Rv2655c Still unknown · low auto-curated
H37Rv Rv2655c · MTBC0 mtbc0_002829 ·
475 aa · 2999434–3000861 (-) ·
RefSeq NP_217171.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | prophage protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF3631 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3631. 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 |
I6Y1F0
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible PhiRv2 prophage protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3631) |
| Orthologous group | COG0464 |
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 | 0.796 · 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 0.40% of strains (585) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF3631 | PF12307.14 | 2.1e-61 | 195–375 | Protein of unknown function (DUF3631) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2656c (prophage protein), high confidence from genomic context alone (score 830 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2656c |
prophage protein | 831 | 830 ctx | neighborhood:799 |
Rv2659c |
prophage integrase | 819 | 819 ctx | neighborhood:746 |
Rv2657c |
prophage protein | 800 | 800 ctx | neighborhood:798 |
Rv2654c |
antitoxin | 784 | 784 ctx | neighborhood:781 |
Rv2658c |
prophage protein | 747 | 748 ctx | neighborhood:746 |
Rv2653c |
toxin | 585 | 586 ctx | neighborhood:567 |
Rv2652c |
prophage protein | 513 | 512 ctx | neighborhood:504 |
Rv2660c hyp |
hypothetical protein | 469 | 469 ctx | neighborhood:461 |
Rv2661c hyp |
hypothetical protein | 464 | 464 ctx | neighborhood:461 |
Rv3578 arsB2 |
arsenic transport integral membrane protein ArsB | 440 | 441 ctx | cooccurence:437 |
Rv3875 esxA |
ESAT-6 protein EsxA | 422 | 423 ctx | cooccurence:421 |
Rv3660c ssd hyp |
hypothetical protein | 421 | 421 ctx | cooccurence:416 |
Rv2650c |
prophage protein | 402 | 371 | |
Rv2896c dprA hyp |
hypothetical protein | 655 | 51 | textmining:652 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 570 | 46 | textmining:568 |
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: DUF3631 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF3631 PF12307.14 (E=2e-61)
- (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_217171.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3631 (PF12307.14)
- 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
COG0464 - Curated reference: UniProt I6Y1F0 (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 —
19 functional partner(s); context anchor
Rv2656c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002829|Rv2655c| MADIPYGRDYPDPIWCDEDGQPMPPVGAELLDDIRAFLRRFVVYPSDHELIAHTLWIAHCWFMEAWDSTPRIAFLSPEPGSGKSRALEVTEPLVPRPVHAINCTPAYLFRRVADPVGRPTVLYDECDTLFGPKAKEHEEIRGVINAGHRKGAVAGRCVIRGKIVETEELPAYCAVALAGLDDLPDTIMSRSIVVRMRRRAPTEPVEPWRPRVNGPEAEKLHDRLANWAAAINPLESGWPAMPDGVTDRRADVWESLVAVADTAGGHWPKTARATAETDATANRGAKPSIGVLLLRDIRRVFSDRDRMRTSDILTGLNRMEEGPWGSIRRGDPLDARGLATRLGRYGIGPKFQHSGGEPPYKGYSRTQFEDAWSRYLSADDETPEERDLSVSAVSAVSPPVGDPGDATGATDATDLPEAGDLPYEPPAPNGHPNGDAPLCSGPGCPNKLLSTEAKAAGKCRPCRGRAAASARDGAR