vapC11 Resolved · high auto-curated
H37Rv Rv1561 · MTBC0 mtbc0_001669 ·
134 aa · 1776943–1777347 (+) ·
RefSeq NP_216077.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC11 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system toxin ribonuclease VapC11 |
| Revised (this work) | Type II toxin-antitoxin system toxin ribonuclease VapC11. 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 |
P9WFA5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC11 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. Acts as an RNase. Upon expression in E.coli and M.smegmatis inhibits translation, cell growth and colony formation. Its toxic effects on cell growth and colony formation are neutralized by coexpression with cognate antitoxin VapB11; the effect on translation has not been tested but is probably also neutralized. |
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 | COG1487 |
| Gene Ontology (69) |
GO:0003674, GO:0003824, GO:0004518, GO:0004540, GO:0006139, GO:0006417, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0009605, GO:0009607 +57 more
|
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.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.688 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
PIN | PF01850.28 | 1.2e-18 | 2–124 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB11 (antitoxin VapB11), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1560 vapB11 |
antitoxin VapB11 | 999 | 1000 ctx | neighborhood:882 cooccurence:703 coexpression:817 experimental:999 |
Rv2009 vapB15 |
antitoxin VapB15 | 872 | 872 | experimental:853 |
Rv3677c |
beta lactamase | 765 | 765 | coexpression:765 |
Rv2531c |
amino acid decarboxylase | 687 | 687 | coexpression:687 |
Rv1559 ilvA |
threonine dehydratase IlvA | 668 | 668 ctx | neighborhood:659 |
Rv0624 vapC30 |
ribonuclease VapC30 | 795 | 653 | coexpression:514 textmining:434 |
Rv0158 |
transcriptional regulator | 651 | 651 | coexpression:651 |
Rv1558 hyp |
hypothetical protein | 566 | 566 ctx | neighborhood:563 |
Rv1557 mmpL6 |
transmembrane transport protein MmpL6 | 561 | 561 ctx | neighborhood:556 |
Rv2759c vapC42 |
ribonuclease VapC42 | 460 | 458 | |
Rv0300 vapB2 |
antitoxin VapB2 | 438 | 439 | experimental:412 |
Rv3263 |
DNA methylase | 432 | 432 | coexpression:431 |
Rv2601A vapB41 |
antitoxin VapB41 | 430 | 408 | |
Rv1952 vapB14 |
antitoxin VapB14 | 429 | 407 | |
Rv2010 vapC15 |
ribonuclease VapC15 | 473 | 375 |
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 VapC11
- MTBC0 PGAP product: type II toxin-antitoxin system toxin ribonuclease VapC11
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=1e-18)
- (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_216077.1)
- 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 P9WFA5 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
32 functional partner(s); context anchor
vapB11 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001669|Rv1561|vapC11 MILIDTSAWVEYFRATGSIAAVEVRRLLSEEAARIAMCEPIAMEILSGALDDNTHTTLERLVNGLPSLNVDDAIDFRAAAGIYRAARRAGETVRSINDCLIAALAIRHGARIVHRDADFDVIARITNLQAASFR