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Table 1 Single-strand breaks repair 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
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