vapC29 Resolved · high auto-curated
H37Rv Rv0617 · MTBC0 mtbc0_000650 ·
133 aa · 714558–714959 (+) ·
RefSeq NP_215131.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC29 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system ribonuclease VapC29 |
| Revised (this work) | Type II toxin-antitoxin system ribonuclease VapC29. 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 |
P9WF79
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC29 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. Its cognate antitoxin is VapB29 (By similarity). Has ribonuclease activity. |
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 | COG1848 |
| KEGG orthology |
K07064
|
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 | 0.349 · 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 | 6.7e-14 | 3–121 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB29 (antitoxin VapB29), high confidence from genomic context alone (score 801 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0616A vapB29 |
antitoxin VapB29 | 906 | 801 ctx | neighborhood:801 textmining:548 |
Rv0616c |
Hypothetical protein; Rv0616c, (MTCY19H5.05), len: 88 aa. Hypothetical unknown protein. | 580 | 579 ctx | neighborhood:577 |
Rv0618 galTa |
Rv0618, (MTCY19H5.03c), len: 231 aa (probable partial CDS). Probable galTa, first part of galactose-1-phosphate uridylyltransferase, highly | 514 | 514 ctx | neighborhood:508 |
Rv0619 galTb |
Rv0619, (MTCY19H5.02c), len: 181 aa (probable partial CDS). Probable galTb, second part of galactose-1-phosphate uridylyltransferase, highly | 510 | 511 ctx | neighborhood:508 |
Rv2018 vapB45 hyp |
hypothetical protein | 505 | 506 ctx | cooccurence:502 |
Rv0620 galK |
galactokinase | 499 | 500 ctx | neighborhood:500 |
Rv1114 vapC32 |
ribonuclease VapC32 | 878 | 409 ctx | cooccurence:403 textmining:803 |
Rv2871 vapB43 |
antitoxin VapB43 | 406 | 407 | |
Rv0748 vapB31 |
antitoxin VapB31 | 402 | 403 | |
Rv0624 vapC30 |
ribonuclease VapC30 | 563 | 303 | |
Rv2010 vapC15 |
ribonuclease VapC15 | 719 | 218 | textmining:656 |
Rv0609 vapC28 |
ribonuclease VapC28 | 833 | 191 | textmining:803 |
Rv2548 vapC19 |
ribonuclease VapC19 | 761 | 185 | textmining:720 |
Rv0065 vapC1 |
ribonuclease VapC1 | 830 | 183 | textmining:801 |
Rv1561 vapC11 |
ribonuclease VapC11 | 832 | 170 | textmining:807 |
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 VapC29
- MTBC0 PGAP product: type II toxin-antitoxin system ribonuclease VapC29
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=7e-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_215131.1)
- 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 P9WF79 (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
vapB29 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000650|Rv0617|vapC29 MTVLLDANVLIALVVAEHVHHDAAADWLMASDTGFATCPMTQGSLVRFLVRSGQSAAAARDVVSAVQCTSRHEFWPDALSFAGVEVAGVVGHRQVTDAYLAQLARSHDGQLATLDSGLAHLHGDVAVLIPTTT