ampR (PA4109, P24734) notes

No deep-research provider was available. Literature: PMID:22479525 and PMID:16251297 (full text
cached and read); PMID:25182487 (abstract only).

Biology

Direct binding at PampC PMID:25182487.
Possible membrane association PMID:25182487.
Regulon by mutant transcriptome PMID:22479525; direct targets not determined
PMID:22479525.
Phenotypes: more biofilm PMID:22479525; less pyocyanin PMID:22479525. PMID:16251297 reported the opposite for pyocyanin and LasA.
Consistency: ampD, ampDh2, ampDh3 and ampG (genes/PSEAE) are the peptidoglycan-recycling enzymes and
permease whose muropeptides feed AmpR; none of those reviews assigns them regulation-of-transcription
terms, which is consistent with AmpR being the only transcriptional component here.

GO:0003700 (IBA, IEA, IDA), GO:0006355 (IBA, IEA, IDA), GO:0005737 (IEA): ACCEPT.
GO:0006351 (IDA, UniProt): MODIFY to GO:0006355.
GO:0016020 (IEA, NAS), GO:0046677, GO:1900232, GO:1900378: KEEP_AS_NON_CORE.
GO:0045862, GO:0050714 (PseudoCAP IMP): MARK_AS_OVER_ANNOTATED (gene-expression effects, probably
indirect).
Action counts: ACCEPT 7, MODIFY 1, KEEP_AS_NON_CORE 5, MARK_AS_OVER_ANNOTATED 2.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000794521	GO:0006355 regulation of DNA-templated transcription	6	174 (18 taxa)	GO:0006355, IDA, PMID:22479525 (PseudoCAP)	SOUND	Full text: the term is right (ampR deletion changes >500 transcripts; AmpR binds PampC per PMID:25182487), but the evidence is a mutant transcriptome, so IDA should be IMP (PSEUDOCAP WRONG_EVIDENCE_CODE, CONFIRMED).	trpI P11720 (SOUND), E. coli GcvA, TtdR, DmlR, PgrR	Yes; see the node record in genes/PSEAE/trpI/trpI-notes.md

Node-level assessment for PTN000794521 is recorded once on trpI. No GO_CENTRAL defect.