Rv2653c Resolved · medium auto-curated
H37Rv Rv2653c · MTBC0 mtbc0_002827 ·
107 aa · 2998789–2999112 (-) ·
RefSeq NP_217169.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | toxin |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system toxin |
| Revised (this work) | Type II toxin-antitoxin system toxin. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ13
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Toxin Rv2653c |
| 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 Rv2654c. |
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.719 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.21% of strains (299) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2652c (prophage protein), medium confidence from genomic context alone (score 693 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2652c |
prophage protein | 693 | 693 ctx | neighborhood:685 |
Rv2655c |
prophage protein | 585 | 586 ctx | neighborhood:567 |
Rv2656c |
prophage protein | 724 | 578 ctx | neighborhood:573 |
Rv2654c |
antitoxin | 934 | 571 ctx | neighborhood:567 textmining:853 |
Rv2657c |
prophage protein | 679 | 568 ctx | neighborhood:567 |
Rv2658c |
prophage protein | 770 | 543 ctx | neighborhood:541 textmining:516 |
Rv2659c |
prophage integrase | 695 | 536 ctx | neighborhood:533 |
Rv2650c |
prophage protein | 431 | 431 ctx | neighborhood:424 |
Rv2651c |
prophage protease | 429 | 429 ctx | neighborhood:426 |
Rv1397c vapC10 |
ribonuclease VapC10 | 446 | 47 | textmining:443 |
Rv0837c hyp |
hypothetical protein | 435 | 47 | textmining:432 |
Rv2526 vapB17 |
antitoxin VapB17 | 437 | 45 | textmining:435 |
Rv0909 |
antitoxin | 680 | 44 | textmining:679 |
Rv0656c vapC6 |
ribonuclease VapC6 | 517 | 43 | textmining:516 |
Rv1102c mazF3 |
mRNA interferase MazF3 | 432 | 42 | textmining:432 |
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: type II toxin-antitoxin system toxin
- (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_217169.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt P9WJ13 (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 —
23 functional partner(s); context anchor
Rv2652c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002827|Rv2653c| MTHKRTKRQPAIAAGLNAPRRNRVGRQHGWPADVPSAEQRRAQRQRDLEAIRRAYAEMVATSHEIDDDTAELALLSMHLDDEQRRLEAGMKLGWHPYQFPDEPDSKQ