vapC16 Resolved · medium auto-curated
H37Rv Rv2231A · MTBC0 - ·
141 aa · 2505736–2506161 (-) ·
RefSeq YP_007410917.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC16 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Ribonuclease VapC16. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P0CV93
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Ribonuclease VapC16 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase. The cognate antitoxin is VapB16 (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | ribonuclease activity |
| Orthologous group | COG3744 |
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 | 0.524 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PPE8 (PPE family protein PPE8), high confidence from genomic context alone (score 767 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2308 hyp |
hypothetical protein | 791 | 791 ctx | cooccurence:742 |
Rv0355c PPE8 |
PPE family protein PPE8 | 767 | 767 ctx | cooccurence:767 |
Rv3350c PPE56 |
PPE family protein PPE56 | 765 | 765 ctx | cooccurence:765 |
Rv3347c PPE55 |
PPE family protein PPE55 | 765 | 765 ctx | cooccurence:765 |
Rv1917c PPE34 |
PPE family protein PPE34 | 764 | 764 ctx | cooccurence:764 |
Rv0304c PPE5 |
PPE family protein PPE5 | 762 | 762 ctx | cooccurence:762 |
Rv2209 |
integral membrane protein | 762 | 762 ctx | cooccurence:762 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 761 | 761 ctx | cooccurence:761 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 761 | 761 ctx | cooccurence:761 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 760 | 760 ctx | cooccurence:760 |
Rv3343c PPE54 |
PPE family protein PPE54 | 760 | 760 ctx | cooccurence:760 |
Rv1004c |
membrane protein | 760 | 760 ctx | cooccurence:760 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 752 | 752 ctx | cooccurence:752 |
Rv0305c PPE6 |
PPE family protein PPE6 | 749 | 749 ctx | cooccurence:749 |
Rv2082 hyp |
hypothetical protein | 747 | 747 ctx | cooccurence:747 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): ribonuclease VapC16
- (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 YP_007410917.1)
- 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
COG3744 - Curated reference: UniProt P0CV93 (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 —
94 functional partner(s); context anchor
PPE8 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2231A|vapC16 MTMACTACPTIWTLRCQTTCSNAFTGEALPHRHPRLAADAVNETRAIVQDVRNSILLSAASAWEIAINYRLGKLPPPEPSASYVPDRMRRCGTSPLSVDHAHTAHRRASGSPSTSIRPCAHRPGTAAWPDDHHRRRPVSCL