pvdD (PA2399, Q9I182) notes

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

Fetched with just fetch-gene PSEAE Q9I182 --alias pvdD; accession matches the
worklist. Unreviewed TrEMBL entry. No deep-research provider was used. NCBI
E-utilities, Europe PMC and the PubMed MCP search were unavailable (errors/503);
the PMC copy of PMID:12700264 returned no body text. All three seed papers were
read as abstracts.

Literature

Two NRPS modules (C-A-PCP x2) plus a C-terminal thioesterase (PF00975), PTHR45527.
PMID:15271355
PMID:15271355
PMID:12700264
The abstract describes only the purified first module, no mutant.
PMID:9770291
pvdD is an expression read-out in this quorum-sensing paper.

Decisions

ACCEPT: pyoverdine biosynthetic process (IMP x3; two with defects), cytosol
(IBA), phosphopantetheine binding (IBA, IEA).
MODIFY: catalytic activity (IMP x3, IEA) -> GO:1904091 non-ribosomal peptide
synthetase activity; obsolete GO:0043041 (IBA, IEA) -> GO:0002049.
TOO_GENERAL: cytoplasm (IBA), secondary metabolite biosynthetic process (IBA, IEA).
Counts: ACCEPT 6, MODIFY 6, TOO_GENERAL 3.

PseudoCAP IBA-seed assessment

PTN002378821 is a broad NRPS node (72 leaf IBAs, 22 taxa) with 13 seeds; PvdD and
PvdJ (genes/PSEAE/pvdJ) are the two PAO1 seeds. The node-level assessment is
recorded here, on the gene with the most direct evidence; pvdJ cross-references it.

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:15271355 (PseudoCAP)	SOUND	pvdD mutant makes no pyoverdine and is complemented; PvdD is the NRPS that incorporates two L-Thr, so it does part of the work. Pyoverdine biosynthesis is_a the node term.	E. coli EntF (P11454), S. pombe SPAC23G3.02c, Aspergillus NRPSs (Q4WYG2, Q5BFS3, Q4WMJ7, C8VPS9, Q4WR82, Q4WLW8, Q4WAW3, Q4WF53), M. tuberculosis P9WQ63, PvdJ (Q9I181)	Yes; eleven non-Pseudomonas NRPS seeds
PTN002378821	same	13	72	GO:0002049, IMP, PMID:12700264 (PseudoCAP)	SOUND	Term right (purified module activates L-Thr, a pyoverdine residue); evidence should be IDA, not IMP (PSEUDOCAP WRONG_EVIDENCE_CODE, PROBABLE).	as above	Yes
PTN002378821	same	13	72	GO:0002049, IMP, PMID:9770291 (PseudoCAP)	UNVERIFIABLE	Abstract uses pvdD as an expression read-out in lasR/lasI mutants and reports no pvdD mutant; a pvdD control strain could be in the full text (PSEUDOCAP WRONG_REFERENCE, SUSPECTED).	as above	Yes

The node term is generic enough for a clade of NRPSs making different products and
suits it. No GO_CENTRAL defect. Defects: PSEUDOCAP 2 (one PROBABLE, one SUSPECTED),
each recorded once on the GO:0002049 row and covering the paired GO:0003824 row.