vapC28 Family assigned · medium auto-curated
H37Rv Rv0609 · MTBC0 mtbc0_000639 ·
133 aa · 707038–707439 (+) ·
RefSeq NP_215123.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC28 |
|---|---|
| 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 |
P9WF81
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC28 |
| 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 VapB28. |
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
|
| Gene Ontology (6) |
GO:0008150, GO:0040008, GO:0045926, GO:0048519, GO:0050789, GO:0065007
|
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 | 0.114 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 | 1.9e-18 | 1–124 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB30 (antitoxin VapB30), high confidence from genomic context alone (score 945 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0623 vapB30 |
antitoxin VapB30 | 950 | 945 ctx | cooccurence:772 experimental:754 |
Rv0608 vapB28 |
antitoxin VapB28 | 932 | 930 ctx | neighborhood:882 |
Rv0609A hyp |
hypothetical protein | 836 | 835 ctx | neighborhood:801 |
Rv1740 vapB34 |
antitoxin VapB34 | 785 | 763 | experimental:754 |
Rv0607 hyp |
hypothetical protein | 679 | 679 ctx | neighborhood:675 |
Rv0606 |
Possible transposase (fragment); Rv0606, (MTCY19H5.16c), len: 247 aa. Possible truncated transposase for IS_1536 element, highly similar to | 569 | 569 ctx | neighborhood:552 |
Rv0605 |
IS1536 family serine type transposase | 568 | 568 ctx | neighborhood:552 |
Rv1560 vapB11 |
antitoxin VapB11 | 544 | 544 ctx | cooccurence:540 |
Rv0919 |
GCN5-like N-acetyltransferase | 480 | 480 ctx | cooccurence:477 |
Rv2760c vapB42 |
antitoxin VapB42 | 457 | 435 | |
Rv1982A vapB36 |
antitoxin VapB36 | 464 | 430 | |
Rv2010 vapC15 |
ribonuclease VapC15 | 840 | 383 | textmining:753 |
Rv1561 vapC11 |
ribonuclease VapC11 | 758 | 317 | textmining:660 |
Rv1114 vapC32 |
ribonuclease VapC32 | 846 | 236 | textmining:807 |
Rv2530c vapC39 |
ribonuclease VapC39 | 738 | 232 | textmining:673 |
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 VapC28
- MTBC0 PGAP product: type II toxin-antitoxin system VapC family toxin
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=2e-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_215123.1)
- 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 P9WF81 (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 —
29 functional partner(s); context anchor
vapB30 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000639|Rv0609|vapC28 MIVDTSAIIAILRDEDDAAAYADALANADVRRLSAASYLECGIVLDSQRDPVISRALDELIEEAEFVVEPVTERQARLARAAYADFGRGSGHPAGLNFGDCLSYALAIDRREPLLWKGNDFGHTGVQRALDRR