vapC27 Family assigned · medium auto-curated
H37Rv Rv0598c · MTBC0 mtbc0_000628 ·
137 aa · 700706–701119 (-) ·
RefSeq NP_215112.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC27 |
|---|---|
| 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 |
P9WF83
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC27 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Probably the toxic component of a type II toxin-antitoxin (TA) system. An RNase (By similarity). Its cognate antitoxin is VapB27. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | PIN domain |
| Orthologous group | COG1848 |
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | 0.582 · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
PIN | PF01850.28 | 1.9e-14 | 7–127 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB27 (antitoxin VapB27), high confidence from genomic context alone (score 909 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0599c vapB27 |
antitoxin VapB27 | 957 | 909 ctx | neighborhood:882 textmining:546 |
Rv0600c |
two component sensor kinase HK1 | 526 | 526 ctx | neighborhood:523 |
Rv0597c hyp |
hypothetical protein | 450 | 449 ctx | neighborhood:424 |
Rv0596c vapB4 |
antitoxin VapB4 | 514 | 306 | |
Rv0595c vapC4 |
ribonuclease VapC4 | 696 | 291 | textmining:590 |
Rv0609 vapC28 |
ribonuclease VapC28 | 672 | 164 | textmining:624 |
Rv3181c vapB49 |
antitoxin VapB45 | 446 | 74 | textmining:427 |
Rv0301 vapC2 |
ribonuclease VapC2 | 631 | 73 | textmining:618 |
Rv2010 vapC15 |
ribonuclease VapC15 | 400 | 73 | |
Rv3320c vapC44 |
ribonuclease VapC44 | 662 | 68 | textmining:653 |
Rv0617 vapC29 |
ribonuclease VapC29 | 525 | 67 | textmining:512 |
Rv2530c vapC39 |
ribonuclease VapC39 | 635 | 55 | textmining:630 |
Rv0627 vapC5 |
ribonuclease VapC5 | 469 | 55 | textmining:461 |
Rv2103c vapC37 |
ribonuclease VapC37 | 660 | 53 | textmining:656 |
Rv2494 vapC38 |
ribonuclease VapC38 | 656 | 53 | textmining:652 |
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 VapC27
- MTBC0 PGAP product: type II toxin-antitoxin system VapC family toxin
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=2e-14)
- (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_215112.1)
- 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
COG1848 - Curated reference: UniProt P9WF83 (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 —
31 functional partner(s); context anchor
vapB27 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000628|Rv0598c|vapC27 MKPPLAVDTSVAIPLLVRTHTAHAAVVAWWAHREAALCGHALAETYSVLTRLPRDLRLAPMDAARLLTERFAAPLLLSSRTTEHLPRVLAQFEITGGAVYDALVALAAAEHRAELATRDARAKDTYEKIGVHVVVAA