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 |
---|---|---|---|---|---|---|---|
Direct repair | |||||||
phrB | PhrB protein | Repairs UV radiation-induced DNA damage by catalyzing light-dependent monomerization of cyclobutyl pyrimidine dimers between adjacent bases | LHK_02646 | L. nitroferrum | 58.73 | 3.00E-131 | |
ogt | Ogt | Repairs alkylated guanine by transferring alkyl group at O-6 position to a cysteine residue in the enzyme | LHK_00364 | Dechloromonas aromatica | 46.67 | 4.00E-30 | |
ada | Regulatory protein Ada | Repairs alkylated guanine in DNA by transferring alkyl group at the O-6 position to a cysteine residue in the enzyme | LHK_00147 | Colwellia psychrerythraea | 44.29 | 1.00E-60 | |
Base excision repair | |||||||
DNA glycosylases | alkA | AlkA | Excises damaged DNA polymer formed due to alkylation lesions by hydrolyzing deoxyribose N-glycosidic bond | LHK_01743 | Thiobacillus denitrificans | 61.95 | 2.00E-62 |
mutY | MutY | Adenine glycosylase active on G-A mispairs. Also corrects error-prone DNA synthesis due to oxidized guanine | LHK_02781 | L. nitroferrum | 63.29 | 1.00E-92 | |
ung | UNG | Excises uracil residues arised from misincorporation of dUMP residues by DNA polymerase or cytosine deamination | LHK_00013 | L. nitroferrum | 56.14 | 3.00E-58 | |
LHK_00723 | Ralstonia pickettii | 59.26 | 2.00E-33 | ||||
Bifunctional glycosylases | mutM (fpg) | Formamido-pyrimidine-DNA glycosylase | Recognizes and removes damaged bases. Cleaves DNA backbone to generate single-strand break at site of base removal | LHK_00316 | Neisseria flavescens | 57.25 | 9.00E-90 |
nth | Endonuclease III | Apurinic and/or apyrimidinic endonuclease activity and DNA N-glycosylase activity | LHK_01218 | Methylococcus capsulatus | 72.04 | 1.00E-81 | |
AP endonucleases | xthA | Exodeoxyribo-nuclease III | Removes damaged DNA at cytosines and guanines | LHK_02447 | C. violaceum | 67.06 | 5.00E-94 |
exoA (xthA2) | Exodeoxyribo-nuclease | Posseses 3' to 5' exonuclease, 3' phosphatase activities and makes DNA single-strand breaks at apurinic sites | LHK_03213 | L. nitroferrum | 73.73 | 1.00E-108 | |
Nucleotide excision repair | |||||||
Global genome repair factors | uvrA | Protein UvrA | DNA-binding ATPase, forms recognition complex composed of 2 UvrA and 2 UvrB subunits and scans DNA for abnormalities | LHK_01605 | L. nitroferrum | 82.89 | 0 |
uvrB | Protein UvrB | Causes local melting of the DNA helix, probes one DNA strand for the presence of a lesion | LHK_00960 | L. nitroferrum | 82.18 | 0 | |
uvrC | Protein UvrC | Incises 5' and 3' sides of lesion | LHK_02627 | L. nitroferrum | 71 | 0 | |
Transcription coupled repair factors | |||||||
DNA-directed RNA polymerase (RNAP) complex | rpoB | RNAP subunit beta | Subunit of DNA-dependent RNA polymerase | LHK_00246 | L. nitroferrum | 85.26 | 0 |
rpoC | RNAP subunit beta | Subunit of DNA-dependent RNA polymerase | LHK_00247 | C. violaceum | 87.09 | 0 | |
rpoA | RNAP subunit alpha | Subunit of DNA-dependent RNA polymerase | LHK_00279 | L. nitroferrum | 90.83 | 1.00E-171 | |
rpoE | RNAP delta factor | Participates in initiation and recycling phases of transcription | LHK_01458 | L. nitroferrum | 63.82 | 7.00E-54 | |
rpoZ | RNAP omega subunit | Promotes RNA polymerase assembly | LHK_00457 | Methylobacillus flagellatus | 73.91 | 1.00E-21 | |
Transcription-repair coupling factor (TRCF) | mfd | TRCF | Recognizes RNAP-DNA-RNA complex blocked at template strand lesion, replaces RNAP, releases truncated transcript and recruits UvrABC repair system | LHK_00629 | L. nitroferrum | 73.95 | 0 |
Mismatch excision repair | |||||||
Mismatch and loop recognition factors | mutS | DNA mismatch repair protein MutS | Mismatch recognition | LHK_00373 | C. violaceum | 67.73 | 0 |
Molecular matchmarker | mutL | DNA mismatch repair protein MutL | Promotes formation of a stable complex between two or more DNA-binding proteins | LHK_01012 | C. violaceum | 55.51 | 0 |
DNA exonucleases | xseA | Exodeoxyribo-nuclease 7 large subunit | Bidirectionally degrades single-stranded DNA | LHK_01101 | C. violaceum | 59.51 | 4.00E-125 |
xseB | Exodeoxyribo-nuclease 7 small subunit | Bidirectionally degrades single-stranded DNA | LHK_02322 | C. violaceum | 65.28 | 6.00E-20 | |
DNA polymerase III holoenzyme | dnaE | DNA polymerase III subunit alpha | Subunit of DNA polymerase | LHK_01389 | L. nitroferrum | 74.13 | 0 |
dnaN | DNA polymerase III subunit beta | Subunit of DNA polymerase, initiates replication | LHK_03241 | L. nitroferrum | 72.5 | 3.00E-131 | |
holC | DNA polymerase III subunit chi | Subunit of DNA polymerase | LHK_01415 | C. violaceum | 50 | 2.00E-27 | |
holA | DNA polymerase III subunit delta | Subunit of DNA polymerase, interacts with gamma subunit to transfer beta subunit on DNA | LHK_00117 | C. violaceum | 67.28 | 7.00E-79 | |
holB | DNA polymerase III subunit delta | Subunit of DNA polymerase | LHK_02696 | L. nitroferrum | 57.36 | 3.00E-75 | |
dnaQ | DNA polymerase III subunit epsilon | Subunit of DNA polymerase, a 3'-5' exonuclease posseses proofreading function | LHK_00881 | C. violaceum | 71.74 | 6.00E-85 | |
LHK_01009 | C. violaceum | 62.7 | 4.00E-60 | ||||
LHK_02526 | C. violaceum | 51.52 | 3.00E-105 | ||||
dnaX | DNA polymerase III subunits gamma and tau | Subunits of DNA polymerase, tau subunit serves as scaffold in dimerization of the core complex while gamma subunit interacts with delta subunit to transfer beta subunit on DNA | LHK_00963 | C. violaceum | 82.17 | 2.00E-154 | |
Other MMR factors | dam | DNA adenine methylase | Methylates DNA sequence GATC and protects DNA from cleavage by restriction endonuclease | LHK_01749 | C. violaceum | 83.92 | 8.00E-131 |
LHK_02602 | C. violaceum | 75 | 9.00E-113 | ||||
LHK_00398 | C. violaceum | 75 | 9.00E-113 | ||||
vsr | Very short patch repair protein | Endonuclease, nicks double-stranded DNA | LHK_03243 | Limnobacter sp. MED105 | 61.38 | 5.00E-48 |