Rv0909 Resolved · high auto-curated
H37Rv Rv0909 · MTBC0 mtbc0_000964 ·
59 aa · 1017896–1018075 (+) ·
RefSeq NP_215424.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin |
|---|---|
| MTBC0 PGAP re-annotation | antitoxin |
| Revised (this work) | Antitoxin. Pfam: MT0933_antitox (PF14013.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ07
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin Rv0909 |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin Rv0910. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | MT0933-like antitoxin protein |
| Orthologous group | 2EJAX |
| 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) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.08% of strains (1571) · clonal |
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 |
|---|---|---|---|---|
MT0933_antitox | PF14013.12 | 1.7e-19 | 4–50 | MT0933-like antitoxin protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0910 (toxin), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0910 |
toxin | 978 | 887 ctx | neighborhood:882 textmining:814 |
Rv3301c phoY1 |
phosphate transport system transcriptional regulator PhoY | 733 | 733 | coexpression:733 |
Rv0911 hyp |
hypothetical protein | 619 | 620 ctx | neighborhood:604 |
Rv0906 hyp |
hypothetical protein | 582 | 583 ctx | neighborhood:544 |
Rv0908 ctpE |
metal cation transporter ATPase E | 576 | 576 ctx | neighborhood:544 |
Rv0907 hyp |
hypothetical protein | 546 | 546 ctx | neighborhood:544 |
Rv0905 echA6 |
enoyl-CoA hydratase EchA6 | 545 | 545 ctx | neighborhood:544 |
Rv0273c |
transcriptional regulator | 533 | 533 | coexpression:533 |
Rv2418c octT hyp |
hypothetical protein | 500 | 476 | experimental:425 |
Rv1075c hyp |
hypothetical protein | 498 | 474 | experimental:425 |
Rv1740 vapB34 |
antitoxin VapB34 | 474 | 474 | coexpression:474 |
Rv0518 hyp |
hypothetical protein | 494 | 470 | experimental:425 |
Rv0912 |
transmembrane protein | 445 | 445 ctx | neighborhood:442 |
Rv1975 hyp |
hypothetical protein | 440 | 440 | coexpression:430 |
Rv0157A hyp |
hypothetical protein | 438 | 438 | coexpression:428 |
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: antitoxin
- Pfam (hmmscan --cut_ga): MT0933_antitox PF14013.12 (E=2e-19)
- (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_215424.1)
- Domains: Pfam-A via hmmscan --cut_ga — MT0933_antitox (PF14013.12)
- 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
2EJAX - Curated reference: UniProt P9WJ07 (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 —
37 functional partner(s); context anchor
Rv0910 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000964|Rv0909| MGILDKVKNLLSQNADKVETVINKAGEFVDEQTQGNYSDAIHKLQDAASNVVGMSDQQS