Rv0299 Resolved · high auto-curated
H37Rv Rv0299 · MTBC0 mtbc0_000318 ·
100 aa · 366815–367117 (+) ·
RefSeq NP_214813.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | toxin |
|---|---|
| MTBC0 PGAP re-annotation | toxin-antitoxin system toxin |
| Revised (this work) | Toxin-antitoxin system toxin. Pfam: Rv0299_toxin (PF27466.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07226
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Toxin Rv0299 |
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis inhibits colony formation. Its toxic effect is neutralized by coexpression with cognate antitoxin Rv0298/MT0312. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2BJJP |
|---|---|
| Gene Ontology (6) |
GO:0008150, GO:0040008, GO:0045926, GO:0048519, 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 | 1.132 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Rv0299_toxin | PF27466.1 | 2.5e-41 | 5–98 | Type II toxin-antitoxin system toxin Rv0299 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0298 (antitoxin), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0298 |
antitoxin | 989 | 887 ctx | neighborhood:882 textmining:912 |
Rv0300 vapB2 |
antitoxin VapB2 | 781 | 781 ctx | neighborhood:667 |
Rv0301 vapC2 |
ribonuclease VapC2 | 683 | 683 ctx | neighborhood:667 |
Rv0297 PE_PGRS5 |
PE-PGRS family protein PE_PGRS5 | 499 | 498 ctx | neighborhood:498 |
Rv0302 |
transcriptional regulator | 430 | 430 ctx | neighborhood:423 |
Rv0303 |
dehydrogenase/reductase | 421 | 421 ctx | neighborhood:421 |
Rv3697c vapC48 |
ribonuclease VapC48 | 550 | 54 | textmining:544 |
Rv0910 |
toxin | 551 | 53 | textmining:546 |
Rv3749c vapC50 hyp |
hypothetical protein | 810 | 50 | textmining:809 |
Rv3750c vapB50 |
excisionase | 804 | 50 | textmining:803 |
Rv0461 |
transmembrane protein | 653 | 47 | textmining:651 |
Rv0909 |
antitoxin | 549 | 47 | textmining:547 |
Rv0624 vapC30 |
ribonuclease VapC30 | 437 | 47 | textmining:434 |
Rv0424c hyp |
hypothetical protein | 652 | 46 | textmining:651 |
Rv2021c higA2 |
transcriptional regulator | 552 | 46 | textmining:550 |
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: toxin
- MTBC0 PGAP product: toxin-antitoxin system toxin
- Pfam (hmmscan --cut_ga): Rv0299_toxin PF27466.1 (E=2e-41)
- (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_214813.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv0299_toxin (PF27466.1)
- 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
2BJJP - Curated reference: UniProt O07226 (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 —
27 functional partner(s); context anchor
Rv0298 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000318|Rv0299| MIAPGDIAPRRDSEHELYVAVLSNALHRAADTGRVITCPFIPGRVPEDLLAMVVAVEQPNGTLLPELVQWLHVAALGAPLGNAGVAALREAASVVTALLC