vapC9 Family assigned · medium auto-curated
H37Rv Rv0960 · MTBC0 mtbc0_001025 ·
127 aa · 1080760–1081143 (+) ·
RefSeq NP_215475.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC9 |
|---|---|
| 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 |
P9WFA9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC9 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase. The cognate antitoxin is VapB9 (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 | COG4113 |
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 | 0.371 · 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 | 1.1e-16 | 2–115 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB9 (antitoxin VapB9), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0959A vapB9 |
antitoxin VapB9 | 882 | 882 ctx | neighborhood:882 |
Rv0549c vapC3 |
ribonuclease VapC3 | 813 | 775 ctx | cooccurence:774 |
Rv3098A |
PemK-like protein | 762 | 754 ctx | cooccurence:753 |
Rv0959 hyp |
hypothetical protein | 658 | 658 ctx | neighborhood:653 |
Rv0958 |
magnesium chelatase | 629 | 629 ctx | neighborhood:627 |
Rv3384c vapC46 |
ribonuclease VapC46 | 621 | 622 ctx | cooccurence:616 |
Rv2801A mazE9 |
antitoxin MazE9 | 609 | 610 ctx | cooccurence:609 |
Rv3407 vapB47 |
antitoxin VapB47 | 558 | 559 ctx | cooccurence:543 |
Rv0456A mazF1 |
toxin MazF1 | 539 | 523 ctx | cooccurence:519 |
Rv2018 vapB45 hyp |
hypothetical protein | 534 | 523 ctx | cooccurence:522 |
Rv1962c vapC35 |
ribonuclease VapC35 | 523 | 523 ctx | cooccurence:522 |
Rv0961 |
integral membrane protein | 503 | 503 ctx | neighborhood:496 |
Rv2103c vapC37 |
ribonuclease VapC37 | 485 | 485 ctx | cooccurence:480 |
Rv3408 vapC47 |
ribonuclease VapC47 | 646 | 478 ctx | cooccurence:473 |
Rv0749 vapC31 |
ribonuclease VapC31 | 474 | 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 VapC9
- MTBC0 PGAP product: type II toxin-antitoxin system VapC family toxin
- 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_215475.1)
- 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
COG4113 - Curated reference: UniProt P9WFA9 (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 —
40 functional partner(s); context anchor
vapB9 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001025|Rv0960|vapC9 MIVVDASAALAALLNDGQARQLIAAERLHVPHLVDSEIASGLRRLAQRDRLGAADGRRALQTWRRLAVTRYPVVGLFERIWEIRANLSAYDASYVALAEALNCALVTADLRLSDTGQAQCPITVVPR