All families / PF10073
PF10073: GapR_DNA-bd
GapR-like, DNA-binding domain
- Curation status
- SEEDED
- Seed status
- EX DUF
- Characterization
- UNSCORED
Grounding
PF10073: GapR-like, DNA-binding domain
IPR046367: integrated entry for GapR-like, DNA-binding domain
Source description
GapR is a nucleoid-associated protein (NAP) critical for cellular function in Caulobacter crescentus (also known as Caulobacter vibrioides). Loss of GapR causes severe defects in growth, cell division, DNA replication, and chromosome segregation [InterPro reference PUB00100154,InterPro reference PUB00100155]. This is a DNA-binding protein which has mainly an alpha-helical secondary structure. In the absence of DNA, GapR is a dimer, with each monomer folded into two extended alpha-helices, while in the presence of DNA, GapR forms a tetramer, with the C-terminal alpha-helix of each monomer reorganised into two shorter helices, which allows GapR to encircle the DNA [InterPro reference PUB00070793,InterPro reference PUB00100154,InterPro reference PUB00100155]. This is the DNA-binding domain of GapR from Caulobacter crescentus and related sequences. This domain is not only highly conserved in Alphaproteobacteria, it is also present in cyanobacteria, firmicutes, planctomycetes, actinobacteria, and even archaea and eukaryotes, possibly through horizontal gene transfer. This domain is also found in phages, in which it is associated to DNA-related processes [InterPro reference PUB00100154].
Evidence and references
- InterPro entry and its literature references. PUB identifiers are internal InterPro references, not PubMed identifiers. Unresolved citations link to the originating entry.
- Frozen description source: InterPro/Pfam API
Source descriptions and links are provenance, not independent functional validation.
Evidence counts: not scored.
Curated functional assertions
No curated functional assertions supplied.
Protein sequence examples
3 verified sequence examples. FASTA
| UniProt | Protein / organism | Sequence | Provenance |
|---|---|---|---|
| A4YMG9 | UPF0335 protein BRADO1188 Bradyrhizobium sp. (strain ORS 278) | 91 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| A5ERF9 | UPF0335 protein BBta_6866 Bradyrhizobium sp. (strain BTAi1 / ATCC BAA-1182) | 91 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| A6WY25 | UPF0335 protein Oant_1161 Brucella anthropi (strain ATCC 49188 / DSM 6882 / CCUG 24695 / JCM 21032 / LMG 3331 / NBRC 15819 / NCTC 12168 / Alc 37) | 85 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
Pfam membership is not functional evidence. Whole-protein sequences do not establish domain boundaries. A coverage gap here is not absence from UniProt.
Sequences and metadata: UniProt Consortium, CC BY 4.0.
Domain matches
No residue-level domain match evidence is available in this build. Structure and AlphaFold counters do not supply coordinates or establish function.
Snapshot counters
- proteins
- 3,528
- matches
- 3,530
- proteomes
- 2,569
- taxa
- 3,722
- structures
- 9
- alphafold models
- 2,397
- domain architectures
- 10
Classification basis
pfam previous unknown name
No scoring reasons supplied.
Related Mech records
This family joined the worklist after the frozen cross-Mech scan, so other Mechs were not searched for it. Missing links here are not evidence that other Mechs lack it; rows shown come from mentions of a former DUF/UPF name.
No cross-Mech examples are present in the supplied snapshot.
Curation history and reviews
No retained curation events supplied.
No retained review supplied.
Record source
Status and evidence
- Seed status
- A name-based classification of frozen InterPro/Pfam metadata. UNKNOWN CANDIDATE means the metadata explicitly says the function is unknown. KNOWN HISTORICAL DUF means a DUF name matched without that wording; this heuristic is not proof of a known function and does not establish experimental characterization. EX DUF means Pfam renamed the family away from a DUF/UPF name, as recorded in Pfam's previous identifiers; a rename usually follows published work on some members but is naming history, not proof of function for every member. Some EX DUF families' current names or descriptions still say the function is unknown; their classification basis lists this, and scoring does not treat them as characterized. FALSE POSITIVE TEXT HIT means the naming rules did not match.
- Characterization
- A separate evidence-scoring result. UNSCORED means no score has been calculated; it is not evidence that the family lacks a known function. Missing scores are not negative evidence. PARTIALLY CHARACTERIZED has partial support; KNOWN HISTORICAL DUF can inherit the seed label or reflect a known-function signal. Neither label implies experimental validation.
- Evidence counts
- Source-specific signals, not unique proteins, publications, or confidence scores. Known counts Rhea reactions and experimentally supported GO molecular-function annotations. Partial counts functional/domain assignments. Context counts structural, environmental, orthology, interaction and neighborhood signals; context alone does not assign function. Repeated annotations may not be independent.
- Curation status
- Reported separately from seed classification and characterization. SNAPSHOT ONLY means no curated metadata was supplied for this build. SEEDED denotes a source-derived record, not an expert-reviewed functional claim.
- Missing counts
- Not available means the source did not supply that counter. A zero is a reported count. Not scored means evidence counts are unavailable.