All families / PF04480
PF04480: DUF559
Protein of unknown function (DUF559)
- Curation status
- SEEDED
- Seed status
- UNKNOWN CANDIDATE
- Characterization
- UNSCORED
Grounding
PF04480: Protein of unknown function (DUF559)
IPR007569: integrated entry for Protein of unknown function (DUF559)
Source description
No description supplied.
Evidence and references
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 |
|---|---|---|---|
| P36434 | Type II nicking enzyme V.HpaIIP Haemophilus parainfluenzae | 141 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| P45736 | Uncharacterized protein YcjD Escherichia coli (strain K12) | 117 aa; version 1 UniProt 2026_03 | PTM REGISTRY MIRROR |
| Q9RLM5 | Type II nicking enzyme V.NmeDIP Neisseria meningitidis serogroup C | 148 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
- 12,664
- matches
- 12,670
- proteomes
- 6,339
- taxa
- 9,510
- structures
- 2
- alphafold models
- 7,682
- domain architectures
- 192
Classification basis
short name matches duf; name says unknown function
No scoring reasons supplied.
Related Mech records
| Family | Mech | Record | Protein | Link basis |
|---|---|---|---|---|
| DUF559 (PF04480) | ProteinTraitsMech | DUF559 domain-containing protein | P45736 Uncharacterized protein YcjD | canonical example family classification |
| DUF559 (PF04480) | ProteinTraitsMech | Endonuclease_DUF559 | P45736 Uncharacterized protein YcjD | canonical example family classification |
| DUF559 (PF04480) | ProteinTraitsMech | Domain of unknown function DUF559 | P45736 Uncharacterized protein YcjD | canonical example family classification |
| DUF559 (PF04480) | ProteinTraitsMech | Domain of unknown function DUF559 | trait identifier | |
| DUF559 (PF04480) | ProteinTraitsMech | Putative endonuclease DUF559, bacteria | P45736 Uncharacterized protein YcjD | canonical example family classification |
| DUF559 (PF04480) | ProteinTraitsMech | Protein of unknown function (DUF559) | P36434 Type II nicking enzyme V.HpaIIP | canonical example family classification |
| DUF559 (PF04480) | ProteinTraitsMech | Protein of unknown function (DUF559) | P45736 Uncharacterized protein YcjD | canonical example family classification |
| DUF559 (PF04480) | ProteinTraitsMech | Protein of unknown function (DUF559) | Q9RLM5 Type II nicking enzyme V.NmeDIP | canonical example family classification |
| DUF559 (PF04480) | ProteinTraitsMech | Protein of unknown function (DUF559) | trait identifier | |
| DUF559 (PF04480) | ProteinTraitsMech | VSR Endonuclease | P45736 Uncharacterized protein YcjD | 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.