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Table 3 Other proteins involved in DNA repair

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

TLS (translesion DNA synthesis) factors

       

Y-family DNA polymerases

dinB

DNA Polymerase IV

Poorly processive, error-prone DNA polymerase involves in translesional DNA synthesis

LHK_01833

L. nitroferrum

69.32

2.00E-128

 

umuD

Protein UmuD

Essential for induced (or SOS) mutagenesis, modifies DNA replication machinery to allow bypass synthesis across a damaged template

LHK_01580

Legionella pneumophila subsp. pneumophila

48.65

9.00E-32

Other SOS response factors

dinG

Probable ATP-dependent helicase DinG

Damage-inducible helicase, unwinds DNA duplex with a 5'-3'-polarity

LHK_02134

L. nitroferrum

64.79

0

 

dnaA

Chromosomal replication initiator protein DnaA

Initiates and regulates chromosomal replication

LHK_03240

L. nitroferrum

76.72

0

Modulation of nucleotide pools

dut

dUTPase

Produces dUMP, immediate precursor of thymidine nucleotides and decreases intracellular concentration of dUTP

LHK_01910

L. nitroferrum

78.45

1.00E-46

 

nrdA

Ribonucleoside-diphosphate reductase 1 subunit alpha

Catalyzes biosynthesis of deoxyribo-nucleotides from the corresponding ribonucleotides

LHK_01803

L. nitroferrum

71

0

 

nrdB

Ribonucleoside-diphosphate reductase 1 subunit beta

Catalyzes biosynthesis of deoxyribo-nucleotides from the corresponding ribonucleotides

LHK_01801

L. nitroferrum

83.1

5.00E-177

 

nrdE

Ribonucleoside-diphosphate reductase 2 subunit alpha

Catalyzes biosynthesis of deoxyribo-nucleotides from the corresponding ribonucleotides

LHK_01596

L. nitroferrum

79.73

0

 

mutT

Mutator MutT protein

Removes oxidatively damaged guanine from DNA and the nucleotide pool, degrades 8-oxo-dGTP to monophosphate

LHK_02262

C. violaceum

60.12

2.00E-56

Other factors involved in DNA repair

ligA

DNA ligase

Catalyzes phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA, essential for DNA replication and repair

LHK_02877

Cupriavidus taiwanensis

65.83

0

 

recJ

Single-stranded-DNA-specific exonuclease RecJ

Single-stranded-DNA-specific exonuclease required for many recombinational events

LHK_02397

L. nitroferrum

71.58

0

 

polA

DNA polymerase I

DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity

LHK_02983

C. violaceum

68.03

0

 

ssb

Single-stranded DNA binding protein, SSB

Forms homotetramer and binds single-stranded DNA to protect susceptible ssDNA from nucleolytic digestion and prevents secondary-structure formation

LHK_01479

M. flagellatus

82.24

4.00E-46

 

ssb2

Single-stranded DNA binding protein

Forms a homotetramer and binds single-stranded DNA to protect susceptible ssDNA from nucleolytic digestion and prevents secondary-structure formation

LHK_01496

L. hongkongensis HLHK9 (SSB protein)

68

3E-57

 

recA

Protein RecA

Catalyzes ATP-dependent uptake of single-stranded DNA by duplex DNA, and hybridization of homologous single-stranded DNA

LHK_00793

L. nitroferrum

86.75

4.00E-137

 

recN

DNA repair protein RecN

Coordinates alignment of broken segments with intact duplexes to facilitate recombination

LHK_01210

C. violaceum

62.43

5.00E-159

 

uvrD

DNA helicase II

ATPase and helicase involves in post-incision events of nucleotide excision repair and methyl-directed mismatch repair

LHK_00065

C. violaceum

65.68

0

 

rep

ATP-dependent DNA helicase Rep

Helicase and ATPase involves in DNA replication, binds to single-stranded DNA, initiates unwinding at a nick

LHK_00318

L. nitroferrum

72.86

0