gbdR (PA5380, Q9HTI4) review notes

AraC-family transcriptional activator, 367 aa: N-terminal DJ-1/PfpI-like
(class I glutamine amidotransferase-like) effector domain and C-terminal
AraC-type HTH domain (residues 227-325). PANTHER PTHR43130 (AraC-family
regulator). Reviewed UniProt entry. 44% identical to CdhR (PA5389).

Literature (no deep-research provider available; own reading)

Wargo et al. 2008 (abstract only). Transposon screen for growth on glycine
betaine (GB); gbdR identified as a predicted AraC regulator required for
growth on GB and DMG and for induction of the GB/DMG catabolic genes
[PMID:17951379 "Our screen also identified a predicted AraC"; "that is
required for growth on GB and DMG and for the induction of gbcA, gbcB, and
dgcAB in response"]. The catabolic steps are performed by GbcAB (GB to DMG)
and DgcAB (DMG to sarcosine), not by GbdR.
Wargo et al. 2009 (full text read). GbdR is required for GB/DMG induction of
plcH and pchP transcription; MBP-GbdR binds the plcH and pchP promoters in
EMSA, and a 2-bp promoter mutation abolishes binding and induction
[PMID:19103776 "Here we report that the induction of plcH and pchP
transcription by glycine betaine is mediated by GbdR, an AraC family
transcription factor."; "In electrophoretic mobility shift assays, a
GbdR-maltose binding protein fusion bound specifically to both the plcH and
pchP promoters."]. Effects on PlcH and PchP enzyme activity are downstream of
transcriptional induction; GbdR does not act on the enzymes.
Hampel et al. 2014 (full text read). GbdR regulon: 26 genes from 12
promoters, 11 bound in vitro; DNase I footprint on plcH; consensus site;
choE added PMID:24097953. Direct control of all steps from GB to
pyruvate PMID:24097953.

PseudoCAP IBA-seed assessment

Other seeds' experimental support queried live in QuickGO on 2026-11-05.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000111456	GO:0006355 regulation of DNA-templated transcription	4	50 (13 taxa)	GO:0006355, IDA, PMID:17951379 (PseudoCAP)	SOUND	Abstract states GbdR is required for induction of the GB/DMG catabolic genes; later papers show direct promoter binding. Term correct (the IDA code is generous for a genetics abstract, but the claim is true).	P. aeruginosa ArgR G3XCU2 (CollecTF EXP/IMP/IPI), S. coelicolor AdpA Q9L062 (CollecTF EXP), P. aeruginosa CdhR Q9HTH5 (PseudoCAP IMP)	Yes; ArgR and AdpA have experimental support
PTN000111456	GO:0006355 regulation of DNA-templated transcription	4	50 (13 taxa)	GO:0006355, IMP, PMID:24097953 (PseudoCAP)	SOUND	Full text: regulon defined, direct EMSA binding to 11 promoters, footprint.	as above	Yes

The node term is the generic AraC-regulator process and suits a 13-taxon
clade of AraC activators. No PSEUDOCAP defect on the seed rows and no
GO_CENTRAL defect on PTN000111456. CdhR (Q9HTH5) shares this node and is being
reviewed in parallel; no node-level defect needs recording there.

Other PseudoCAP rows (not seeds)

term	verdict	defect
GO:0031457 glycine betaine catabolic process (IMP, PMID:17951379)	WRONG (regulator annotated to the process its targets perform)	PSEUDOCAP WRONG_TERM, CONFIRMED (abstract says gbdR encodes a regulator required for induction; PMID:24097953 full text shows direct transcriptional control). Repoint to GO:0009896.
GO:0010518 positive regulation of phospholipase activity (IMP, PMID:19103776)	WRONG	PSEUDOCAP WRONG_TERM, CONFIRMED (full text): GbdR induces plcH transcription; it does not modulate PlcH activity.
GO:0010922 positive regulation of phosphatase activity (IMP, PMID:19103776)	WRONG	PSEUDOCAP WRONG_TERM, CONFIRMED (full text): GbdR induces pchP transcription.
GO:0009896 positive regulation of catabolic process	SOUND	none; no GB-specific regulation term exists.
GO:0045764 positive regulation of amino acid metabolic process	SOUND, non-core	none (DMG, sarcosine, glycine, serine catabolic genes are direct targets).