vapB43 Family assigned · medium auto-curated
H37Rv Rv2871 · MTBC0 mtbc0_003053 ·
85 aa · 3203804–3204061 (+) ·
RefSeq NP_217387.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB43 |
|---|---|
| MTBC0 PGAP re-annotation | ribbon-helix-helix domain-containing protein |
| Revised (this work) | Ribbon-helix-helix domain-containing protein. Pfam: RHH_1 (PF01402.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL41
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB43 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin VapC43. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | vapB43 |
| eggNOG description | Ribbon-helix-helix protein, copG family |
| Orthologous group | COG3905 |
| Gene Ontology (12) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040008, GO:0044464, GO:0045927, GO:0048518, GO:0050789, GO:0065007, GO:0071944
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
RHH_1 | PF01402.28 | 6.5e-08 | 1–38 | Ribbon-helix-helix protein, copG family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC43 (ribonuclease VapC43), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2872 vapC43 |
ribonuclease VapC43 | 999 | 1000 ctx | neighborhood:800 experimental:999 textmining:803 |
Rv2103c vapC37 |
ribonuclease VapC37 | 964 | 965 | experimental:960 |
Rv3697c vapC48 |
ribonuclease VapC48 | 869 | 869 | experimental:858 |
Rv2873 mpt83 |
cell surface lipoprotein | 565 | 564 ctx | neighborhood:562 |
Rv2870c dxr |
1-deoxy-D-xylulose 5-phosphate reductoisomerase | 552 | 551 ctx | neighborhood:550 |
Rv2869c rip |
zinc metalloprotease | 549 | 549 ctx | neighborhood:549 |
Rv0749 vapC31 |
ribonuclease VapC31 | 526 | 527 | experimental:508 |
Rv0277c vapC25 |
ribonuclease VapC25 | 526 | 527 | experimental:508 |
Rv2868c gcpE |
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) | 527 | 526 ctx | neighborhood:526 |
Rv1242 vapC33 |
ribonuclease VapC33 | 525 | 526 | experimental:508 |
Rv2867c |
GCN5-like N-acetyltransferase | 426 | 425 ctx | neighborhood:425 |
Rv0617 vapC29 |
ribonuclease VapC29 | 406 | 407 | |
Rv3408 vapC47 |
ribonuclease VapC47 | 696 | 405 | textmining:511 |
Rv1838c vapC13 |
ribonuclease VapC13 | 650 | 405 | textmining:437 |
Rv2494 vapC38 |
ribonuclease VapC38 | 404 | 405 |
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: antitoxin VapB43
- MTBC0 PGAP product: ribbon-helix-helix domain-containing protein
- Pfam (hmmscan --cut_ga): RHH_1 PF01402.28 (E=6e-08)
- (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_217387.1)
- Domains: Pfam-A via hmmscan --cut_ga — RHH_1 (PF01402.28)
- 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
COG3905 - Curated reference: UniProt P9WL41 (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
vapC43 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003053|Rv2871|vapB43 MRTTIRIDDELYREVKAKAARSGRTVAAVLEDAVRRGLNPPKPQAAGRYRVQPSGKGGLRPGVDLSSNAALAEAMNDGVSVDAVR