xcpS (PA3102, Q00513) review notes

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

Fetched with just fetch-gene PSEAE xcpS (first attempt timed out at UniProt, second succeeded);
accession Q00513 matches the worklist (rank 46, PA3102). No deep-research provider was used;
these are manual notes from the cached publications, PubMed searches and the UniProt record.
Publications PMID:17464073, PMID:18832308 (and, not used, PMID:12581354, PMID:1389315) were
cached with ai-gene-review fetch-pmid; all abstract-only.

What XcpS is

GspF-family inner-membrane platform protein of the Xcp T2SS. UniProt: "Belongs to the GSP F
family"; NCBIfam TIGR02120 (GspF), InterPro IPR011850 (T2SS_GspF), PANTHER PTHR30012:SF0.
Similar to type IV pilus PilC PMID:1588814.
Inner-membrane core component; stabilised by XcpR (GspE) and XcpY (GspL) via its cytoplasmic
loop; P. putida swap hybrids define species-specific functional domains [PMID:17464073 "One of
the core components of the Xcp system is the inner-membrane protein XcpS (GspF)"; "XcpS was
shown to be stabilized by co-expression of the XcpR (GspE) and XcpY (GspL) components of the
machinery, demonstrating an interaction between these three proteins"; "The cytoplasmic loop of
XcpS was found to be involved in the stabilization by XcpR and XcpY"]. UniProt curates the
topology (cytoplasmic 1..168, periplasmic 190..219, cytoplasmic 240..376) from this paper.
XcpRSYZ subcomplex co-purified under native conditions PMID:16168578.
Polar localisation; tagged XcpS is functional [PMID:18832308 "Fusion of the Lumio tag to the C
termini of the XcpR and XcpS proteins did not affect the functionality of these proteins";
"labelled XcpS was still found to locate at the poles, whereas XcpR was evenly distributed in the
cell"].
Ca2+ binding sites in the cytoplasmic domain are only By-similarity (P45780); not annotated.

I did not find a PAO1 paper whose abstract reports an xcpS single-deletion secretion phenotype;
the 2003 pseudopilus paper uses xcpRS double deletions (PMID:12700254). Primary support for the
process term is therefore the functional analysis in PMID:17464073 and PMID:18832308.

PseudoCAP rows

GO:0015627 IDA PMID:16168578: direct co-purification; correct.
GO:0015628 IDA PMID:9818381: a review (FEMS Microbiol Rev 1998, PubMed type Review). Same
defect as recorded on xcpX: WRONG_EVIDENCE_CODE, CHECK; term correct.

PAINT node composition

genes/PSEAE/xcpV/xcpV-bioinformatics/node_leaves.py (shared analysis for the three Xcp genes)
lists current QuickGO leaves of PTN000768597 for GO:0015628: 911 proteins, 846 T2SS-named,
7 named PilC/HofC/MshG, 58 generic. The node also carries a plasma membrane IBD seeded by E. coli
HofC (P36646, PTHR30012:SF7) and GspF (P41441), so the node spans both the GspF and the
HofC/PilC subfamilies. The T2SS process term at this node therefore leaks to a few type IV
pilus/MSHA platform proteins. Small fraction; noted, no defect filed.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN000768597	GO:0015628 protein secretion by the type II secretion system	1 (sole seed)	25 (12 taxa) in worklist; 911 proteins in current QuickGO	GO:0015628, IDA, PMID:9818381	SOUND (term); evidence code WRONG (cited paper is a review with no original secretion data; full text checked)	XcpS is a core Xcp component (PMID:16168578, PMID:17464073). PMID:9818381 is a review, so IDA is invalid; re-key to a primary paper (PMID:17464073) or TAS. Node term suits a GspF clade; a few PilC/HofC/MshG leaves receive it (minor over-propagation).