All families / PF03990
PF03990: DUF348
G5-linked-Ubiquitin-like domain
- Curation status
- SEEDED
- Seed status
- KNOWN HISTORICAL DUF
- Characterization
- UNSCORED
Grounding
PF03990: G5-linked-Ubiquitin-like domain
IPR007137: integrated entry for G5-linked-Ubiquitin-like domain
Source description
This domain normally occurs as tandem repeats; however it is found as a single copy in the S. cerevisiae DNA-binding nuclear protein YCR593 (P25357 (UniProtKB protein)). This protein is involved in sporulation part of the SET3C complex, which is required to repress early/middle sporulation genes during meiosis ([InterPro reference PUB00019472]). The bacterial proteins are likely to be involved in a cell wall function as they are found in conjunction with the PF07501 (Pfam entry) domain, which is involved in various cell surface processes. This domain is also present in the resuscitation-promoting factors RpfB from Mycobacterium tuberculosis and Rpf2 from Corynebacterium glutamicum. These are factors that stimulate resuscitation of dormant cells [InterPro reference PUB00075582]. This domain has a beta grasp fold. Structural description of this domain revealed a structural conservation between these domains and ubiquitin, hence it is termed UBL-G5 [InterPro reference PUB00137668].
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 |
|---|---|---|---|
| H8EZH5 | Resuscitation-promoting factor RpfB Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) | 362 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| P37546 | Putative cell wall shaping protein YabE Bacillus subtilis (strain 168) | 407 aa; version 2 UniProt 2026_03 | PTM REGISTRY MIRROR9 sibling references
|
| P9WG29 | Resuscitation-promoting factor RpfB Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) | 362 aa; version 1 UniProt 2026_03 | UNIPROT FETCH2 sibling references |
| Q6M6N7 | Resuscitation-promoting factor Rpf2 Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534) | 374 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
- 4,937
- matches
- 12,547
- proteomes
- 4,394
- taxa
- 5,839
- structures
- 1
- alphafold models
- 3,055
- domain architectures
- 44
Classification basis
short name matches duf
No scoring reasons supplied.
Related Mech records
| Family | Mech | Record | Protein | Link basis |
|---|---|---|---|---|
| DUF348 (PF03990) | ProteinTraitsMech | DPBB_YuiC-like | P37546 Putative cell wall shaping protein YabE | canonical example family classification |
| DUF348 (PF03990) | ProteinTraitsMech | 3D domain | P37546 Putative cell wall shaping protein YabE | canonical example family classification |
| DUF348 (PF03990) | ProteinTraitsMech | G5 domain | P37546 Putative cell wall shaping protein YabE | canonical example family classification |
| DUF348 (PF03990) | ProteinTraitsMech | Resuscitation-promoting factor, domain of unknown function DUF348 | P37546 Putative cell wall shaping protein YabE | canonical example family classification |
| DUF348 (PF03990) | ProteinTraitsMech | Resuscitation-promoting factor, domain of unknown function DUF348 | trait identifier | |
| DUF348 (PF03990) | ProteinTraitsMech | 3D domain | P37546 Putative cell wall shaping protein YabE | canonical example family classification |
| DUF348 (PF03990) | ProteinTraitsMech | G5-linked-Ubiquitin-like domain | H8EZH5 Resuscitation-promoting factor RpfB | canonical example family classification |
| DUF348 (PF03990) | ProteinTraitsMech | G5-linked-Ubiquitin-like domain | P9WG29 Resuscitation-promoting factor RpfB | canonical example family classification |
| DUF348 (PF03990) | ProteinTraitsMech | G5-linked-Ubiquitin-like domain | Q6M6N7 Resuscitation-promoting factor Rpf2 | canonical example family classification |
| DUF348 (PF03990) | ProteinTraitsMech | G5-linked-Ubiquitin-like domain | trait identifier | |
| DUF348 (PF03990) | ProteinTraitsMech | G5 domain profile | P37546 Putative cell wall shaping protein YabE | canonical example family classification |
| DUF348 (PF03990) | ProteinTraitsMech | Resuscitation-promoting factor rpfb. | P37546 Putative cell wall shaping protein YabE | canonical example family classification |
| DUF348 (PF03990) | TraitMech | dormancy | P9WG29 Resuscitation-promoting factor RpfB | uniprot pfam xref |
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.