Rv0298 Family assigned · medium auto-curated
H37Rv Rv0298 · MTBC0 mtbc0_000317 ·
75 aa · 366591–366818 (+) ·
RefSeq NP_214812.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin |
|---|---|
| MTBC0 PGAP re-annotation | ribbon-helix-helix protein%2C CopG family |
| Revised (this work) | Ribbon-helix-helix protein%2C CopG family. 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 |
P9WJ09
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin Rv0298 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin Rv0299. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Ribbon-helix-helix protein, copG family |
| Orthologous group | 2B37W |
| 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.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.333 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
RHH_1 | PF01402.28 | 8.5e-11 | 5–42 | Ribbon-helix-helix protein, copG family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0299 (toxin), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0299 |
toxin | 989 | 887 ctx | neighborhood:882 textmining:912 |
Rv0300 vapB2 |
antitoxin VapB2 | 681 | 681 ctx | neighborhood:667 |
Rv0301 vapC2 |
ribonuclease VapC2 | 675 | 675 ctx | neighborhood:667 |
Rv0297 PE_PGRS5 |
PE-PGRS family protein PE_PGRS5 | 499 | 498 ctx | neighborhood:498 |
Rv0302 |
transcriptional regulator | 426 | 427 ctx | neighborhood:423 |
Rv0303 |
dehydrogenase/reductase | 421 | 421 ctx | neighborhood:421 |
Rv0909 |
antitoxin | 630 | 55 | textmining:625 |
Rv0910 |
toxin | 629 | 55 | textmining:624 |
Rv3182 higB3 hyp |
hypothetical protein | 657 | 50 | textmining:654 |
Rv3750c vapB50 |
excisionase | 806 | 47 | textmining:805 |
Rv3697c vapC48 |
ribonuclease VapC48 | 617 | 47 | textmining:615 |
Rv2018 vapB45 hyp |
hypothetical protein | 450 | 46 | textmining:448 |
Rv3749c vapC50 hyp |
hypothetical protein | 861 | 45 | textmining:861 |
Rv2021c higA2 |
transcriptional regulator | 631 | 44 | textmining:630 |
Rv3183 higA3 |
transcriptional regulator | 630 | 44 | textmining:629 |
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
- MTBC0 PGAP product: ribbon-helix-helix protein%2C CopG family
- Pfam (hmmscan --cut_ga): RHH_1 PF01402.28 (E=9e-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_214812.1)
- 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
2B37W - Curated reference: UniProt P9WJ09 (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 —
24 functional partner(s); context anchor
Rv0299 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000317|Rv0298| MTKEKISVTVDAAVLAAIDADARAAGLNRSEMIEQALRNEHLRVALRDYTAKTVPALDIDAYAQRVYQANRAAGS