Rv2652c Resolved · high auto-curated
H37Rv Rv2652c · MTBC0 - ·
208 aa · 2975928–2976554 (-) ·
RefSeq NP_217168.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | prophage protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Prophage protein. Pfam: Terminase_4 (PF05119.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P71949
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable PhiRv2 prophage protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Phage terminase, small subunit |
| Orthologous group | COG3747 |
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 | 1.421 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 12 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.16% of strains (230) · 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 |
|---|---|---|---|---|
Terminase_4 | PF05119.18 | 1.4e-22 | 96–188 | Phage terminase, small subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2653c (toxin), medium confidence from genomic context alone (score 693 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2653c |
toxin | 693 | 693 ctx | neighborhood:685 |
Rv2651c |
prophage protease | 636 | 617 ctx | neighborhood:493 |
Rv2650c |
prophage protein | 602 | 588 ctx | neighborhood:493 |
Rv2655c |
prophage protein | 513 | 512 ctx | neighborhood:504 |
Rv2656c |
prophage protein | 499 | 499 ctx | neighborhood:496 |
Rv2654c |
antitoxin | 497 | 496 ctx | neighborhood:493 |
Rv2657c |
prophage protein | 495 | 495 ctx | neighborhood:493 |
Rv2658c |
prophage protein | 476 | 476 ctx | neighborhood:473 |
Rv2659c |
prophage integrase | 485 | 475 ctx | neighborhood:472 |
Rv1378c hyp |
hypothetical protein | 401 | 401 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): prophage protein
- Pfam (hmmscan --cut_ga): Terminase_4 PF05119.18 (E=1e-22)
- (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_217168.1)
- Domains: Pfam-A via hmmscan --cut_ga — Terminase_4 (PF05119.18)
- 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
COG3747 - Curated reference: UniProt P71949 (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 —
10 functional partner(s); context anchor
Rv2653c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2652c| MPSPATARPDTATVGERVRAQVLWGVFWHHGIRDPKPGKRRVVLKMGRRGPAPAPAQLKLLGGRSPGRDSGGRRVTPPAAFERVAPECPDWLPPGAKDMWGRVVPELAALNLLKESDLGVLTSFCVAWDQLMQAVTAYREQGFIATNARSRRVTVHPAVAAARAATRDVLVLARELGCTPSAEANLAAVLAAAGDPDDDEFNPFAPDR