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 |