gntR (PA2320, Q9I1F6) review notes

Review session 2026-11-05 (PseudoCAP IBA-seed protocol, tier 2)

Fetched with just fetch-gene PSEAE Q9I1F6 --alias gntR; accession matches the worklist.
Swiss-Prot entry. No deep-research provider was used. Literature search: PubMed esearch was
unavailable (NCBI SOLR 500 errors) during the session; a Europe PMC query
(GntR AND PA2320) returned no further P. aeruginosa GntR papers. The only paper on this gene
product is the seed paper PMID:28752954 (abstract cached; full text not available).

Literature

PMID:28752954 (Daddaoua et al. 2017). GntR is a LacI-family regulator in PAO1:
PMID:28752954; PMID:28752954; operator
overlaps the RNA polymerase site; PMID:28752954; GntR does not affect toxA; PMID:28752954
UniProt FUNCTION text (ECO:0000269, PubMed:28752954) restates the above.

Annotation decisions

GO:0003700 (IBA, IDA seed): MODIFY to GO:0001217 DNA-binding transcription repressor activity.
GO:0006355 (IBA, IEA): MODIFY to GO:0045892 negative regulation of DNA-templated transcription.
GO:0000976 (IBA): ACCEPT. GO:0003677 (IEA): TOO_GENERAL.
GO:0010906 regulation of glucose metabolic process (IMP): KEEP_AS_NON_CORE (gluconate uptake
is a route of glucose catabolism in Pseudomonas; consequence of gntP repression).
Action counts: ACCEPT 1, MODIFY 4, KEEP_AS_NON_CORE 1, TOO_GENERAL 1.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN001248758	GO:0003700 DNA-binding transcription factor activity	11	219 (28 taxa)	GO:0003700, IDA, PMID:28752954 (PseudoCAP)	SOUND	Abstract states purified GntR binds PgntR/PgntP operators, effector release, and repression in vivo; DNA binding plus repression is direct TF evidence. Generic node term suits a LacI/GalR clade.	E. coli LacI, MalI, XylR, RbsR, PurR, AscG, TreR; B. subtilis CcpA; Shewanella NagR; P. aeruginosa PtxS	Yes

Confidence note: abstract-only reading, but the abstract states the binding and repression data
outright, so the SOUND call does not depend on what the abstract omits.

PtxS (genes/PSEAE/ptxS/ptxS-notes.md) shares PTN001248758; the node-level verdict (all three
IBDs at this node stand, no GO_CENTRAL defect) is recorded there. No PSEUDOCAP or GO_CENTRAL
defect on gntR.