Rv2651c Family assigned · medium auto-curated
H37Rv Rv2651c · MTBC0 mtbc0_001684 ·
177 aa · 1794033–1794566 (-) ·
RefSeq NP_217167.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | prophage protease |
|---|---|
| MTBC0 PGAP re-annotation | HK97 family phage prohead protease |
| Revised (this work) | HK97 family phage prohead protease. Pfam: Peptidase_S78 (PF04586.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XEX3
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible PhiRv2 prophage protease |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Caudovirus prohead serine protease |
| Orthologous group | COG3740 |
| KEGG orthology |
K06904
|
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 | 0.372 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (212) · 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 |
|---|---|---|---|---|
Peptidase_S78 | PF04586.23 | 7.0e-20 | 19–161 | Caudovirus prohead serine protease |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2650c (prophage protein), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2650c |
prophage protein | 989 | 988 ctx | neighborhood:787 cooccurence:686 coexpression:838 |
Rv1576c |
phage capsid protein | 931 | 925 ctx | cooccurence:648 coexpression:783 |
Rv1577c |
phage prohead protease | 848 | 847 | coexpression:846 |
Rv2652c |
prophage protein | 636 | 617 ctx | neighborhood:493 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 502 | 503 ctx | cooccurence:496 |
Rv3350c PPE56 |
PPE family protein PPE56 | 479 | 479 ctx | cooccurence:476 |
Rv3347c PPE55 |
PPE family protein PPE55 | 473 | 474 ctx | cooccurence:469 |
Rv0355c PPE8 |
PPE family protein PPE8 | 471 | 471 ctx | cooccurence:468 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 471 | 471 ctx | cooccurence:464 |
Rv1749c |
integral membrane protein | 458 | 459 ctx | cooccurence:456 |
Rv1956 higA |
antitoxin HigA | 446 | 446 ctx | cooccurence:446 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 445 | 446 ctx | cooccurence:438 |
Rv0304c PPE5 |
PPE family protein PPE5 | 443 | 444 ctx | cooccurence:440 |
Rv2653c |
toxin | 429 | 429 ctx | neighborhood:426 |
Rv3343c PPE54 |
PPE family protein PPE54 | 426 | 426 ctx | cooccurence:421 |
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 protease
- MTBC0 PGAP product: HK97 family phage prohead protease
- Pfam (hmmscan --cut_ga): Peptidase_S78 PF04586.23 (E=7e-20)
- (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_217167.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_S78 (PF04586.23)
- 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
COG3740 - Curated reference: UniProt I6XEX3 (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 —
25 functional partner(s); context anchor
Rv2650c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001684|Rv2651c| MSSILFRMAELRSGEGRTVHGTIVPYNEATTVRDFDGEFQEMFAPGAFRRSIAERGHKLKLLVSHDARTRYPVGRAVELREEPHGLFGAFEIADTPDGDEALANVKAGVVDSFSVGFRPIRDRREGDVLVRVEAALLEVSLTGVPAYSGAQIAGVRAESLTVVSRSTAEAWLSLLDW