Table 3.

Other proteins involved in DNA repair

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