All families / PF04167
PF04167: DUF402
Protein of unknown function (DUF402)
- Curation status
- SEEDED
- Seed status
- UNKNOWN CANDIDATE
- Characterization
- UNSCORED
Grounding
PF04167: Protein of unknown function (DUF402)
IPR007295: integrated entry for Protein of unknown function (DUF402)
Source description
Family member FomD is a protein encoded in the fosfomycin biosynthesis gene cluster [InterPro reference PUB00009885,InterPro reference PUB00100530], which hydrolyses (S)-HPP-CMP to give (S)-HPP and CMP in the presence of Mn2 or Co2 [InterPro reference PUB00100530]. FomD also hydrolyses cytidylyl 2-hydroxyethylphosphonate (HEP-CMP), which is a biosynthetic intermediate before C-methylation. FomD structure revealed that it has a beta-barrel fold consisting of a large twisted antiparallel beta-sheet, a key feature of DUF402-containing proteins. The function of this domain is unknown. It has a Tyr residue which activates a water molecule to promote nucleophilic attack on the phosphorus atom of the phosphonate moiety [InterPro reference PUB00100530]. This domain has also been found in Ntdp (nucleoside tri- and diphosphatase, also known as Sa1684) from Staphylococcus aureus [InterPro reference PUB00100531].
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
4 verified sequence examples. FASTA
| UniProt | Protein / organism | Sequence | Provenance |
|---|---|---|---|
| O83033 | Cytidylyl-2-hydroxypropylphosphonate hydrolase Streptomyces wedmorensis | 209 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| Q2G2M8 | Nucleoside triphosphate/diphosphate phosphatase Staphylococcus aureus (strain NCTC 8325 / PS 47) | 180 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| Q796Z1 | Nucleoside triphosphate/diphosphate phosphatase Bacillus subtilis (strain 168) | 176 aa; version 2 UniProt 2026_03 | PTM REGISTRY MIRROR |
| Q7A4T2 | Nucleoside triphosphate/diphosphate phosphatase Staphylococcus aureus (strain N315) | 180 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
- 8,509
- matches
- 8,523
- proteomes
- 5,477
- taxa
- 7,221
- structures
- 12
- alphafold models
- 5,048
- domain architectures
- 23
Classification basis
short name matches duf; name says unknown function; description says unknown function
No scoring reasons supplied.
Related Mech records
| Family | Mech | Record | Protein | Link basis |
|---|---|---|---|---|
| DUF402 (PF04167) | ProteinTraitsMech | hypothetical protein | Q796Z1 Nucleoside triphosphate/diphosphate phosphatase | canonical example family classification |
| DUF402 (PF04167) | ProteinTraitsMech | nucleoside tri-diphosphate phosphatase | Q796Z1 Nucleoside triphosphate/diphosphate phosphatase | canonical example family classification |
| DUF402 (PF04167) | ProteinTraitsMech | Domain of unknown function DUF402 | Q796Z1 Nucleoside triphosphate/diphosphate phosphatase | canonical example family classification |
| DUF402 (PF04167) | ProteinTraitsMech | Domain of unknown function DUF402 | trait identifier | |
| DUF402 (PF04167) | ProteinTraitsMech | Protein of unknown function (DUF402) | O83033 Cytidylyl-2-hydroxypropylphosphonate hydrolase | canonical example family classification |
| DUF402 (PF04167) | ProteinTraitsMech | Protein of unknown function (DUF402) | Q2G2M8 Nucleoside triphosphate/diphosphate phosphatase | canonical example family classification |
| DUF402 (PF04167) | ProteinTraitsMech | Protein of unknown function (DUF402) | Q7A4T2 Nucleoside triphosphate/diphosphate phosphatase | canonical example family classification |
| DUF402 (PF04167) | ProteinTraitsMech | Protein of unknown function (DUF402) | trait identifier | |
| DUF402 (PF04167) | ProteinTraitsMech | FomD-like superfamily | Q796Z1 Nucleoside triphosphate/diphosphate phosphatase | canonical example family classification |
| DUF402 (PF04167) | ProteinTraitsMech | FomD-like | Q796Z1 Nucleoside triphosphate/diphosphate phosphatase | canonical example family classification |
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.