PA3697 (Q9HXU3) notes

No deep-research provider was available; this is a manual literature review
(PubMed search, cached abstracts). Both P. aeruginosa papers are abstract-only.

Identity

UniProt Q9HXU3 (TrEMBL, PE 4 predicted), 431 aa. Name "Flavohemoglobin
expression-modulating QEGLA motif protein" is a ProtNLM machine name
(ECO:0008006), not curated.
Domains: Pfam PF08014 MATCAP (formerly DUF1704), InterPro IPR012548 MATCAP and
IPR012656 CHP02421_QEGLA, NCBIfam TIGR02421 QEGLA, SMART SM01154 DUF1704,
PANTHER PTHR31817. Zn2+ cofactor and the Hydrolase / Metalloprotease / Protease
keywords are ARBA predictions only (unvetted).
The MATCAP domain is named after the animal microtubule-associated tyrosine
carboxypeptidase, a metalloprotease that detyrosinates alpha-tubulin
PMID:35482892. Bacterial members have no characterised
activity; tubulin is absent from P. aeruginosa, so the animal substrate does
not transfer. No activity is proposed here.

Literature

Koskenkorva et al. 2008 (PMID:18043907, PseudoCAP seed paper). The fhp-fhpR
intergenic region was used as bait "to isolate proteins affecting the
transcription of fhp and fhpR", identifying FhpR plus PA0779 and PA3697.
"Both PA0779 and PA3697 were found to be essential for NO3(-) and NO2(-)
induced Pfhp activity under aerobic and low-oxygen conditions, and needed for
the full function of Pfhp/PfhpR as NO responsive regulatory circuit under
aerobic conditions." PMID:18043907. The measured readout is promoter
activity of the flavohemoglobin gene in mutants; NO levels or NO metabolism
were not reported in the abstract. Whether PA3697 binds the promoter directly
(affinity isolation could be indirect or nonspecific) cannot be judged from
the abstract.
Koskenkorva-Frank and Kallio 2009 (PMID:19767835): ROS-induced fhp promoter
activity also depended on FhpR, PA0779 and PA3697 PMID:19767835.
Again a promoter-reporter phenotype.
PubMed searches for PA3697 return only these two papers.

GO term reasoning

GO:0080164 regulation of nitric oxide metabolic process: "Any process that
modulates the frequency, rate or extent of the chemical reactions and pathways
involving nitric oxide". The evidence is that PA3697 is needed for full
induction of the fhp promoter. Fhp detoxifies NO, so an effect on NO
metabolism is a plausible downstream consequence, but it is two steps removed
(gene -> fhp transcription -> Fhp protein -> NO) and was not measured. The
mechanism (direct DNA binding? proteolysis of a regulator, as the MATCAP
domain would suggest?) is unknown. Mutant reporter phenotype ->
INDIRECT-PHENOTYPE.
A more literal reading would be regulation of transcription of fhp (e.g.
GO:0045893 positive regulation of DNA-templated transcription), but without
evidence that PA3697 is a transcription factor or acts directly, proposing it
would just restate the same phenotype with a different term. No NEW.
Node breadth: QuickGO (2026-10-28) lists 175 GO:0080164 IBA rows citing
PANTHER:PTN002422332 (worklist: 5 leaf IBAs in 5 taxa in the reference set).
Leaves include dozens of Legionella spp. (Lfee_, Lbru_, LHA_, ...),
Chondromyces (CMC5_), Planctomycetes (Pla133_, Poly30_) and many other
lineages. A single promoter-fusion phenotype in one Pseudomonas strain, whose
mechanism is unknown and which depends on the presence of the Fhp/FhpR system,
cannot be inherited across such a clade.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002422332	GO:0080164 regulation of nitric oxide metabolic process	1 (sole seed)	5 (5 taxa) in worklist; 175 in current GOA	GO:0080164 regulation of nitric oxide metabolic process, IMP, PMID:18043907 (PseudoCAP)	INDIRECT-PHENOTYPE	The paper shows PA3697 mutants lose NO3-/NO2--induced activity of the flavohemoglobin (fhp) promoter; NO metabolism itself was not measured and the mechanism is unknown. PA3697 is a MATCAP/QEGLA-domain protein of unknown activity (putative metalloprotease, ARBA only), not a known regulator. A reporter phenotype tied to the P. aeruginosa Fhp/FhpR circuit is not a heritable family function, and the node spans Legionella, myxobacteria, planctomycetes and others. The IBD should be withdrawn.

Decisions summary

regulation of nitric oxide metabolic process, IMP: MARK_AS_OVER_ANNOTATED
(real gene-specific phenotype, but the term goes beyond the assay); PSEUDOCAP
WRONG_TERM CHECK (SUSPECTED).
regulation of nitric oxide metabolic process, IBA: MARK_AS_OVER_ANNOTATED
(consistent with the IMP row); GO_CENTRAL defect asking to withdraw the IBD at
PTN002422332.
No core MF can be assigned; core_functions records only the observed role in
fhp expression, without a GO MF.