xcpW (PA3098, Q00517) review notes

Review session 2026-10-28 (PseudoCAP IBA-seed protocol)

Fetched with just fetch-gene PSEAE xcpW; accession Q00517 matches the worklist (rank 47,
PA3098). UniProt synonym pddD. No deep-research provider was used; manual notes from cached
publications, PubMed and the UniProt record. PMID:9282737, PMID:21245534 and PMID:1309616 were
cached with ai-gene-review fetch-pmid (abstract only). PMID:8331069 has a PMC id
(PMC204877) but the PubMed MCP full-text call returned an empty body.

What XcpW is

• GspJ-family minor pseudopilin (UniProt "Belongs to the GSP J family"; NCBIfam TIGR01711,
  InterPro IPR010055, Pfam PF11612 T2SSJ, PANTHER PTHR39583:SF2).
• Prepilin-like precursor processed and N-methylated by PilD; inner membrane before and after
  processing [PMID:8331069 "Sequence analysis of XcpT-W has shown that these proteins, like mature
  pilin, contain N-methylphenylalanine as the N-terminal amino acid"; "the precursor forms of
  XcpT-W are located predominantly in the bacterial inner membrane, and their localization is not
  altered after PilD-mediated removal of the leader sequence"].
• Required for excretion: the four pdd genes (= xcpT-W) PMID:1309616.
• Cross-links with PilA and XcpT [PMID:9282737 "XcpW and XcpU can also be crosslinked to form
  dimeric complexes with PilA"; "When expression of XcpT is increased, its homodimers, as well as
  XcpT/XcpW heterodimers, can be detected"].
• Tip complex XcpU-V-W-X; XcpW recruits XcpU PMID:19828448.
• Structure: type IVa pilin fold; disordered C-terminal 31 residues dispensable for secretion
  PMID:21245534.
• XcpVW is the core of the tip; xcpW mutant has reduced LasB secretion, complemented
  [PMID:30346996 "The absence of either XcpV or -W resulted in the non-functional T2SS"; "The
  supernatant of the xcpW mutant also had less LasB activity than the mutants of xcpU and -X"].

PseudoCAP rows

• GO:0015628 IDA PMID:9818381: the paper is a review (FEMS Microbiol Rev 1998, PubMed type Review);
  IDA not supported: full text checked, no original secretion data. Same WRONG_EVIDENCE_CODE / CHECK defect as on xcpX and xcpS. Term correct; primary
  IMP evidence: PMID:30346996, PMID:1309616.
• GO:0015627 IDA PMID:8331069: the paper is primary research (not a review), but its abstract
  reports leader cleavage, N-methylation and inner-membrane fractionation of XcpT-W. That supports
  plasma membrane (UniProt already has EXP from it) but does not assay T2SS complex membership; the
  abstract presupposes it ("Four components of the apparatus of extracellular protein secretion").
  Full text not obtainable. Row accepted (term true; curator saw the full text); recorded a
  SUSPECTED WRONG_REFERENCE / CHECK defect suggesting re-keying to PMID:19828448.

PAINT node identity

The worklist and .cache/paint/seed_support.json place the XcpW seeds at PTN002446812 (terms
GO:0015628, GO:0015627, and GO:0005886 from the UniProt EXP). Current GOA carries only a
GO:0015628 IBA on XcpW, from PTN002218419 with XcpW as WITH/FROM, and no GO:0015627 IBA. QuickGO
has no annotations citing PTN002446812, while PTN002218419 has 618 leaf proteins for GO:0015628,
542 GspJ/T2SS-named (genes/PSEAE/xcpV/xcpV-bioinformatics/RESULTS.md). Likely a PANTHER
version renumbering; not verified. The PAINT file for PTHR39583 is not cached in
interpro/panther/.

PseudoCAP IBA-seed assessment