vapC44 Family assigned · medium auto-curated
H37Rv Rv3320c · MTBC0 mtbc0_003530 ·
142 aa · 3729780–3730208 (-) ·
RefSeq NP_217837.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC44 |
|---|---|
| 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 |
P9WF53
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC44 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase. Its cognate antitoxin is VapB44 (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | PIN domain |
| Orthologous group | COG1848 |
| KEGG orthology |
K07064
|
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | 0.167 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 | 1.9e-11 | 4–128 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB44 (antitoxin VapB44), high confidence from genomic context alone (score 911 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3321c vapB44 |
antitoxin VapB44 | 911 | 911 ctx | neighborhood:882 |
Rv3322c |
methyltransferase | 566 | 567 ctx | neighborhood:564 |
Rv3323c moaX |
MoaD-MoaE fusion protein MoaX | 565 | 565 ctx | neighborhood:564 |
Rv3324c moaC3 |
cyclic pyranopterin monophosphate synthase accessory protein | 522 | 522 ctx | neighborhood:519 |
Rv3324A |
Rv3324A, len: 44 aa. Probable pseudogene moaB3,fragment of pterin-4-alpha-carbinolamine dehydratase,equivalent to C-terminus of MT3426|Q8VJ3 | 521 | 522 ctx | neighborhood:519 |
Rv1838c vapC13 |
ribonuclease VapC13 | 710 | 508 ctx | cooccurence:505 textmining:436 |
Rv2018 vapB45 hyp |
hypothetical protein | 502 | 502 ctx | cooccurence:500 |
Rv1114 vapC32 |
ribonuclease VapC32 | 416 | 417 ctx | cooccurence:411 |
Rv2954c hyp |
hypothetical protein | 616 | 416 ctx | cooccurence:406 |
Rv1113 vapB32 |
antitoxin VapB32 | 407 | 408 ctx | cooccurence:407 |
Rv0748 vapB31 |
antitoxin VapB31 | 406 | 406 | |
Rv2871 vapB43 |
antitoxin VapB43 | 402 | 403 | |
Rv0240 vapC24 |
ribonuclease VapC24 | 654 | 317 | textmining:515 |
Rv2829c vapC22 |
ribonuclease VapC22 | 501 | 277 | |
Rv3377c |
type B diterpene cyclase | 444 | 208 |
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 VapC44
- MTBC0 PGAP product: type II toxin-antitoxin system VapC family toxin
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=2e-11)
- (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_217837.1)
- 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 P9WF53 (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 —
27 functional partner(s); context anchor
vapB44 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003530|Rv3320c|vapC44 MRALLDVNVLLALLDRDHVDHERARAWITGQIERGWASCAITQNGFVRVISQPRYPSPISVAHAIDLLARATHTRYHEFWSCTVSILDSKVIDRSRLHSPKQVTDAYLLALAVAHDGRFVTFDQSIALTAVPGATKQHLATL