vapC42 Family assigned · medium auto-curated
H37Rv Rv2759c · MTBC0 mtbc0_002936 ·
131 aa · 3093290–3093685 (-) ·
RefSeq NP_217275.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC42 |
|---|---|
| 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 |
P9WF57
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC42 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase. Its cognate antitoxin is VapB42 (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 | COG3742 |
| KEGG orthology |
K19686
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 | 1.1e-19 | 1–125 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB42 (antitoxin VapB42), high confidence from genomic context alone (score 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2760c vapB42 |
antitoxin VapB42 | 987 | 987 ctx | neighborhood:882 coexpression:834 |
Rv0623 vapB30 |
antitoxin VapB30 | 959 | 944 ctx | cooccurence:772 experimental:754 |
Rv2761c hsdS |
type I restriction/modification system specificity determinant HsdS | 811 | 810 ctx | neighborhood:801 |
Rv2762c hyp |
hypothetical protein | 802 | 803 ctx | neighborhood:800 |
Rv1740 vapB34 |
antitoxin VapB34 | 792 | 769 | experimental:754 |
Rv2757c vapC21 |
ribonuclease VapC21 | 828 | 764 ctx | neighborhood:753 |
Rv2758c vapB21 |
antitoxin VapB21 | 756 | 756 ctx | neighborhood:753 |
Rv3439c hyp |
hypothetical protein | 730 | 730 | coexpression:730 |
Rv1560 vapB11 |
antitoxin VapB11 | 623 | 624 ctx | cooccurence:529 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 615 | 615 | coexpression:615 |
Rv2755c hsdS.1 |
Rv2755c, (MTV002.20c), len: 91 aa. Possible hsdS.1,fragment of type I restriction/modification system specificity determinant (S protein), s | 600 | 600 ctx | neighborhood:530 |
Rv2763c dfrA |
dihydrofolate reductase | 595 | 596 ctx | neighborhood:593 |
Rv0273c |
transcriptional regulator | 580 | 580 | coexpression:580 |
Rv2756c hsdM |
type I restriction/modification system DNA methylase HsdM | 553 | 552 ctx | neighborhood:532 |
Rv0919 |
GCN5-like N-acetyltransferase | 475 | 475 ctx | cooccurence:472 |
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 VapC42
- MTBC0 PGAP product: type II toxin-antitoxin system VapC family toxin
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=1e-19)
- (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_217275.1)
- 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
COG3742 - Curated reference: UniProt P9WF57 (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 —
25 functional partner(s); context anchor
vapB42 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002936|Rv2759c|vapC42 MIVDTSAIVAIVSGESGAQVLKEALERSPNSRMSAPNYVELCAIMQRRDRPEISRLVDRLLDDYGIQVEAVDADQARVAAQAYRDYGRGSGHPARLNLGDTYSYALAQVTGEPLLFRGDDFTHTDIRPACT