No deep-research provider was available. Sources: UniProt record (TrEMBL), cached
abstracts of PMID:21204920, PMID:24082078 and PMID:24928312 (none with full text).
PubMed and Europe PMC searches failed on 2026-11-05 (server errors), so later CtpA
literature could not be retrieved.
PseudoCAP cites PMID:24928312 for three PA5134 rows (IDA signal transduction, IDA cell wall
biogenesis, ISS serine-type endopeptidase with E. coli Prc P23865). The abstract is about
the S. aureus CtpA only
PMID:24928312.
It cannot provide IDA evidence for a P. aeruginosa protein, and it reports neither signal
transduction nor cell wall biogenesis (it reports cell-wall localisation, stress sensitivity
and virulence). The two IDA rows are removed with CONFIRMED PSEUDOCAP WRONG_REFERENCE
defects. The ISS row's term (serine-type endopeptidase) is correct from family membership, so
it is accepted; only its reference is odd.
| PTN node | node term | n_seeds | leaf IBAs | seed annotation (term, evidence, PMID) | verdict | rationale | other seeds | IBD stands without this seed? |
|---|---|---|---|---|---|---|---|---|
| PTN001279639 | GO:0007165 signal transduction | 3 | 58 (32 taxa) | GO:0007165 signal transduction, IDA, PMID:24928312 (PseudoCAP) | WRONG | The cited paper is about S. aureus CtpA and reports no signalling role; no P. aeruginosa CtpA paper seen here shows one. PSEUDOCAP WRONG_REFERENCE, CONFIRMED. | B. subtilis CtpB O35002 (SpoIVFA cleavage in sigma-K activation); P. aeruginosa Prc Q9HYY3 (PMID:24373018, cell-surface signalling; reviewed in this batch, seed SOUND) | Partly. The two remaining seeds support signal transduction for their own proteins, so the IBD is not baseless, but they are paralogous CTP lineages that each acquired a signalling role. Placed at their common ancestor, the term reaches CtpA-type members (PA5134) and E. coli Prc/Tsp (P23865), which have no signalling role on record. GO_CENTRAL defect recorded here (now CONFIRMED after the tree check, CHECK): drop Q9HU50 from WITH/FROM and move the term to the subfamily nodes that support it. |
Cross-reference: prc (PA3257, Q9HYY3) seeds the same node term; its seed is SOUND, and the
node-level defect is recorded once, here, as PA5134 has the decisive (wrong-reference) evidence.
Defects recorded: PSEUDOCAP 2 (WRONG_REFERENCE x2, CONFIRMED); GO_CENTRAL 1 (OTHER on
PTN001279639, CONFIRMED, CHECK).
Topology of PTN001279639 in PTHR32060 fetched with projects/PSEUDOCAP/panther_tree.py node
PTN001279639 --depth 3, then --contains for each seed and --family PTHR32060 for the subclades.
The node is a DUPLICATION with 58 leaves spanning three subfamilies (SF22 9, SF29 2, SF30 47) and
exactly two children.
| Node | Event | Leaves | Subfamilies | Contents | Verdict |
|---|---|---|---|---|---|
| PTN004918760 | SPECIATION (Eubacteria) | 9 | SF22 | Prc / tail-specific proteases: Rhodopirellula prc + PTN000786025 | signalling supported (Prc lineage) |
| PTN000786025 | SPECIATION (Gammaproteobacteria) | 8 | SF22 | Haemophilus, Shewanella, Vibrio, Xanthomonas prc; PAO1 Prc Q9HYY3; PTN002078873 (Enterobacteriaceae, incl. E. coli Prc/Tsp P23865) | smallest clade holding both Prc seeds |
| PTN008644010 | SPECIATION (Eubacteria) | 49 | SF29 + SF30 | the CtpA branch (Terrabacteria, Cyanobacteria, Bacteroidetes, PVC, Proteobacteria ...) | no signalling evidence except CtpB |
| PTN002078920 | SPECIATION (Bacillus) | 2 | SF29 | B. subtilis CtpB O35002, B. cereus BC_5184 | signalling supported (CtpB) |
| PTN002078922 | SPECIATION (Gammaproteobacteria) | 6 | SF30 | Coxiella, Shewanella, three Xanthomonas, PA5134 Q9HU50 (PTN002424651) | no signalling evidence |
--contains Q9HYY3,P23865 returns PTN000786025 (8 leaves); --contains O35002,Q9HU50 returns
PTN008644010 (49 leaves). So the two sound seeds sit on opposite sides of the duplication that
defines PTN001279639, which is exactly why the IBD landed at the family root and reaches all 58
leaves. B. subtilis CtpA (O34666) is a separate SF30 leaf in the same Firmicutes clade as CtpB's
SF29 pair, so even within Bacillales the signalling role belongs to the CtpB subfamily, not to
CtpA-type proteases.
Verdict: concern CONFIRMED, raised from SUSPECTED (topology is primary data checked here). Requested
fix in the defect: drop Q9HU50 from the WITH/FROM (its seed row is mis-referenced - note that a gene
appearing in its own WITH/FROM is not in itself circular), and move GO:0007165 to PTN000786025 (or
PTN004918760) for the Prc lineage and PTN002078920 for CtpB, removing it from PTN001279639.