PA2127 (CgrA, Q9I1Y8) review notes

PAPS reductase-like domain (Pfam PF01507 x2) plus DUF3440; adenine nucleotide alpha-hydrolase superfamily; 408 aa. Gene names from McManus and Dove 2011: CgrA residues 2-408 and CgrC
residues 2-211 match PA2127 (408 aa) and PA2126 (211 aa).

Literature (no deep-research provider; own reading, 2026-11-05)

Vallet-Gely et al. 2007 (abstract only; PMC2168922 returned no body text via
the PubMed MCP): cgrABC and Anr are positive regulators of cupA; PMID:17890313 and cgr expression is
PMID:17890313. Source of the
PseudoCAP IEP rows.
Trunk et al. 2010 (abstract only): Anr/Dnr regulons after oxygen depletion
PMID:20553552; the abstract does not name the cgr genes.
McManus and Dove 2011 (full text, PMC3209204): CgrA and CgrC interact
directly PMID:21926232; the interaction is needed for cupA expression
PMID:21926232; CgrC, not CgrA, is
at the cupA promoter PMID:21926232; CgrA has a putative PAPS reductase
domain, CgrB is GNAT-like, CgrC ParB-like.
PubMed search via MCP and NCBI eutils returned errors on 2026-11-05.

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?
PTN000764275	GO:0071453 cellular response to oxygen levels	2	12 (5 taxa)	GO:0071453, IEP, PMID:17890313 (PseudoCAP)	SOUND (as IEP)	Abstract states cgr expression is induced by anaerobiosis via Anr. Correct as an expression annotation; anoxia is the more precise stimulus.	the other cgr gene (PA2127/PA2126), same two IEP papers	No. The only other seed is the partner cgr gene with the same IEP evidence; an Anr-dependent expression response in one species is not an inheritable function of the clade
PTN000764275	GO:0071453 cellular response to oxygen levels	2	12 (5 taxa)	GO:0071453, IEP, PMID:20553552 (PseudoCAP)	UNVERIFIABLE	Abstract only; does not name the cgr genes.	as above	as above

No PSEUDOCAP defect: the IEP rows are a conventional use of IEP for a
response term. This review holds the node-level GO_CENTRAL defect (PROBABLE) for PTN000764275.

Other decisions

IEP and IBA rows on GO:0071453 MODIFY to GO:0071454 cellular response to
anoxia (the stimulus is anaerobiosis/oxygen depletion); same action on all
three rows, so the gene-level claim is consistent.
GO:0005515 IPI REMOVE (protein-binding policy); the CgrA-CgrC interaction is
real and is reflected in the coregulator description.
NEW GO:0045893 positive regulation of DNA-templated transcription (IMP,
PMID:21926232), added on both PA2127 and PA2126.
GO:0003824 catalytic activity (InterPro2GO, PAPS reductase domain)
MARK_AS_OVER_ANNOTATED: no activity shown; the protein acts as a coregulator.