Rv2654c Resolved · medium auto-curated
H37Rv Rv2654c · MTBC0 mtbc0_002828 ·
81 aa · 2999192–2999437 (-) ·
RefSeq NP_217170.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system antitoxin |
| Revised (this work) | Type II toxin-antitoxin system antitoxin. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ11
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin Rv2654c |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin Rv2653c. |
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.414 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2656c (prophage protein), high confidence from genomic context alone (score 784 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2656c |
prophage protein | 921 | 784 ctx | neighborhood:781 textmining:652 |
Rv2655c |
prophage protein | 784 | 784 ctx | neighborhood:781 |
Rv2657c |
prophage protein | 896 | 782 ctx | neighborhood:781 textmining:542 |
Rv2658c |
prophage protein | 852 | 747 ctx | neighborhood:746 textmining:441 |
Rv2659c |
prophage integrase | 815 | 738 ctx | neighborhood:737 |
Rv2653c |
toxin | 934 | 571 ctx | neighborhood:567 textmining:853 |
Rv2652c |
prophage protein | 497 | 496 ctx | neighborhood:493 |
Rv2660c hyp |
hypothetical protein | 476 | 476 ctx | neighborhood:461 |
Rv2661c hyp |
hypothetical protein | 462 | 462 ctx | neighborhood:461 |
Rv0909 |
antitoxin | 655 | 46 | textmining:654 |
Rv0298 |
antitoxin | 434 | 44 | textmining:433 |
Rv0910 |
toxin | 653 | 42 | textmining:653 |
Rv1545 hyp |
hypothetical protein | 510 | 42 | textmining:510 |
Rv3622c PE32 |
PE family protein PE32 | 511 | 41 | textmining:511 |
Rv2355 |
Probable transposase; Rv2355, (MTCY98.24), len: 328 aa. Probable IS6110 transposase. Identical to many other M. tuberculosis IS6110 transpos | 433 | 41 | textmining:433 |
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: type II toxin-antitoxin system antitoxin
- (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_217170.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt P9WJ11 (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 —
16 functional partner(s); context anchor
Rv2656c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002828|Rv2654c| MSGHALAARTLLAAADELVGGPPVEASAAALAGDAAGAWRTAAVELARALVRAVAESHGVAAVLFAATAAAAAAVDRGDPP