ohrR / PA2849 (Q9HZZ4) review notes

Summary of the literature

OhrR is a 151-residue MarR/OhrR-family regulator. The UniProtKB entry is unreviewed (SubName
"OhrR") and its only CC line, a cytoplasm location, is ARBA-derived, so it is not usable as
evidence. Usable features: FT DNA_BIND 61..84 (winged-helix recognition region) and the family
assignment [file:PSEAE/ohrR/ohrR-uniprot.txt "PANTHER; PTHR33164:SF5; ORGANIC HYDROPEROXIDE
RESISTANCE TRANSCRIPTIONAL REGULATOR; 1."].

Primary data, Atichartpongkul et al. 2010 PMID:20139188, abstract only — the PubMed MCP
returns no body text for PMC2849439:

PMID:20139188.
PMID:20139188 — direct binding, which is what the CollecTF site records rest on.
Redox switch: PMID:20139188.
Genetics: PMID:20139188 and PMID:20139188.

The abstract therefore states, outright, every claim annotated from this paper by PseudoCAP and
CollecTF (operator binding, repression, redox release, mutant phenotypes). The partner thiol
peroxidase Ohr is further characterised in PMID:22609922 (cached), consistent with this picture.

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?
PTN002109389	GO:0006355 regulation of DNA-templated transcription	8	229 (33 taxa)	GO:0045892, IMP + EXP + IEP, PMID:20139188 (PseudoCAP and CollecTF)	SOUND	Three independent evidence lines on the same gene, and the abstract states both the direct operator binding and the mutant de-repression phenotype. OhrR is a bona fide transcriptional repressor; the node term is a correct generalisation.	B. subtilis OhrR (O34777, IMP GO:0001227 / IMP+IDA GO:0045892), E. coli MarR (P27245, IDA GO:0003677, IMP GO:0045892), SlyA (P0A8W2, IMP GO:0003700, IDA GO:0045893), MprA/EmrR (P0ACR9, IDA GO:0000976/GO:0003677), S. oneidensis OhrR (Q8EI70, EXP GO:0045892), P. aeruginosa PA0942 (Q9I516, IEP GO:0045892), B. subtilis ScoC/Hpr (P11065, IMP GO:0006355) — verified by live QuickGO query 2026-11-05	Yes, strongly: five other seeds carry experimental transcription-regulation annotations. The node term suits the whole MarR clade. No GO_CENTRAL defect.
PTN002109389	GO:0006950 response to stress	2	229 (33 taxa)	not seeded by OhrR	n/a (leaf IBA only)	OhrR receives this IBA but does not seed it. The two seeds are B. subtilis OhrR (IMP GO:0042542 response to hydrogen peroxide) and E. coli MarR (IMP GO:0071236 response to antibiotic, GO:0009408 response to heat). The node term stops at the root precisely because the clade's stresses differ; that is granularity, not unsoundness.	O34777, P27245	Yes. No GO_CENTRAL defect; for OhrR the row is MODIFYed to the hydroperoxide-specific child (see below).

This is a different node from the one shared by the sensor kinases in this batch, so there is no
overlap with pprA/fleS/cbrA, nor with the reviewed genes/PSEAE/fleQ (a sigma-54 activator
on an unrelated family).

Annotation decisions

GO:0045892 (IMP, EXP, IEP) and GO:1900407 (IMP): ACCEPT. Core function; the seed row is sound.
GO:0000976, GO:0001217 (IPI and IMP each): ACCEPT — direct operator binding and repression.
GO:0032993 protein-DNA complex (IPI, IMP): KEEP_AS_NON_CORE, a component restatement of the
binding (the same call as in genes/PSEAE/fleQ).
GO:0003677, GO:0003700, GO:0006355 (IBA, IEA), GO:0006355 (IEA): TOO_GENERAL — each entailed by
an accepted specific term. Note GO:0001217 is_a GO:0003700, so TOO_GENERAL rather than
MODIFY is right there.
GO:0006950 response to stress (IBA): MODIFY to GO:0033194 response to hydroperoxide. Note
that GO:1900407 (regulation of cellular response to oxidative stress) is a regulation class and
does not entail GO:0006950, so TOO_GENERAL would be wrong here; a propagation_review
block records the node reading.
GO:0006351 DNA-templated transcription (IEA, GO_REF:0000104): REMOVE, with a
resource: UNIPROT WRONG_TERM defect (PROBABLE). A repressor does not perform transcription;
the sequence-feature mapping from the MarR HTH should point into the regulation branch. This is
a UniProt/ARBA rule-based row, not a PseudoCAP row, so the defect is filed against UNIPROT.
GO:0005737 cytoplasm (IEA GO_REF:0000044): ACCEPT on biological grounds (the only possible
location for an operator-binding repressor), with the reason noting that the underlying UniProt
statement is ARBA-derived.

No PseudoCAP defect is filed on this gene: the PseudoCAP row (GO:0045892 IMP) and the two
CollecTF rows for the same claim are all correct.