Rv2656c Still unknown · low auto-curated
H37Rv Rv2656c · MTBC0 mtbc0_002830 ·
130 aa · 3000863–3001255 (-) ·
RefSeq NP_217172.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | prophage protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2742 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF2742. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL49
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv2656c |
UniProt still lists this protein as Uncharacterized protein Rv2656c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF2742) |
| Orthologous group | 2AYB0 |
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 | 0.729 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
DUF2742 | PF10888.15 | 2.5e-38 | 35–128 | Protein of unknown function (DUF2742) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2655c (prophage protein), high confidence from genomic context alone (score 830 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2655c |
prophage protein | 831 | 830 ctx | neighborhood:799 |
Rv2657c |
prophage protein | 924 | 787 ctx | neighborhood:785 textmining:657 |
Rv2654c |
antitoxin | 921 | 784 ctx | neighborhood:781 textmining:652 |
Rv2658c |
prophage protein | 901 | 746 ctx | neighborhood:746 textmining:629 |
Rv2659c |
prophage integrase | 857 | 739 ctx | neighborhood:738 textmining:479 |
Rv2653c |
toxin | 724 | 578 ctx | neighborhood:573 |
Rv2652c |
prophage protein | 499 | 499 ctx | neighborhood:496 |
Rv2660c hyp |
hypothetical protein | 476 | 476 ctx | neighborhood:461 |
Rv2661c hyp |
hypothetical protein | 464 | 463 ctx | neighborhood:461 |
Rv1398c vapB10 |
antitoxin VapB10 | 521 | 51 | textmining:516 |
Rv2355 |
Probable transposase; Rv2355, (MTCY98.24), len: 328 aa. Probable IS6110 transposase. Identical to many other M. tuberculosis IS6110 transpos | 548 | 44 | textmining:547 |
Rv2278 |
Rv2278, (MTCY339.32c), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase s | 548 | 44 | textmining:547 |
Rv1511 gmdA |
GDP-D-mannose dehydratase GmdA | 512 | 44 | textmining:511 |
Rv0550c vapB3 |
antitoxin VapB3 | 511 | 44 | textmining:510 |
Rv0718 rpsH |
30S ribosomal protein S8 | 511 | 44 | textmining:510 |
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: prophage protein
- MTBC0 PGAP product: DUF2742 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF2742 PF10888.15 (E=3e-38)
- (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_217172.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2742 (PF10888.15)
- 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
2AYB0 - Curated reference: UniProt P9WL49 (SwissProt, reviewed; Predicted)
- 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 —
18 functional partner(s); context anchor
Rv2655c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002830|Rv2656c| MTAVGGSPPTRRCPATEDRAPATVATPSSTDPTASRAVSWWSVHEYVAPTLAAAVEWPMAGTPAWCDLDDTDPVKWAAICDAARHWALRVETCQAASAEASRDVSAAADWPAVSREIQRRRDAYIRRVVV