vapB30 Resolved · high auto-curated
H37Rv Rv0623 · MTBC0 mtbc0_000656 ·
84 aa · 719963–720217 (+) ·
RefSeq NP_215137.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB30 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system antitoxin VapB30 |
| Revised (this work) | Type II toxin-antitoxin system antitoxin VapB30. Pfam: PSK_trans_fac (PF07704.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ35
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin VapB30 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin VapC30. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon |
| Orthologous group | COG4423 |
| KEGG orthology |
K19687
|
| Gene Ontology (6) |
GO:0008150, GO:0040008, GO:0045927, GO:0048518, GO:0050789, GO:0065007
|
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 |
|---|---|---|---|---|
PSK_trans_fac | PF07704.18 | 1.5e-29 | 1–83 | Rv0623-like transcription factor |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC30 (ribonuclease VapC30), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0624 vapC30 |
ribonuclease VapC30 | 999 | 1000 ctx | neighborhood:882 cooccurence:773 experimental:999 textmining:821 |
Rv0609 vapC28 |
ribonuclease VapC28 | 950 | 945 ctx | cooccurence:772 experimental:754 |
Rv2759c vapC42 |
ribonuclease VapC42 | 959 | 944 ctx | cooccurence:772 experimental:754 |
Rv1982c vapC36 |
ribonuclease VapC36 | 948 | 944 ctx | cooccurence:773 experimental:754 |
Rv1741 vapC34 |
ribonuclease VapC34 | 876 | 864 | experimental:853 |
Rv0622 |
membrane protein | 584 | 584 ctx | neighborhood:583 |
Rv2010 vapC15 |
ribonuclease VapC15 | 752 | 480 ctx | cooccurence:454 textmining:544 |
Rv2021c higA2 |
transcriptional regulator | 651 | 469 ctx | cooccurence:445 |
Rv1560 vapB11 |
antitoxin VapB11 | 445 | 445 ctx | cooccurence:419 |
Rv0621 |
membrane protein | 413 | 413 ctx | neighborhood:410 |
Rv0240 vapC24 |
ribonuclease VapC24 | 403 | 404 ctx | cooccurence:403 |
Rv2549c vapC20 |
ribonuclease VapC20 | 408 | 202 | |
Rv2018 vapB45 hyp |
hypothetical protein | 596 | 196 | textmining:519 |
Rv0608 vapB28 |
antitoxin VapB28 | 687 | 191 | textmining:630 |
Rv0626 vapB5 |
antitoxin VapB5 | 812 | 86 | textmining:803 |
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 VapB30
- MTBC0 PGAP product: type II toxin-antitoxin system antitoxin VapB30
- Pfam (hmmscan --cut_ga): PSK_trans_fac PF07704.18 (E=2e-29)
- (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_215137.1)
- Domains: Pfam-A via hmmscan --cut_ga — PSK_trans_fac (PF07704.18)
- 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
COG4423 - Curated reference: UniProt P9WJ35 (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 —
26 functional partner(s); context anchor
vapC30 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000656|Rv0623|vapB30 MALSIKHPEADRLARALAARTGETLTEAVVTALRERLARETGRARVVPLRDELAAIRHRCAALPVVDNRSAEAILGYDERGLPA