PF03235: GmrSD_N

GmrSD restriction endonuclease, N-terminal domain

Curation status: SEEDED
Seed status: EX DUF
Characterization: UNSCORED

Grounding

PF03235: GmrSD restriction endonuclease, N-terminal domain
IPR004919: integrated entry for GmrSD restriction endonuclease, N-terminal domain

Source description

This entry (previously known as DUF262) represents a domain found N-terminal in the GmrSD family of modification-dependent restriction endonuclease, including BrxU and SspE proteins [InterPro reference PUB00155271,InterPro reference PUB00155272]. BrxU is a type IV DNA modification-dependent restriction enzyme, which is promiscuous and uses a range of nucleotide and metal co-factors to recognise and cleave DNA that contains any of at least three different modifications, and this activity is dependent on the initial nucleotide-driven dissociation of BrxU dimers, and subsequent nucleotide hydrolysis [InterPro reference PUB00155271]. SspE is a dual-function protein that exerts both N-terminal NTPase and C-terminal DNA nicking nuclease activities to defend against phage infection [InterPro reference PUB00155272]. BrxU targets and cleaves DNA containing one of at least three DNA modifications, 5mC, 5hmC or glc-5hmC whereas SspE has a phosphorothioate (PT) modification-binding preference and utilizes epigenetic PT modification to accomplish self-nonself discrimination and to coordinate its NTPase and DNA nicking activities to fight against phages. The domain represented in this entry is involved in nucleotide binding, recognition and hydrolysis.

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

1 verified sequence example. FASTA

UniProt	Protein / organism	Sequence	Provenance
Q58099	Uncharacterized protein MJ0686 Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)	580 aa; version 1 UniProt 2026_03	UNIPROT FETCH 2 sibling references ProteinTraitsMech: InterPro:IPR004919 ProteinTraitsMech: Pfam:PF03235

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: 14,123
matches: 14,176
proteomes: 8,899
taxa: 14,565
structures: 8
alphafold models: 9,036
domain architectures: 93

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.

Family	Mech	Record	Protein	Link basis
GmrSD_N (PF03235)	TaxonMech	Sinorhizobium xinjiangense		record mentions previous pfam name
GmrSD_N (PF03235)	TraitMech	DUF262 Schlafen system		record mentions previous pfam name

Curation history and reviews

No retained curation events supplied.

No retained review supplied.

Record source

data/families/PF03235.yaml
Family YAML in this build

Download this family (JSON)

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.