Rv1582c Family assigned · medium auto-curated
H37Rv Rv1582c · MTBC0 mtbc0_001689 ·
471 aa · 1796457–1797872 (-) ·
RefSeq NP_216098.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phage protein |
|---|---|
| MTBC0 PGAP re-annotation | phage/plasmid primase%2C P4 family |
| Revised (this work) | Phage/plasmid primase%2C P4 family. Pfam: D5_N (PF08706.17), DUF5906 (PF19263.6). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06608
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable PhiRv1 phage protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | D5 N terminal like |
| Orthologous group | COG3378 |
| KEGG orthology |
K06919
|
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, 2 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.10% of strains (150) · 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 |
|---|---|---|---|---|
D5_N | PF08706.17 | 1.8e-35 | 41–185 | D5 N terminal like |
DUF5906 | PF19263.6 | 1.7e-07 | 214–328 | Family of unknown function (DUF5906) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1583c (phage protein), high confidence from genomic context alone (score 779 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1583c |
phage protein | 780 | 779 ctx | neighborhood:777 |
Rv1584c |
phage protein | 777 | 777 ctx | neighborhood:773 |
Rv1586c |
phage integrase | 802 | 757 ctx | neighborhood:634 |
Rv1585c |
phage protein | 628 | 628 ctx | neighborhood:605 |
Rv1587c hyp |
hypothetical protein | 630 | 627 ctx | neighborhood:617 |
Rv1588c hyp |
hypothetical protein | 622 | 619 ctx | neighborhood:617 |
Rv1576c |
phage capsid protein | 597 | 597 ctx | cooccurence:444 |
Rv1578c |
phage protein | 583 | 583 | |
Rv2650c |
prophage protein | 524 | 524 ctx | cooccurence:468 |
Rv1581c |
phage protein | 455 | 455 ctx | neighborhood:447 |
Rv1579c |
phage protein | 445 | 445 ctx | neighborhood:436 |
Rv1580c |
phage protein | 443 | 442 ctx | neighborhood:436 |
Rv2351c plcA |
membrane-associated phospholipase A | 512 | 44 | textmining:511 |
Rv3878 espJ |
ESX-1 secretion-associated protein EspJ | 542 | 42 | textmining:542 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 511 | 41 | textmining:511 |
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/plasmid primase%2C P4 family
- Pfam (hmmscan --cut_ga): D5_N PF08706.17 (E=2e-35), DUF5906 PF19263.6 (E=2e-07)
- (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_216098.1)
- Domains: Pfam-A via hmmscan --cut_ga — D5_N (PF08706.17), DUF5906 (PF19263.6)
- 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
COG3378 - Curated reference: UniProt O06608 (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 —
15 functional partner(s); context anchor
Rv1583c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001689|Rv1582c| MADIPYGTDYPDAPWIDRDGHVLIDDGGKPTQVHRGQARIAYRLAERYQDKLLHVAGIGWHSWDGRRWAADDRGEAKRAVLAELRQALSDSLNDKELRADVRKCESASGVAGVLDLAAALVPFAATVADLDSDPHLLNVANGTLDLHTLKLRPHAPADRITKICRGAYQSDTESPLWQAFLTRVLPDEGVRGFVQRLAGVGLLGTVREHVLAILIGVGANGKSVFDKAIRYALGDYACTAEPDLFMHRENAHPTGEMDLRGVRWVAVSESEKDRRLAESTIKRLTGGDTIRARKMRQDFVEFTPSHTPLLITNHLPRVPGDDTAIWRRIRVVPFEVVIPADEQDRELDARLQLEADSILSWAVAGWSDYQRIGLSQPDAVLAATSNYREDSDTIKRFIDDECVTSSPVLKATTTHLFEAWQRWRVQEGVPEISRKAFGQSLDTHGYPVTDKARDGRWRAGIAVRGADDFDD