Rv1586c Family assigned · low auto-curated
H37Rv Rv1586c · MTBC0 mtbc0_001693 ·
115 aa · 1799056–1800469 (-) ·
RefSeq NP_216102.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phage integrase |
|---|---|
| MTBC0 PGAP re-annotation | recombinase family protein |
| Revised (this work) | Recombinase family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06604
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable PhiRv1 integrase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Recombinase |
| Orthologous group | COG1961 |
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 | 0.116 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (221) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1585c (phage protein), high confidence from genomic context alone (score 971 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1585c |
phage protein | 971 | 971 ctx | neighborhood:801 coexpression:860 |
Rv1587c hyp |
hypothetical protein | 882 | 882 ctx | neighborhood:780 |
Rv1588c hyp |
hypothetical protein | 786 | 786 ctx | neighborhood:780 |
Rv1582c |
phage protein | 802 | 757 ctx | neighborhood:634 |
Rv1584c |
phage protein | 857 | 630 ctx | neighborhood:618 textmining:630 |
Rv1583c |
phage protein | 612 | 611 ctx | neighborhood:606 |
Rv1140 |
integral membrane protein | 431 | 431 | |
Rv2874 dipZ |
integral membrane C-type cytochrome biogenesis protein DipZ | 448 | 426 | coexpression:424 |
Rv2877c |
integral membrane protein | 426 | 426 | coexpression:425 |
Rv0527 ccdA |
cytochrome C-type biogenesis protein CcdA | 425 | 425 | coexpression:424 |
Rv0784 hyp |
hypothetical protein | 416 | 417 | coexpression:417 |
Rv1107c xseB |
exodeoxyribonuclease VII small subunit | 408 | 408 | coexpression:408 |
Rv1576c |
phage capsid protein | 866 | 351 | textmining:803 |
Rv1997 ctpF |
cation transporter ATPase F | 456 | 243 | |
Rv0888 spmT hyp |
hypothetical protein | 577 | 124 | textmining:538 |
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 integrase
- MTBC0 PGAP product: recombinase family protein
- (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_216102.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG1961 - Curated reference: UniProt O06604 (TrEMBL, unreviewed; Evidence at protein level)
- 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 —
19 functional partner(s); context anchor
Rv1585c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001693|Rv1586c| MRYTTPVRAAVYLRISEDRSGEQLGVARQREDCLKLCGQRKWVPVEYLDNDVSPHQPASAAPNLRADVGRHHRRQDRRRGGLGPGPAPSPSHRAGSLHVISRREAAGPGHRRRRR