pvdQ (PA2385, Q9I194) review notes

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

Fetched with just fetch-gene PSEAE Q9I194 --alias pvdQ (first attempt hit a UniProt 429);
accession matches the worklist. Reviewed entry. No deep-research provider was used; literature
from the cached papers. Reviewed together with quiP (PA1032) and PA0305, which share the
PTN002151232 node.

Literature

PMID:16495538 (Sio et al. 2006), full text cached and read. Purified PvdQ deacylates
long-chain AHLs PMID:16495538; GC/MS shows lauric acid release PMID:16495538. No beta-lactam activity PMID:16495538.
Pyoverdine maturation: PMID:19787431; PMID:21892836.
Location: PMID:22498339. The PseudoCAP cytoplasm
IDA from this paper is therefore wrong (it is PvdA that is cytoplasmic/membrane).
Phenotypes (biofilm, swarming, antibiotic resistance) are linked by the authors to pyoverdine
or AHL levels PMID:19778968.
The swarming paper PMID:18245294 used a PA14 mutant.
GO has no AHL acylase term (EC 3.5.1.97); GO:0016811 is the most specific existing term. A
new term is proposed.

Annotation decisions

GO:0016811 (IBA, IDA, IEA): ACCEPT, core MF.
GO:0016787 (IEA): TOO_GENERAL.
GO:0002049 pyoverdine biosynthetic process (IDA, 3x IMP): ACCEPT.
GO:0005737 cytoplasm (IDA): REMOVE; PSEUDOCAP WRONG_TERM -> GO:0042597, CONFIRMED (abstract
states periplasm).
GO:0042597 periplasmic space (IEA): ACCEPT.
GO:0017000 antibiotic biosynthetic process (IEA, InterPro S45): REMOVE.
GO:0042802 identical protein binding (IPI): KEEP_AS_NON_CORE.
GO:0044010, GO:0046677, GO:0071978 x2: MARK_AS_OVER_ANNOTATED (indirect phenotypes).
Action counts: ACCEPT 8, TOO_GENERAL 1, REMOVE 2, KEEP_AS_NON_CORE 1,
MARK_AS_OVER_ANNOTATED 4.

PseudoCAP IBA-seed assessment

Node-level record for PTN002151232 (shared with quiP and PA0305) is kept here.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN002151232	GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	3	21 (13 taxa)	GO:0016811, IDA, PMID:16495538 (PseudoCAP)	SOUND	Purified enzyme deacylates AHLs; fatty acid product shown by GC/MS (full text).	quiP Q9I4U2 (SOUND, heterologous activity in E. coli, full text), PA0305 Q9I6I6 (SOUND, purified enzyme kinetics, abstract)	Yes; each of the three seeds independently supports the node term, which suits an Ntn acylase clade of 21 leaves

No GO_CENTRAL defect on this node. The only PSEUDOCAP defect on pvdQ is the non-seed cytoplasm
row.