Rv2659c Resolved · high auto-curated
H37Rv Rv2659c · MTBC0 mtbc0_002833 ·
375 aa · 3001894–3003021 (-) ·
RefSeq NP_217175.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | prophage integrase |
|---|---|
| MTBC0 PGAP re-annotation | tyrosine-type recombinase/integrase |
| Revised (this work) | Tyrosine-type recombinase/integrase. Pfam: Integrase_N_phage (PF26003.1), Phage_int_SAM_3 (PF14659.13), 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 |
P9WMB3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative prophage phiRv2 integrase |
| Curated function | Integrase is necessary for integration of the phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome (By similarity). |
UniProt still lists this protein as Putative prophage phiRv2 integrase; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | intA |
| eggNOG description | Belongs 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 | 0.17 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (213) · 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 |
|---|---|---|---|---|
Integrase_N_phage | PF26003.1 | 6.9e-25 | 11–60 | Phage integrase, N-terminal domain |
Phage_int_SAM_3 | PF14659.13 | 8.5e-08 | 77–127 | Phage integrase, N-terminal SAM-like domain |
Phage_integrase | PF00589.28 | 1.6e-15 | 182–356 | Phage integrase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2658c (prophage protein), high confidence from genomic context alone (score 953 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2658c |
prophage protein | 993 | 953 ctx | neighborhood:773 coexpression:801 textmining:861 |
Rv2655c |
prophage protein | 819 | 819 ctx | neighborhood:746 |
Rv2657c |
prophage protein | 830 | 742 ctx | neighborhood:740 |
Rv2656c |
prophage protein | 857 | 739 ctx | neighborhood:738 textmining:479 |
Rv2654c |
antitoxin | 815 | 738 ctx | neighborhood:737 |
Rv2653c |
toxin | 695 | 536 ctx | neighborhood:533 |
Rv2661c hyp |
hypothetical protein | 487 | 486 ctx | neighborhood:481 |
Rv2660c hyp |
hypothetical protein | 486 | 486 ctx | neighborhood:481 |
Rv2652c |
prophage protein | 485 | 475 ctx | neighborhood:472 |
Rv3242c hyp |
hypothetical protein | 467 | 468 | coexpression:466 |
Rv2584c apt |
adenine phosphoribosyltransferase | 457 | 458 | coexpression:456 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 452 | 452 | coexpression:434 |
Rv3226c hyp |
hypothetical protein | 455 | 435 | coexpression:435 |
Rv1423 whiA |
transcriptional regulator WhiA | 434 | 434 | coexpression:434 |
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 412 | 413 | coexpression:413 |
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: prophage integrase
- MTBC0 PGAP product: tyrosine-type recombinase/integrase
- Pfam (hmmscan --cut_ga): Integrase_N_phage PF26003.1 (E=7e-25), Phage_int_SAM_3 PF14659.13 (E=8e-08), Phage_integrase PF00589.28 (E=2e-15)
- (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_217175.1)
- Domains: Pfam-A via hmmscan --cut_ga — Integrase_N_phage (PF26003.1), Phage_int_SAM_3 (PF14659.13), 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 P9WMB3 (SwissProt, reviewed; 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 —
30 functional partner(s); context anchor
Rv2658c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002833|Rv2659c| MTQTGKRQRRKFGRIRQFNSGRWQASYTGPDGRVYIAPKTFNAKIDAEAWLTDRRREIDRQLWSPASGQEDRPGAPFGEYAEGWLKQRGIKDRTRAHYRKLLDNHILATFADTDLRDITPAAVRRWYATTAVGTPTMRAHSYSLLRAIMQTALADDLIDSNPCRISGASTARRVHKIRPATLDELETITKAMPDPYQAFVLMAAWLAMRYGELTELRRKDIDLHGEVARVRRAVVRVGEGFKVTTPKSDAGVRDISIPPHLIPAIEDHLHKHVNPGRESLLFPSVNDPNRHLAPSALYRMFYKARKAAGRPDLRVHDLRHSGAVLAASTGATLAELMQRLGHSTAGAALRYQHAAKGRDREIAALLSKLAENQEM