All families / PF01139
PF01139: RtcB
tRNA-splicing ligase RtcB
- Curation status
- SEEDED
- Seed status
- EX DUF
- Characterization
- UNSCORED
Grounding
PF01139: tRNA-splicing ligase RtcB
IPR001233: integrated entry for tRNA-splicing ligase RtcB
Source description
This family of RNA ligases ([ec:6.5.1.3]) join 2',3'-cyclic phosphate and 5'-OH ends. They catalyse the splicing of tRNA and may also participate in tRNA repair and recovery from stress-induced RNA damage [InterPro reference PUB00152168,InterPro reference PUB00057853,InterPro reference PUB00056744].
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
9 verified sequence examples. FASTA
| UniProt | Protein / organism | Sequence | Provenance |
|---|---|---|---|
| O59245 | tRNA-splicing ligase RtcB Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) | 871 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| P46850 | RNA-splicing ligase RtcB Escherichia coli (strain K12) | 408 aa; version 3 UniProt 2026_03 | PTM REGISTRY MIRROR |
| P90838 | RNA-splicing ligase rtcb-1 Caenorhabditis elegans | 505 aa; version 2 UniProt 2026_03 | PTM REGISTRY MIRROR9 sibling references |
| Q58095 | tRNA-splicing ligase RtcB Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) | 968 aa; version 1 UniProt 2026_03 | PTM REGISTRY MIRROR2 sibling references |
| Q6AYT3 | RNA-splicing ligase RTCB Rattus norvegicus | 505 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| Q8IIU6 | RNA-splicing ligase RTCB Plasmodium falciparum (isolate 3D7) | 506 aa; version 1 UniProt 2026_03 | UNIPROT FETCH |
| Q99LF4 | RNA-splicing ligase RTCB Mus musculus | 505 aa; version 1 UniProt 2026_03 | UNIPROT FETCH11 sibling references
|
| Q9VIW7 | RNA-splicing ligase RtcB Drosophila melanogaster | 506 aa; version 1 UniProt 2026_03 | UNIPROT FETCH |
| Q9Y3I0 | RNA-splicing ligase RTCB Homo sapiens | 505 aa; version 1 UniProt 2026_03 | UNIPROT FETCH11 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
- 12,598
- matches
- 15,105
- proteomes
- 9,357
- taxa
- 17,245
- structures
- 20
- alphafold models
- 8,370
- domain architectures
- 66
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.