Rv1577c Resolved · high auto-curated
H37Rv Rv1577c · MTBC0 - ·
170 aa · 1782072–1782584 (-) ·
RefSeq NP_216093.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phage prohead protease |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 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.
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 |
O06613
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable PhiRv1 phage protein |
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 | 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 |
|---|---|---|---|---|
Peptidase_S78 | PF04586.23 | 1.2e-19 | 9–153 | Caudovirus prohead serine protease |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1576c (phage capsid protein), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1576c |
phage capsid protein | 988 | 988 ctx | neighborhood:787 cooccurence:675 coexpression:838 |
Rv2650c |
prophage protein | 955 | 952 ctx | cooccurence:693 coexpression:839 |
Rv2651c |
prophage protease | 848 | 847 | coexpression:846 |
Rv1578c |
phage protein | 665 | 646 ctx | neighborhood:478 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 609 | 609 ctx | cooccurence:604 |
Rv3350c PPE56 |
PPE family protein PPE56 | 590 | 590 ctx | cooccurence:586 |
Rv0355c PPE8 |
PPE family protein PPE8 | 585 | 586 ctx | cooccurence:583 |
Rv3347c PPE55 |
PPE family protein PPE55 | 582 | 582 ctx | cooccurence:578 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 577 | 578 ctx | cooccurence:572 |
Rv0304c PPE5 |
PPE family protein PPE5 | 550 | 551 ctx | cooccurence:548 |
Rv3343c PPE54 |
PPE family protein PPE54 | 540 | 540 ctx | cooccurence:536 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 539 | 539 ctx | cooccurence:533 |
Rv1004c |
membrane protein | 538 | 539 ctx | cooccurence:536 |
Rv1749c |
integral membrane protein | 533 | 533 ctx | cooccurence:532 |
Rv1917c PPE34 |
PPE family protein PPE34 | 532 | 532 ctx | cooccurence:531 |
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): phage prohead protease
- Pfam (hmmscan --cut_ga): Peptidase_S78 PF04586.23 (E=1e-19)
- (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_216093.1)
- 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 O06613 (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 —
45 functional partner(s); context anchor
Rv1576c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1577c| MAELRSGEGRTVHGTIVPYNEATTVRDFDGEFQEMFAPGAFRRSIAERGHKLKLLVSHDARTRYPVGRAVELREEPHGLFGAFEIADTPDGDEALANVKAGVVDSFSVGFRPIRDRREGDVLVRVEAALLEVSLTGVPAYSGAQIAGVRAESLTVVSRSTAEAWLSLLDW