vapC15 Family assigned · medium auto-curated
H37Rv Rv2010 · MTBC0 mtbc0_002138 ·
132 aa · 2281886–2282284 (+) ·
RefSeq NP_216526.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC15 |
|---|---|
| MTBC0 PGAP re-annotation | PIN domain nuclease |
| Revised (this work) | PIN domain nuclease. 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 |
P9WF97
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC15 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. Degrades total E.coli RNA, which is partially inhibited by cognate antitoxin VapB15. Upon expression in M.smegmatis inhibits colony formation, which is neutralized by coexpression with VapB15. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | vapC |
| eggNOG description | nuclease activity |
| Orthologous group | COG1487 |
| Gene Ontology (12) |
GO:0001666, GO:0006950, GO:0008150, GO:0009628, GO:0036293, GO:0040008, GO:0045926, GO:0048519, GO:0050789, GO:0050896, GO:0065007, GO:0070482
|
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 | 0.351 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 | 1.2e-16 | 1–120 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB15 (antitoxin VapB15), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2009 vapB15 |
antitoxin VapB15 | 999 | 1000 ctx | neighborhood:882 experimental:999 textmining:888 |
Rv1560 vapB11 |
antitoxin VapB11 | 961 | 961 ctx | cooccurence:706 experimental:853 |
Rv2008c hyp |
hypothetical protein | 723 | 724 ctx | neighborhood:600 |
Rv0623 vapB30 |
antitoxin VapB30 | 752 | 480 ctx | cooccurence:454 textmining:544 |
Rv0624 vapC30 |
ribonuclease VapC30 | 893 | 478 | textmining:804 |
Rv0300 vapB2 |
antitoxin VapB2 | 814 | 454 | experimental:412 textmining:674 |
Rv2601A vapB41 |
antitoxin VapB41 | 434 | 412 | |
Rv1952 vapB14 |
antitoxin VapB14 | 429 | 407 | |
Rv2549c vapC20 |
ribonuclease VapC20 | 784 | 395 | textmining:658 |
Rv0960 vapC9 |
ribonuclease VapC9 | 401 | 387 | |
Rv0609 vapC28 |
ribonuclease VapC28 | 840 | 383 | textmining:753 |
Rv1561 vapC11 |
ribonuclease VapC11 | 473 | 375 | |
Rv0626 vapB5 |
antitoxin VapB5 | 767 | 356 | textmining:654 |
Rv0582 vapC26 |
ribonuclease VapC26 | 757 | 316 | textmining:659 |
Rv2829c vapC22 |
ribonuclease VapC22 | 482 | 301 |
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 VapC15
- MTBC0 PGAP product: PIN domain nuclease
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=1e-16)
- (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_216526.1)
- 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 P9WF97 (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 —
35 functional partner(s); context anchor
vapB15 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002138|Rv2010|vapC15 MIVDTSVWIAYLSTSESLASRWLADRIAADSTVIVPEVVMMELLIGKTDEDTAALRRRLLQRFAIEPLAPVRDAEDAAAIHRRCRRGGDTVRSLIDCQVAAMALRIGVAVAHRDRDYEAIRTHCGLRTEPLF