xcpV (PA3099, Q00516) review notes

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

Fetched with just fetch-gene PSEAE xcpV; accession Q00516 matches the worklist (rank 51,
PA3099). UniProt synonym pddC. No deep-research provider was used; manual notes from cached
publications, PubMed and the UniProt record. PMID:8331069 full text could not be obtained (PMC204877
returns an empty body through the PubMed MCP).

What XcpV is

GspI-family minor pseudopilin (UniProt "Belongs to the GSP I family"; NCBIfam TIGR01707,
InterPro IPR010052/IPR003413, Pfam PF02501 T2SSI, PANTHER PTHR38779:SF2). 129 aa, leader 1..6,
TM 7..27.
PilD-processed and N-methylated; inner membrane [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"].
Required for excretion (pddC) PMID:1309616.
Complexes with His-XcpT PMID:9282737.
Nucleator of the tip complex PMID:19828448.
XcpVW core; xcpV mutant has the lowest LasB secretion and is complemented [PMID:30346996 "The
absence of either XcpV or -W resulted in the non-functional T2SS"; "The supernatant of the xcpV
mutant, containing secreted proteins, displayed the lowest LasB activity, suggesting that the
secretion of LasB was significantly compromised."].

PseudoCAP rows

GO:0015628 IDA PMID:9818381: review; IDA not supported: full text checked, no original secretion data. Same WRONG_EVIDENCE_CODE / CHECK defect as
xcpX, xcpS, xcpW. Term correct; primary IMP: PMID:30346996, PMID:1309616.
GO:0015627 IDA PMID:8331069: primary paper, but the abstract shows processing, methylation and
inner-membrane fractionation only, not complex membership. Accepted (term true), SUSPECTED
WRONG_REFERENCE / CHECK defect suggesting PMID:19828448. Same treatment as xcpW.

PAINT node breadth (bioinformatics)

xcpV-bioinformatics/node_leaves.py lists the QuickGO leaves of the seed nodes for all three Xcp
genes reviewed in this session (xcpS, xcpW, xcpV) and classifies them by name; see
xcpV-bioinformatics/RESULTS.md. For PTN002446181 (GO:0015627): 49 proteins, 14 T2SS-named,
14 named PilV/MshD/pilin (including N. gonorrhoeae PilV NGO_0453, a type IV pilus minor pilin), 21
generic prepilin-domain names. GspI and PilV are homologous minor pilins; the node appears to span
the split, so both T2SS IBDs at this node leak to type IV pilus proteins. Recorded as GO_CENTRAL
WRONG_TERM / CHECK defects on the two IBA rows (the IBAs on XcpV itself are correct), raised to
CONFIRMED by the tree check below, which also reframes where the fault lies.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002446181	GO:0015627 type II protein secretion system complex	1 (sole seed)	12 (9 taxa) in worklist; 49 proteins in current QuickGO	GO:0015627, IDA, PMID:8331069	SOUND (term for XcpV); seed reference OVER-SPECIFIC; node scope questionable	XcpV is in the tip complex (PMID:19828448, PMID:30346996), but the cited paper shows only membrane localisation and PilD processing (abstract). About 14 of 49 leaves are named PilV/MshD/pilin, so the T2SS complex term is likely over-propagated to type IV pilus minor pilins.
PTN002446181	GO:0015628 protein secretion by the type II secretion system	1 (sole seed)	12 (9 taxa) in worklist; 49 proteins in current QuickGO	GO:0015628, IDA, PMID:9818381	SOUND (term for XcpV); evidence code WRONG; node scope questionable	xcpV mutant loses LasB secretion and is complemented (PMID:30346996). PMID:9818381 is a review, so IDA is invalid; re-key as IMP. Same PilV leakage concern at the node.

PANTHER tree check (2026-11-05)

Topology of PTN002446181 fetched with projects/PSEUDOCAP/panther_tree.py node PTN002446181 --depth 6 and family PTHR38779 --depth 3. PTN002446181 is the root of PTHR38779: a
SPECIATION node (Eubacteria) with 12 reference-proteome leaves, all PTHR38779:SF2, and three
children.

Child node	Event	Leaves	Subfamilies	Contents	Verdict
PTN002446182	LEAF	1	SF2	Aquifex aeolicus ppdD3, "Pilin"	not a T2SS protein
PTN002409471	LEAF	1	SF2	Thermodesulfovibrio yellowstonii THEYE_A0597, bare prepilin-type cleavage/methylation domain	not a T2SS protein
PTN002215342	SPECIATION (Proteobacteria)	10	SF2	Geobacter GspI; PTN002215344 (Gammaproteobacteria, 9): Shewanella GspI, Vibrio EpsI, PTN002215341 (Xanthomonas XpsI/XcsI/XcsJ), PTN002446183 (XcpV Q00516, PA0680), PTN002215349 (E. coli GspI, Yersinia YPO0811)	every T2SS-named leaf in the family

Two corrections to the earlier, name-based reading:

There is no GspI/PilV split in this tree. No PilV or MshD protein is a leaf of PTHR38779's
reference tree. Checking node_leaves.tsv against the tree, the 12 reference leaves are all
present in the 49-protein QuickGO set (Q00516, Q9I5P5, P45760, P45775, Q74S14, Q8EKC4, Q8P5C1,
Q8P5C2, P31738, Q74GC2, O67426, B5YJM5); the other 37, PilV/MshD names included (e.g. Q5F9E5
NGO_0453), are non-reference members grafted into the family by sequence, which the tree cannot
place. So the leakage is a family-assignment/grafting effect, not evidence that the annotated
clade mixes two systems.
The node is nevertheless one level too high. Being the family root, the IBD also covers the
two deep generic prepilin branches, while every T2SS-named leaf sits in PTN002215342. That is a
real, checkable node-placement error with an unambiguous target.

Verdict for both defects (GO:0015627 and GO:0015628): CONFIRMED, raised from SUSPECTED, with the
request changed from "move to a node confined to GspI proteins / add NOT for the PilV clade" to
"move both IBDs to PTN002215342". If grafted PilV/MshD members still receive the terms after the
move, the next thing to check is their PTHR38779:SF2 assignment, not the node. The XcpV IBA rows
themselves stay ACCEPT: XcpV is inside PTN002215342 and the terms are right for it.