vapB10 Family assigned · medium auto-curated
H37Rv Rv1398c · MTBC0 mtbc0_001499 ·
85 aa · 1583854–1584111 (-) ·
RefSeq NP_215914.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB10 |
|---|---|
| MTBC0 PGAP re-annotation | CopG family transcriptional regulator |
| Revised (this work) | CopG family transcriptional regulator. Pfam: RHH_5 (PF07878.18), 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 |
P9WLZ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative antitoxin VapB10 |
| Curated function | Putative antitoxin component of a possible type II toxin-antitoxin (TA) system. The cognate toxin is VapC10. |
UniProt still lists this protein as Putative antitoxin VapB10; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5 |
| Orthologous group | 2EQ3X |
| 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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
RHH_5 | PF07878.18 | 8.2e-07 | 1–42 | CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5 |
RHH_1 | PF01402.28 | 1.5e-11 | 2–40 | Ribbon-helix-helix protein, copG family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC10 (ribonuclease VapC10), high confidence from genomic context alone (score 889 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1397c vapC10 |
ribonuclease VapC10 | 889 | 889 ctx | neighborhood:882 |
Rv3583c carD |
RNA polymerase-binding transcription factor CarD | 740 | 740 | coexpression:740 |
Rv1399c nlhH |
carboxylesterase NlhH | 604 | 604 ctx | neighborhood:604 |
Rv1400c lipI |
lipase | 544 | 544 ctx | neighborhood:543 |
Rv1396c PE_PGRS25 |
PE-PGRS family protein PE_PGRS25 | 452 | 452 ctx | neighborhood:452 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 443 | 55 | textmining:435 |
Rv2656c |
prophage protein | 521 | 51 | textmining:516 |
Rv0581 vapB26 |
antitoxin VapB26 | 514 | 49 | textmining:510 |
Rv2355 |
Probable transposase; Rv2355, (MTCY98.24), len: 328 aa. Probable IS6110 transposase. Identical to many other M. tuberculosis IS6110 transpos | 630 | 47 | textmining:628 |
Rv0718 rpsH |
30S ribosomal protein S8 | 518 | 47 | textmining:515 |
Rv2657c |
prophage protein | 435 | 46 | textmining:433 |
Rv1114 vapC32 |
ribonuclease VapC32 | 415 | 44 | textmining:414 |
Rv2278 |
Rv2278, (MTCY339.32c), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase s | 628 | 41 | textmining:628 |
Rv0661c vapC7 |
ribonuclease VapC7 | 603 | 41 | textmining:603 |
Rv0550c vapB3 |
antitoxin VapB3 | 515 | 41 | textmining:515 |
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 VapB10
- MTBC0 PGAP product: CopG family transcriptional regulator
- Pfam (hmmscan --cut_ga): RHH_5 PF07878.18 (E=8e-07), RHH_1 PF01402.28 (E=1e-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_215914.1)
- Domains: Pfam-A via hmmscan --cut_ga — RHH_5 (PF07878.18), 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
2EQ3X - Curated reference: UniProt P9WLZ1 (SwissProt, reviewed; Evidence at protein level)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
16 functional partner(s); context anchor
vapC10 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001499|Rv1398c|vapB10 MKRTNIYLDEEQTASLDKLAAQEGVSRAELIRLLLNRALTTAGDDLASDLQAINDSFGTLRHLDPPVRRSGGREQHLAQVWRATS