vapB7 Resolved · medium auto-curated
H37Rv Rv0662c · MTBC0 mtbc0_000700 ·
84 aa · 759855–760109 (-) ·
RefSeq NP_215176.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB7 |
|---|---|
| MTBC0 PGAP re-annotation | antitoxin |
| Revised (this work) | Antitoxin. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06777
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Putative antitoxin VapB7 |
| Curated function | Antitoxin component of a possible type II toxin-antitoxin (TA) system. The cognate toxin is VapC7. |
UniProt still lists this protein as Putative antitoxin VapB7; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2ERR5 |
|---|---|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, 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, 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC7 (ribonuclease VapC7), high confidence from genomic context alone (score 886 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0661c vapC7 |
ribonuclease VapC7 | 942 | 886 ctx | neighborhood:882 textmining:511 |
Rv0660c mazE2 |
antitoxin MazE2 | 562 | 562 ctx | neighborhood:560 |
Rv0663 atsD |
arylsulfatase AtsD | 541 | 541 ctx | neighborhood:540 |
Rv0659c mazF2 |
toxin MazF2 | 525 | 525 ctx | neighborhood:524 |
Rv0664 vapB8 |
antitoxin VapB8 | 475 | 476 ctx | neighborhood:473 |
Rv0665 vapC8 |
ribonuclease VapC8 | 475 | 475 ctx | neighborhood:473 |
Rv0666 |
membrane protein | 474 | 475 ctx | neighborhood:473 |
Rv3833 |
AraC family transcriptional regulator | 462 | 55 | textmining:455 |
Rv2640c |
ArsR family transcriptional regulator | 416 | 52 | textmining:410 |
Rv2865 relF |
antitoxin RelF | 440 | 51 | textmining:435 |
Rv2872 vapC43 |
ribonuclease VapC43 | 809 | 50 | textmining:808 |
Rv1960c parD1 |
antitoxin ParD1 | 519 | 50 | textmining:515 |
Rv3167c |
TetR family transcriptional regulator | 518 | 50 | textmining:514 |
Rv1721c vapB12 |
antitoxin VapB12 | 522 | 47 | textmining:519 |
Rv2871 vapB43 |
antitoxin VapB43 | 807 | 46 | textmining:806 |
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 VapB7
- MTBC0 PGAP product: antitoxin
- (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_215176.2)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2ERR5 - Curated reference: UniProt O06777 (SwissProt, reviewed; Predicted)
- 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 —
19 functional partner(s); context anchor
vapC7 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000700|Rv0662c|vapB7 MSMRLAHRLQILLDDECHRRITAVARERGVPVATVVREAIDRGLVSPAGRRKSAGRRLLDAADMSVPEPRELKQELEALRARRG