vapC41 Family assigned · medium auto-curated
H37Rv Rv2602 · MTBC0 mtbc0_002770 ·
146 aa · 2953897–2954337 (+) ·
RefSeq NP_217118.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC41 |
|---|---|
| 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 |
P9WF59
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC41 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase (By similarity). Upon expression in M.smegmatis inhibits colony formation. Its toxic effect is neutralized by coexpression with cognate antitoxin VapB41. |
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
|
| Gene Ontology (8) |
GO:0005575, GO:0005576, GO:0008150, GO:0040008, GO:0045926, GO:0048519, GO:0050789, GO:0065007
|
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 | 1.034 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 | 2.0e-14 | 3–137 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB41 (antitoxin VapB41), high confidence from genomic context alone (score 930 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2601A vapB41 |
antitoxin VapB41 | 930 | 930 ctx | neighborhood:882 coexpression:431 |
Rv2600 |
integral membrane protein | 554 | 553 ctx | neighborhood:551 |
Rv2601 speE |
spermidine synthase | 531 | 531 ctx | neighborhood:528 |
Rv0748 vapB31 |
antitoxin VapB31 | 407 | 408 | |
Rv2871 vapB43 |
antitoxin VapB43 | 403 | 404 | |
Rv2829c vapC22 |
ribonuclease VapC22 | 470 | 71 | textmining:453 |
Rv2494 vapC38 |
ribonuclease VapC38 | 473 | 70 | textmining:458 |
Rv2103c vapC37 |
ribonuclease VapC37 | 544 | 63 | textmining:534 |
Rv2530c vapC39 |
ribonuclease VapC39 | 629 | 55 | textmining:624 |
Rv2548 vapC19 |
ribonuclease VapC19 | 571 | 51 | textmining:567 |
Rv0598c vapC27 |
ribonuclease VapC27 | 532 | 51 | textmining:528 |
Rv0656c vapC6 |
ribonuclease VapC6 | 656 | 48 | textmining:654 |
Rv2757c vapC21 |
ribonuclease VapC21 | 418 | 48 | textmining:414 |
Rv1838c vapC13 |
ribonuclease VapC13 | 610 | 47 | textmining:608 |
Rv3320c vapC44 |
ribonuclease VapC44 | 519 | 47 | textmining:516 |
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 VapC41
- 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_217118.1)
- 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 P9WF59 (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 —
17 functional partner(s); context anchor
vapB41 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002770|Rv2602|vapC41 MLLCDTNIWLALALSGHVHHRASRAWLDTINAPGVIHFCRATQQSLLRLLTNRTVLGAYGSPPLTNREAWAAYAAFLDDDRIVLAGAEPDGLEAQWRAFAVRQSPAPKVWMDAYLAAFALTGGFELVTTDTAFTQYGGIELRLLAK