vapC8 Family assigned · medium auto-curated
H37Rv Rv0665 · MTBC0 mtbc0_000703 ·
112 aa · 762887–763225 (+) ·
RefSeq NP_215179.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC8 |
|---|---|
| MTBC0 PGAP re-annotation | PIN domain-containing protein |
| Revised (this work) | PIN domain-containing protein. Pfam: PIN (PF01850.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFB1
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Ribonuclease VapC8 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase. The cognate antitoxin is VapB8 (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | PIN domain |
| Orthologous group | COG1487 |
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
PIN | PF01850.28 | 4.1e-06 | 10–109 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB5 (antitoxin VapB5), high confidence from genomic context alone (score 977 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0626 vapB5 |
antitoxin VapB5 | 978 | 977 ctx | cooccurence:772 experimental:891 |
Rv0664 vapB8 |
antitoxin VapB8 | 888 | 888 ctx | neighborhood:882 |
Rv0596c vapB4 |
antitoxin VapB4 | 804 | 796 | experimental:784 |
Rv0666 |
membrane protein | 790 | 790 ctx | neighborhood:781 |
Rv0663 atsD |
arylsulfatase AtsD | 709 | 709 ctx | neighborhood:700 |
Rv3407 vapB47 |
antitoxin VapB47 | 642 | 642 ctx | cooccurence:541 |
Rv3181c vapB49 |
antitoxin VapB45 | 606 | 606 ctx | cooccurence:495 |
Rv3408 vapC47 |
ribonuclease VapC47 | 596 | 597 ctx | cooccurence:594 |
Rv0659c mazF2 |
toxin MazF2 | 536 | 535 | |
Rv3479 |
transmembrane protein | 514 | 515 ctx | cooccurence:512 |
Rv3385c vapB46 |
antitoxin VapB46 | 502 | 502 | |
Rv3180c vapC49 |
ribonuclease VapC45 | 492 | 492 ctx | cooccurence:490 |
Rv1995 hyp |
hypothetical protein | 484 | 484 ctx | cooccurence:484 |
Rv3384c vapC46 |
ribonuclease VapC46 | 488 | 477 ctx | cooccurence:473 |
Rv0661c vapC7 |
ribonuclease VapC7 | 515 | 475 ctx | neighborhood:475 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: ribonuclease VapC8
- MTBC0 PGAP product: PIN domain-containing protein
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=4e-06)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215179.1)
- Domains: Pfam-A via hmmscan --cut_ga — PIN (PF01850.28)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG1487 - Curated reference: UniProt P9WFB1 (SwissProt, reviewed; Inferred from homology)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
26 functional partner(s); context anchor
vapB5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000703|Rv0665|vapC8 MTEGEVGVGLLDTSVFIARESGGAIADLPERVALSVMTIGELQLGLLNAGDSATRSRRADTLALARTADQIPVSEAVMISLARLVADCRAAGVRRSVKLTDALIAATAEIKV