azoR1 (PA0785, Q9I5F3) notes

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

Fetched with just fetch-gene PSEAE Q9I5F3 --alias azoR1; accession matches the
worklist. Reviewed Swiss-Prot entry. No deep-research provider was used; literature
was gathered from the UniProt record's citations and fetched with just fetch-pmid.
PMID:24915188 and PMID:22355582 have full text in the cache; PMID:17904577,
PMID:20057057, PMID:20417637 and PMID:19666717 are abstract-only. The PubMed MCP
search returned API errors during this session.

Literature

PA0785, annotated as acpD, is an FMN azoreductase
PMID:17904577,
with one FMN per subunit
PMID:17904577.
Quinone reductase activity of the purified enzyme, NADPH as donor
PMID:24915188;
quinones are far better substrates than azo compounds
PMID:24915188.
The paper frames the family as two-electron reducers
PMID:24915188
but did not determine the product.
Nitrofurazone reduction
PMID:22355582.
E. coli ortholog AzoR protects against electrophilic quinones
PMID:19666717.
No P. aeruginosa mutant phenotype is reported for any of the three azoR genes.

Decisions

NEW: GO:0003955 NAD(P)H dehydrogenase (quinone) activity, IDA PMID:24915188 (core).
TOO_GENERAL: catalytic activity (IEA); GO:0016655 (IBA, PseudoCAP IDA, IEA).
MODIFY: GO:0003960 quinone reductase (NADPH) activity (EXP, IEA Rhea) to
GO:0003955, because GO:0003960 is the semiquinone-forming reaction (UNIPROT
WRONG_TERM, SUSPECTED).
ACCEPT: FMN binding (IEA).
KEEP_AS_NON_CORE: response to oxidative stress (IBA PTN000811013, E. coli seed).
MARK_AS_OVER_ANNOTATED: electron transfer activity (IEA), consistent with PA0949.
REMOVE: GO:0016652 (NAD(P)+ as acceptor; UniRule mapping wrong; UNIPROT
WRONG_TERM, CONFIRMED by the GO definition). This defect is recorded once, here;
the same UniRule row on azoR2 and azoR3 cross-references it.
Counts: NEW 1, TOO_GENERAL 4, MODIFY 2, ACCEPT 1, KEEP_AS_NON_CORE 1,
MARK_AS_OVER_ANNOTATED 1, REMOVE 1.

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?
PTN000024600	GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	4	38 (25 taxa)	GO:0016655, IDA, PMID:24915188 (PseudoCAP)	SOUND	Full text read: purified paAzoR1 assayed with a quinone panel (NADPH oxidation at 340 nm). The term is correct; GO:0003955 is the specific child, added as NEW.	E. coli AzoR (P41407; EcoCyc IDA GO:0016655, PMID:19666717); paralogs azoR2 (Q9I2E2) and azoR3 (Q9HZ17), same paper	Yes; E. coli AzoR alone carries independent experimental evidence

No PSEUDOCAP and no GO_CENTRAL defect. The node term is the general quinone-acceptor
term, which suits a 38-leaf, 25-taxon clade of azoreductase type 1 proteins
(HAMAP MF_01216) in which quinone reduction has been shown in both E. coli and
P. aeruginosa. The three P. aeruginosa paralogs are seeds of the same node from
the same paper; their seed verdicts (SOUND) and actions are kept consistent in the
azoR2 and azoR3 reviews.

Other defects (not node-level): UNIPROT WRONG_TERM on the GO:0003960 EXP row
(SUSPECTED); UNIPROT WRONG_TERM on the UniRule UR000101231 GO:0016652 mapping
(CONFIRMED), recorded here only.