vapC6 Resolved · medium auto-curated
H37Rv Rv0656c · MTBC0 mtbc0_000694 ·
127 aa · 757070–757453 (-) ·
RefSeq NP_215170.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC6 |
|---|---|
| MTBC0 PGAP re-annotation | ribonuclease VapC6 |
| Revised (this work) | Ribonuclease VapC6. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFB5
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Ribonuclease VapC6 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II type II toxin-antitoxin (TA) system. An RNase. The cognate antitoxin is VapB6 (By similarity). |
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 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 6 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (214) · clonal |
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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB6 (antitoxin VapB6), medium confidence from genomic context alone (score 680 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0657c vapB6 |
antitoxin VapB6 | 680 | 680 ctx | neighborhood:599 |
Rv0300 vapB2 |
antitoxin VapB2 | 434 | 435 | experimental:412 |
Rv0658c |
integral membrane protein | 416 | 416 ctx | neighborhood:407 |
Rv2601A vapB41 |
antitoxin VapB41 | 431 | 409 | |
Rv1952 vapB14 |
antitoxin VapB14 | 429 | 407 | |
Rv1720c vapC12 |
ribonuclease VapC12 | 675 | 74 | textmining:664 |
Rv2103c vapC37 |
ribonuclease VapC37 | 536 | 55 | textmining:530 |
Rv0277c vapC25 |
ribonuclease VapC25 | 444 | 53 | textmining:437 |
Rv1102c mazF3 |
mRNA interferase MazF3 | 441 | 53 | textmining:434 |
Rv2526 vapB17 |
antitoxin VapB17 | 655 | 51 | textmining:652 |
Rv2274c mazF8 |
toxin MazF8 | 575 | 51 | textmining:571 |
Rv2602 vapC41 |
ribonuclease VapC41 | 656 | 48 | textmining:654 |
Rv3408 vapC47 |
ribonuclease VapC47 | 653 | 48 | textmining:651 |
Rv0549c vapC3 |
ribonuclease VapC3 | 561 | 48 | textmining:558 |
Rv1397c vapC10 |
ribonuclease VapC10 | 658 | 47 | textmining:656 |
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 VapC6
- MTBC0 PGAP product: ribonuclease VapC6
- (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_215170.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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 P9WFB5 (SwissProt, reviewed; Inferred from homology)
- 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 —
18 functional partner(s); context anchor
vapB6 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000694|Rv0656c|vapC6 MAAATTTGTHRGLELRAAQRAVGSCEPQRAEFCRSARNADEFDQMSRMFGDVYPDVPVPKSVWRWIDSAQHRLARAGAVGALSVVDLLICDTAAARGLVVLHDDADYELAERHLPDIRVRRVVSADD