Fetched with just fetch-gene PSEAE PA4504 (UniProt read timeouts on early
attempts; a re-run completed). Accession Q9HVR7 matches the worklist (rank 75).
The entry is unreviewed (PE 3), named "Probable permease of ABC transporter",
with no gene symbol, so the folder uses the locus tag. No deep-research provider
was used. Reviewed together with PA4503 (DppB); see
genes/PSEAE/PA4503/PA4503-notes.md for the shared literature analysis.
PMID:25338022 (Pletzer et al. 2014, full text cached) deleted the whole
dppBCDF operon in PA14 PMID:25338022 and scored dipeptide use as N source by Biolog
PMID:25338022 and phaseolotoxin sensitivity
PMID:25338022. There was no direct transport, binding or ATPase assay, no
single-gene dppC mutant and no complementation of the operon deletion. The
evidence is therefore IMP-type, not IDA. The claim that DppC is part of the
dipeptide transporter is still sound: the two permeases form the translocation
pathway (they do the work of moving the substrate), and DppC is the only
OppC-type permease in the operon.
Qualifier: transport is a property of the DppA-BCDF complex, so contributes_to
is the strict GO qualifier for a subunit; E. coli DppB/DppC (EcoCyc) and
NikB/NikC use enables, so the existing rows are kept as enables and
contributes_to is used in core_functions.
The 12 leaves (6 taxa; cached PAINT leaf GAF) are E. coli DppC, DdpC, NikC and
GsiD; Salmonella DppC and GsiD; Haemophilus DppC; Yersinia (two), Vibrio (two)
and PA4504. Experimental MF annotations of these leaves in QuickGO:
- NikC (P0AFA9): nickel transmembrane transporter activity (IMP, EcoCyc).
- GsiD (P75799): glutathione transmembrane transporter activity (EXP, EcoCyc).
Nickel and glutathione (a tripeptide) are not dipeptides, so the node term is
over-specific for this mixed-specificity clade, in which the binding protein
sets the substrate PMID:25338022. The parent PTN000765620 carries GO:0022857 transmembrane transporter
activity (5 seeds: PA4504, E. coli GsiD, NikC and two others), which suits a
clade of 96 leaves in 31 taxa.
| PTN node | node term | n_seeds | leaf IBAs | seed annotation (term, evidence, PMID) | verdict | rationale |
|---|---|---|---|---|---|---|
| PTN000766696 | GO:0071916 dipeptide transmembrane transporter activity | 1 (sole) | 12 (6 taxa) | GO:0071916, IDA, PMID:25338022 (PseudoCAP) | OVER-SPECIFIC | Sound for PA4504 (DppC), though the evidence is an operon-deletion phenotype (IMP, not IDA). The node also contains NikC (nickel) and GsiD (glutathione) permeases with experimental annotations for those substrates; in this family the binding protein sets substrate specificity. |
| PTN000765620 | GO:0022857 transmembrane transporter activity | 5 | 96 (31 taxa) | GO:0071916, IDA, PMID:25338022 (PseudoCAP) | SOUND | A general transporter term suits an OppC-type permease clade; other seeds are experimentally characterised E. coli permeases. |
Defects filed: PSEUDOCAP WRONG_EVIDENCE_CODE (IDA should be IMP) on the IDA row;
GO_CENTRAL WRONG_TERM (CHECK) for the PTN000766696 IBD on the IBA row. The IBA
on PA4504 itself remains correct.