 in PTHR30543 (chromate reductase), subfamily SF21 (Lot6-like); UniProt: SsuE family.

Search: PubMed metadata for all GOA-cited PMIDs; PMID:24915188 full text cached and read for PA1204 passages; PMID:25085734 and PMID:16552139 abstract only. 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?
PTN001254275	GO:0003955 NAD(P)H dehydrogenase (quinone) activity	4	167 (74 taxa)	GO:0003955, IMP, PMID:25085734	SOUND	The abstract reports in vitro quinone reduction by the purified P. aeruginosa orthologs, and Ryan et al. name PA1204 among them. The term is right; the evidence code should be IDA (PSEUDOCAP WRONG_EVIDENCE_CODE, PROBABLE).	yeast Lot6 (SGD:S000004001), E. coli ChrR (P0AGE6), Synechocystis ArsH (P74312), all characterised quinone reductases	Yes

Node term suits the clade (SsuE/ChrR/ArsH/Lot6 FMN-dependent quinone reductases). No GO_CENTRAL defect.

Other PseudoCAP row: GO:0016655 IDA from PMID:24915188 is true but the paper only cites PA1204's activity (WRONG_EVIDENCE_CODE, PROBABLE); set TOO_GENERAL because GO:0003955 is_a GO:0016655.

The GO:0034599 IBA rests on yeast Lot6 alone; no oxidative-stress phenotype has been shown for PA1204, so marked over-annotated (not a seed of this gene).