Rv2658c Family assigned · low
H37Rv Rv2658c · MTBC0 mtbc0_002832 ·
120 aa · 3001529–3001891 (-) ·
RefSeq NP_217174.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | prophage protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Protein of prophage phiRv2, within region-of-difference RD11; hypoxia-induced and recognised as an antigen. A prophage-encoded protein whose enzymatic/molecular function is unknown. |
Curated reference (UniProt)
| UniProt |
P9WL47
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2658c |
UniProt still lists this protein as Uncharacterized protein Rv2658c; the revised annotation above is ahead of the current UniProt record.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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: Rv2659c (prophage integrase), high confidence from genomic context alone (score 953 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2659c |
prophage integrase | 993 | 953 ctx | neighborhood:773 coexpression:801 textmining:861 |
Rv2657c |
prophage protein | 877 | 757 ctx | neighborhood:755 textmining:514 |
Rv2655c |
prophage protein | 747 | 748 ctx | neighborhood:746 |
Rv2654c |
antitoxin | 852 | 747 ctx | neighborhood:746 textmining:441 |
Rv2656c |
prophage protein | 901 | 746 ctx | neighborhood:746 textmining:629 |
Rv2653c |
toxin | 770 | 543 ctx | neighborhood:541 textmining:516 |
Rv2661c hyp |
hypothetical protein | 816 | 484 ctx | neighborhood:481 textmining:659 |
Rv2660c hyp |
hypothetical protein | 485 | 484 ctx | neighborhood:481 |
Rv2652c |
prophage protein | 476 | 476 ctx | neighborhood:473 |
Rv1986 lysE |
amino acid transporter | 444 | 55 | textmining:436 |
Rv1978 hyp |
hypothetical protein | 439 | 51 | textmining:434 |
Rv1981c nrdF1 |
ribonucleoside-diphosphate reductase subunit beta NrdF1 | 548 | 47 | textmining:546 |
Rv1511 gmdA |
GDP-D-mannose dehydratase GmdA | 630 | 41 | textmining:630 |
Rv3429 PPE59 |
PPE family protein PPE59 | 511 | 41 | textmining:511 |
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
- Prophage phiRv2 / RD11 protein; expression varies with stress (Fan 2016, PMID 25855385)
- Hypoxia-induced antigen (Gideon 2010, PMID 21203487)
- Curated from the literature crible (project 'Still unknown gene function', 2026-06-09)
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_217174.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt P9WL47 (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 —
14 functional partner(s); context anchor
Rv2659c - Primary literature: Fan X, Abd Alla AA, Xie J (2016). Distribution and function of prophage phiRv1 and phiRv2 among Mycobacterium tuberculosis complex J Biomol Struct Dyn 34(2):233-8. doi:10.1080/07391102.2015.1022602 PMID:25855385
- Primary literature: Gideon HP, Wilkinson KA, Rustad TR, Oni T, Guio H, Kozak RA, Sherman DR, Meintjes G, Behr MA, Vordermeier HM, Young DB, Wilkinson RJ (2010). Hypoxia induces an immunodominant target of tuberculosis specific T cells absent from common BCG vaccines PLoS Pathog 6(12):e1001237. doi:10.1371/journal.ppat.1001237 PMID:21203487
Ancestral MTBC0 protein sequence
>mtbc0_002832|Rv2658c| MADAVKYVVMCNCDDEPGALIIAWIDDERPAGGHIQMRSNTRFTETQWGRHIEWKLECRACRKYAPISEMTAAAILDGFGAKLHELRTSTIPDADDPSIAEARHVIPFSALCLRLSQLGG