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Table 2 Homologous recombination proteins in L. hongkongensis and their closest homologues

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

       

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