vapC33 Family assigned · medium auto-curated
H37Rv Rv1242 · MTBC0 mtbc0_001331 ·
143 aa · 1392979–1393410 (+) ·
RefSeq NP_215758.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC33 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system VapC family toxin |
| Revised (this work) | Type II toxin-antitoxin system VapC family toxin. 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 |
P9WF69
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC33 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase (By similarity). Upon expression in M.smegmatis inhibits colony formation. Its toxic effect is neutralized by coexpression with cognate antitoxin VapB33. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Toxic component of a toxin-antitoxin (TA) module. An RNase |
| Orthologous group | COG1848 |
| KEGG orthology |
K07064
|
| Gene Ontology (12) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040008, GO:0044464, GO:0045926, GO:0048519, GO:0050789, GO:0065007, GO:0071944
|
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 | 2.4e-06 | 2–134 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB33 (antitoxin VapB33), high confidence from genomic context alone (score 896 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1241 vapB33 |
antitoxin VapB33 | 896 | 896 ctx | neighborhood:882 |
Rv1240 mdh |
malate dehydrogenase | 630 | 630 ctx | neighborhood:611 |
Rv0748 vapB31 |
antitoxin VapB31 | 526 | 527 | experimental:508 |
Rv2871 vapB43 |
antitoxin VapB43 | 525 | 526 | experimental:508 |
Rv0595c vapC4 |
ribonuclease VapC4 | 815 | 493 ctx | cooccurence:488 textmining:651 |
Rv0626 vapB5 |
antitoxin VapB5 | 488 | 489 ctx | cooccurence:478 |
Rv1720c vapC12 |
ribonuclease VapC12 | 438 | 439 ctx | cooccurence:438 |
Rv1239c corA |
magnesium and cobalt transport transmembrane protein CorA | 424 | 425 ctx | neighborhood:421 |
Rv0960 vapC9 |
ribonuclease VapC9 | 414 | 414 ctx | cooccurence:411 |
Rv2548 vapC19 |
ribonuclease VapC19 | 595 | 409 ctx | cooccurence:407 |
Rv1114 vapC32 |
ribonuclease VapC32 | 861 | 326 | textmining:803 |
Rv1838c vapC13 |
ribonuclease VapC13 | 406 | 316 | |
Rv0065 vapC1 |
ribonuclease VapC1 | 545 | 308 | |
Rv2549c vapC20 |
ribonuclease VapC20 | 653 | 295 | textmining:529 |
Rv2010 vapC15 |
ribonuclease VapC15 | 725 | 242 | textmining:653 |
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 VapC33
- MTBC0 PGAP product: type II toxin-antitoxin system VapC family toxin
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=2e-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_215758.1)
- 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
COG1848 - Curated reference: UniProt P9WF69 (SwissProt, reviewed; Evidence at protein level)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
30 functional partner(s); context anchor
vapB33 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001331|Rv1242|vapC33 MIIPDINLLLYAVITGFPQHRRAHAWWQDTVNGHTRIGLTYPALFGFLRIATSARVLAAPLPTADAIAYVREWLSQPNVDLLTAGPRHLDIALGLLDKLGTASHLTTDVQLAAYGIEYDAEIHSSDTDFARFADLKWTDPLRE