vapB19 Family assigned · medium auto-curated
H37Rv Rv2547 · MTBC0 mtbc0_002714 ·
85 aa · 2892151–2892408 (+) ·
RefSeq NP_217063.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB19 |
|---|---|
| MTBC0 PGAP re-annotation | CopG family transcriptional regulator |
| Revised (this work) | CopG family transcriptional regulator. 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 |
P95006
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative antitoxin VapB19 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin VapC19. |
UniProt still lists this protein as Putative antitoxin VapB19; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Ribbon-helix-helix protein, copG family |
| Orthologous group | 2BT7R |
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 | 0.37 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 | 3.9e-12 | 1–38 | Ribbon-helix-helix protein, copG family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC19 (ribonuclease VapC19), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2548 vapC19 |
ribonuclease VapC19 | 941 | 884 ctx | neighborhood:882 textmining:518 |
Rv2546 vapC18 |
ribonuclease VapC18 | 740 | 740 ctx | neighborhood:739 |
Rv2545 vapB18 |
antitoxin VapB18 | 811 | 511 ctx | neighborhood:508 textmining:630 |
Rv2544 lppB |
lipoprotein LppB | 475 | 476 ctx | neighborhood:473 |
Rv2543 lppA |
lipoprotein LppA | 461 | 461 ctx | neighborhood:458 |
Rv3321c vapB44 |
antitoxin VapB44 | 807 | 64 | textmining:803 |
Rv2493 vapB38 |
antitoxin VapB38 | 635 | 55 | textmining:630 |
Rv2550c vapB20 |
antitoxin VapB20 | 634 | 53 | textmining:630 |
Rv0599c vapB27 |
antitoxin VapB27 | 517 | 51 | textmining:512 |
Rv1494 mazE4 |
antitoxin MazE4 | 579 | 50 | textmining:576 |
Rv0623 vapB30 |
antitoxin VapB30 | 515 | 50 | textmining:511 |
Rv3320c vapC44 |
ribonuclease VapC44 | 416 | 50 | textmining:411 |
Rv2530A vapB39 |
antitoxin VapB39 | 552 | 47 | textmining:550 |
Rv0608 vapB28 |
antitoxin VapB28 | 521 | 47 | textmining:518 |
Rv2601A vapB41 |
antitoxin VapB41 | 444 | 47 | textmining:441 |
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 VapB19
- MTBC0 PGAP product: CopG family transcriptional regulator
- Pfam (hmmscan --cut_ga): RHH_1 PF01402.28 (E=4e-12)
- (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_217063.1)
- 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
2BT7R - Curated reference: UniProt P95006 (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 —
30 functional partner(s); context anchor
vapC19 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002714|Rv2547|vapB19 MRTQVTLGKEELELLDRAAKASGASRSELIRRAIHRAYGTGSKQERLAALDHSRGSWRGRDFTGTEYVDAIRGDLNERLARLGLA