Rv2646 Resolved · high auto-curated
H37Rv Rv2646 · MTBC0 mtbc0_002821 ·
332 aa · 2994112–2995110 (+) ·
RefSeq NP_217162.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integrase |
|---|---|
| MTBC0 PGAP re-annotation | tyrosine-type recombinase/integrase |
| Revised (this work) | Tyrosine-type recombinase/integrase. Pfam: Phage_integrase (PF00589.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XEU5
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable integrase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | to the 'phage' integrase family |
| Orthologous group | COG0582 |
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 | 0.357 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.82% of strains (1194) · 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 |
|---|---|---|---|---|
Phage_integrase | PF00589.28 | 2.2e-22 | 186–319 | Phage integrase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: xerC (tyrosine recombinase XerC), high confidence from genomic context alone (score 798 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2645 hyp |
hypothetical protein | 952 | 953 ctx | neighborhood:774 coexpression:799 |
Rv2647 hyp |
hypothetical protein | 872 | 866 ctx | neighborhood:520 coexpression:732 |
Rv2894c xerC |
tyrosine recombinase XerC | 798 | 798 ctx | cooccurence:773 |
Rv2748c ftsK |
DNA translocase FtsK | 682 | 553 ctx | cooccurence:549 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 495 | 496 | coexpression:434 |
Rv3242c hyp |
hypothetical protein | 467 | 468 | coexpression:466 |
Rv2584c apt |
adenine phosphoribosyltransferase | 459 | 460 | coexpression:458 |
Rv1708 |
initiation inhibitor protein | 470 | 444 | |
Rv3918c parA |
chromosome partitioning protein ParA | 470 | 444 ctx | cooccurence:420 |
Rv3226c hyp |
hypothetical protein | 456 | 436 | coexpression:436 |
Rv1423 whiA |
transcriptional regulator WhiA | 434 | 434 | coexpression:434 |
Rv3917c parB |
chromosome partitioning protein ParB | 448 | 419 ctx | cooccurence:412 |
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 416 | 416 | coexpression:416 |
Rv3213c |
SOJ/ParA-like protein | 435 | 408 | |
Rv0186 bglS |
beta-glucosidase BglS | 811 | 98 | textmining:800 |
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: integrase
- MTBC0 PGAP product: tyrosine-type recombinase/integrase
- Pfam (hmmscan --cut_ga): Phage_integrase PF00589.28 (E=2e-22)
- (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_217162.1)
- Domains: Pfam-A via hmmscan --cut_ga — Phage_integrase (PF00589.28)
- 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
COG0582 - Curated reference: UniProt I6XEU5 (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 —
16 functional partner(s); context anchor
xerC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002821|Rv2646| MNTATRVRLARKRADRLNLKLIKNGHHFRLRDADEITLAVGHLGVVEAFLAAAKSQNKPPGPPPSLHAPPSWRRDIDDYLLNLNAAGQRPATIRLRKTVLCAAAHGLGRPPADVTAEHLLDWLGKQQHLSPEGRKTYRSTLRGFFVWAYEMDRVRDYVADSLPKVRCPKQPPRPAGDDVWQAALAKADRRTELMIRLAGEAGLRRAEAAQAHTGDLMDGGLLLVHGKGGKRRIVPISDYLAALIRDTPHGYLFPNGTGGHLTAEHVGKLVSRALPGDATMHTLRHRYATRAYRGSHNLRAVQQLLGHASIVTTERYTALCDDEVRAAAAAAW