Rv2657c Family assigned · medium auto-curated
H37Rv Rv2657c · MTBC0 mtbc0_002831 ·
86 aa · 3001252–3001512 (-) ·
RefSeq NP_217173.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | prophage protein |
|---|---|
| MTBC0 PGAP re-annotation | helix-turn-helix domain-containing protein |
| Revised (this work) | Helix-turn-helix domain-containing protein. Pfam: HTH_17 (PF12728.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YE30
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable PhiRv2 prophage protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | DNA binding domain, excisionase family |
| Orthologous group | 2DRZR |
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 | 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
HTH_17 | PF12728.14 | 1.2e-09 | 32–76 | Helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2655c (prophage protein), high confidence from genomic context alone (score 800 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2655c |
prophage protein | 800 | 800 ctx | neighborhood:798 |
Rv2656c |
prophage protein | 924 | 787 ctx | neighborhood:785 textmining:657 |
Rv2654c |
antitoxin | 896 | 782 ctx | neighborhood:781 textmining:542 |
Rv2658c |
prophage protein | 877 | 757 ctx | neighborhood:755 textmining:514 |
Rv2659c |
prophage integrase | 830 | 742 ctx | neighborhood:740 |
Rv2653c |
toxin | 679 | 568 ctx | neighborhood:567 |
Rv2652c |
prophage protein | 495 | 495 ctx | neighborhood:493 |
Rv2660c hyp |
hypothetical protein | 511 | 464 ctx | neighborhood:461 |
Rv2661c hyp |
hypothetical protein | 464 | 464 ctx | neighborhood:461 |
Rv1584c |
phage protein | 464 | 96 | textmining:432 |
Rv0500A |
DNA-binding protein | 521 | 47 | textmining:518 |
Rv2310 |
excisionase | 521 | 47 | textmining:518 |
Rv2355 |
Probable transposase; Rv2355, (MTCY98.24), len: 328 aa. Probable IS6110 transposase. Identical to many other M. tuberculosis IS6110 transpos | 482 | 46 | textmining:480 |
Rv1398c vapB10 |
antitoxin VapB10 | 435 | 46 | textmining:433 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 434 | 46 | 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: prophage protein
- MTBC0 PGAP product: helix-turn-helix domain-containing protein
- Pfam (hmmscan --cut_ga): HTH_17 PF12728.14 (E=1e-09)
- (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_217173.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_17 (PF12728.14)
- 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
2DRZR - Curated reference: UniProt I6YE30 (TrEMBL, unreviewed; 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_002831|Rv2657c| MCAFPSPSLGWTVSHETERPGMADAPPLSRRYITISEAAEYLAVTDRTVRQMIADGRLRGYRSGTRLVRLRRDEVDGAMHPFGGAA