From: Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis
Repair pathways/Types of enzymes | Gene | Protein | Function of protein encoded | CDS | Closest match organism | Amino acid Identity (%) | Best E-value |
---|---|---|---|---|---|---|---|
Initiation | Â | Â | Â | Â | Â | Â | Â |
RecBCD pathway | recB | Exodeoxyribonuclease V beta chain | Catalyzes unwinding of double-stranded DNA and cleavage of single-stranded DNA, stimulates local genetic recombination | LHK_01202 | Pseudomonas entomophila | 45.33 | 0 |
 | recC | Exodeoxyribonuclease V gamma chain | ATP-dependent exonuclease and helicase, DNA-dependent ATPase and ATP-stimulated endonuclease | LHK_01203 | Pseudomonas aeruginosa | 48.11 | 0 |
 | recD | Exodeoxyribonuclease V alpha chain | ATP-dependent exonuclease, ATPase and ATP-stimulated endonuclease | LHK_01201 | Pseudomonas putida | 50.47 | 1.00E-126 |
RecFOR pathway | recF | DNA replication and repair protein RecF | DNA metabolism, DNA replication and normal SOS inducibility | LHK_01798 | Bordetella petrii | 43.67 | 4.00E-91 |
 | recO | DNA repair protein RecO | Acts with RecF and RecR | LHK_01467 | L. nitroferrum | 50.41 | 6.00E-43 |
 | recR | Recombination protein RecR | Acts with RecF and RecO | LHK_00965 | L. nitroferrum | 70.71 | 5.00E-79 |
 | recQ | ATP-dependent DNA helicase RecQ | Helicase involved in the RecFOR recombination pathway | LHK_02771 | C. violaceum | 68.49 | 0 |
Branch migration and resolution | recG | ATP-dependent DNA helicase RecG | Catalyzes branch migration in processing Holliday junction intermediates to mature products. Unwinds DNA with a 3' to 5' polarity | LHK_02776 | L. nitroferrum | 71.3 | 0 |
 | ruvA | Holiday junction ATP-dependent DNA helicase RuvA | Forms complex with RuvB, RuvAB is a helicase that mediates Holliday junction migration by localized denaturation and reannealing | LHK_03111 | C. violaceum | 59.7 | 1.00E-54 |
 | ruvB | Holiday junction ATP-dependent DNA helicase RuvB | Possesses weak ATPase activity, stimulated by the RuvA protein in the presence of DNA. Forms complex with RuvA | LHK_00086 | L. nitroferrum | 92.35 | 8.00E-165 |
 | ruvC | Crossover junction endodeoxyribonuclease RuvC | Resolves Holliday junction intermediates in recombination, cleaves cruciform structure in supercoiled DNA | LHK_03190 | L. nitroferrum | 79.89 | 6.00E-58 |
Other recombination repair related proteins | priA | Primosomal protein N' | Replication restart protein, catalyzes reactivation of replication forks that have stalled at sites of DNA damage | LHK_02821 | L. nitroferrum | 58.37 | 0 |
 | radA | DNA repair and recombination protein RadA | Binds and assembles on single-stranded DNA, promotes DNA strand exchange between homologous DNA molecules | LHK_02039 | L. nitroferrum | 79.42 | 0 |
 | rusA | Crossover junction endodeoxyribonuclease RusA | Resolves Holliday junction intermediates made during homologous genetic recombination and DNA repair | LHK_01785 | Ralstonia eutropha | 62.04 | 3.00E-40 |
 | rdgC | Recombination-associated protein RdgC | Inhibits RecA promoted DNA strand exchange, ATPase activity, and RecA-dependent LexA cleavage, a potential negative regulator of RecA | LHK_00720 | L. nitroferrum | 58.92 | 3.00E-92 |
 | recX | Regulatory protein RecX | Inhibits RecA recombinase and coprotease activities | LHK_00794 | Burkholderia phymatum | 52.45 | 8E-25 |
 | yqgF | Putative Holliday junction resolvase | Nuclease resolves Holliday junction intermediates | LHK_02882 | L. nitroferrum | 66.67 | 8E-46 |
 | bet | Single-stranded DNA annealing protein | Mediates annealing of (partially) single-stranded regions of DNA containing regions of complementary sequence | LHK_01498 | Providencia rettgeri | 69 | 9E-74 |
 | exo | Alkaline exonuclease | Single-stranded DNA exonuclease that digests double-stranded DNA ends with 5'- to 3'-polarity to generate long 3'-ssDNA ends | LHK_01497 | Klebsiella pneumoniae subsp. rhinoscleromatis | 70 | 7E-76 |