pvdJ (PA2400, Q9I181) notes

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

Fetched with just fetch-gene PSEAE Q9I181 --alias pvdJ; accession matches the
worklist. Unreviewed TrEMBL entry. No deep-research provider was used. NCBI
E-utilities, Europe PMC and PubMed MCP search were unavailable; a search of the
local publication cache for "pvdJ" found no PAO1 pvdJ mutant study (hits were
P. syringae, P. putida, PA14 genomics and expression papers).

Literature

Two NRPS modules (C-A-PCP x2), PTHR45527:SF1; adjacent to pvdD (PA2399).
PAO1 pyoverdine NRPSs PMID:15271355
(abstract only; PvdJ is not named in the abstract).
The PseudoCAP seed paper is about another species, read in full:
PMID:19854904;
its pvdJ is described as a PMID:19854904 (an L-Thr-L-Ser component).

Decisions

ACCEPT: pyoverdine biosynthetic process (IMP; claim true, evidence defect),
cytosol (IBA), phosphopantetheine binding (IBA, IEA).
MODIFY: catalytic activity (IMP, IEA) -> GO:1904091; obsolete GO:0043041 (IBA,
IEA) -> GO:0002049.
TOO_GENERAL: cytoplasm (IBA), secondary metabolite biosynthetic process (IEA).
REMOVE: enterobactin biosynthetic process, enterobactin synthetase complex,
2,3-dihydroxybenzoate-serine ligase activity (IBA from E. coli EntF at
PTN002378853; P. aeruginosa makes no enterobactin).
Counts: ACCEPT 4, MODIFY 4, TOO_GENERAL 2, REMOVE 3.

PseudoCAP IBA-seed assessment

Node-level assessment for PTN002378821 is recorded in genes/PSEAE/pvdD/pvdD-notes.md
(PvdD has the direct PAO1 evidence); summary below.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN002378821	GO:0044550 secondary metabolite biosynthetic process	13	72 (22 taxa)	GO:0002049, IMP, PMID:19854904 (PseudoCAP)	WRONG	The mutant is P. syringae pv. tabaci 6605 pvdJ, not PAO1 PA2400; an IMP cannot rest on another species' mutant (PSEUDOCAP WRONG_EVIDENCE_CODE, CONFIRMED, full text read). The claim itself is true for PAO1 PvdJ on other grounds, so the error is in the evidence, not the term.	PvdD (PAO1 mutant, PMID:15271355) plus eleven non-Pseudomonas NRPS seeds (EntF, Aspergillus, S. pombe, M. tuberculosis)	Yes

No GO_CENTRAL defect for PTN002378821. Separately, the EntF-seeded
enterobactin-specific IBDs at PTN002378853 reach PvdJ; they are REMOVEd here with
propagation_review and raised as a suggested question, not filed as a GO_CENTRAL
defect, because that node is not one PvdJ seeds.