Rv1578c Family assigned · medium auto-curated
H37Rv Rv1578c · MTBC0 mtbc0_001685 ·
156 aa · 1794719–1795189 (-) ·
RefSeq NP_216094.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phage protein |
|---|---|
| MTBC0 PGAP re-annotation | phage terminase small subunit P27 family |
| Revised (this work) | Phage terminase small subunit P27 family. 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.
Curated reference (UniProt)
| UniProt |
O06612
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable PhiRv1 phage 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 | 1.128 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
Terminase_4 | PF05119.18 | 2.3e-28 | 48–144 | Phage terminase, small subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1576c (phage capsid protein), medium confidence from genomic context alone (score 675 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1576c |
phage capsid protein | 687 | 675 ctx | neighborhood:478 |
Rv1577c |
phage prohead protease | 665 | 646 ctx | neighborhood:478 |
Rv1582c |
phage protein | 583 | 583 | |
Rv1579c |
phage protein | 563 | 563 ctx | neighborhood:557 |
Rv1580c |
phage protein | 560 | 560 ctx | neighborhood:557 |
Rv1588c hyp |
hypothetical protein | 549 | 549 | |
Rv1587c hyp |
hypothetical protein | 547 | 547 | |
Rv1581c |
phage protein | 545 | 546 ctx | neighborhood:543 |
Rv0613c hyp |
hypothetical protein | 469 | 469 ctx | cooccurence:469 |
Rv2650c |
prophage protein | 441 | 421 | |
Rv2651c |
prophage protease | 443 | 413 | |
Rv1749c |
integral membrane protein | 401 | 401 ctx | cooccurence: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
- Legacy H37Rv annotation: phage protein
- MTBC0 PGAP product: phage terminase small subunit P27 family
- Pfam (hmmscan --cut_ga): Terminase_4 PF05119.18 (E=2e-28)
- (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_216094.1)
- 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 O06612 (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 —
12 functional partner(s); context anchor
Rv1576c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001685|Rv1578c| MPRPPKPARLKLVEGRSPGRDSGGRKVPESPKFIRQAPDAPDWLDAEALAEWRRVAPTLERLDLLKPEDRALLSAYCETWSVYVAAVQRVRAEGLTITSPKSGVVHRNPAVTVAETARMHLLRLASEFGLTPAAEQRLAVAPGDDGDGLNPFAPDR