vapC17 Family assigned · medium auto-curated
H37Rv Rv2527 · MTBC0 mtbc0_002691 ·
133 aa · 2874205–2874606 (+) ·
RefSeq NP_217043.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC17 |
|---|---|
| MTBC0 PGAP re-annotation | PIN domain-containing protein |
| Revised (this work) | PIN domain-containing protein. 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 |
P9WF95
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC17 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase. The cognate antitoxin is VapB17 (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 | 0.331 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 | 2.0e-05 | 27–118 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB17 (antitoxin VapB17), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2526 vapB17 |
antitoxin VapB17 | 887 | 887 ctx | neighborhood:882 |
Rv0300 vapB2 |
antitoxin VapB2 | 433 | 434 | experimental:412 |
Rv2601A vapB41 |
antitoxin VapB41 | 472 | 415 | |
Rv1952 vapB14 |
antitoxin VapB14 | 430 | 408 | |
Rv3436c glmS |
glucosamine--fructose-6-phosphate aminotransferase | 468 | 76 | textmining:449 |
Rv2549c vapC20 |
ribonuclease VapC20 | 444 | 63 | textmining:432 |
Rv2528c mrr |
restriction system protein | 443 | 61 | textmining:432 |
Rv2534c efp |
elongation factor P | 517 | 53 | textmining:511 |
Rv0749 vapC31 |
ribonuclease VapC31 | 653 | 51 | textmining:650 |
Rv2530c vapC39 |
ribonuclease VapC39 | 442 | 50 | textmining:437 |
Rv2035 hyp |
hypothetical protein | 623 | 47 | textmining:621 |
Rv2801A mazE9 |
antitoxin MazE9 | 441 | 46 | textmining:439 |
Rv0627 vapC5 |
ribonuclease VapC5 | 414 | 46 | textmining:411 |
Rv1766 hyp |
hypothetical protein | 513 | 45 | textmining:511 |
Rv1048c hyp |
hypothetical protein | 513 | 45 | textmining:511 |
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 VapC17
- MTBC0 PGAP product: PIN domain-containing protein
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=2e-05)
- (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_217043.1)
- 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
COG1487 - Curated reference: UniProt P9WF95 (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 —
28 functional partner(s); context anchor
vapB17 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002691|Rv2527|vapC17 MTTWILDKSAHVRLVAGATPPAGIDLTDLAICDIGELEWLYSARSATDYDSQQTSLRAYQILRAPSDIFDRVRHLQRDLAHHRGMWHRTPLPDLFIAETALHHRAGVLHHDRDYKRIAVVRPGFQACELSRGR