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Table 4 Replication proteins and their closest homologues

From: Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis

Types of enzymes Gene Protein Function of protein encoded CDS Closest match organism Amino acid identity (%) Best E-value
Initiation factors hupB1 DNA-binding protein hu-beta Beta chain of heterodimeric histone-like DNA-binding protein, wraps DNA to stabilize and prevent denaturation under extreme environmental conditions LHK_02345 C. violaceum 79.78 2.00E-33
  hupB2 DNA-binding protein hu-beta Beta chain of heterodimeric histone-like DNA-binding protein, wraps DNA to stabilize and prevent denaturation under extreme environmental conditions LHK_02180 C. violaceum 46.59 1.00E-14
  ihfA/himA Integration host factor subunit alpha One of the two subunits of integration host factor, a specific DNA-binding protein LHK_02751 L. nitroferrum 91.84 8.00E-46
  ihfB/himD Integration host factor subunit beta One of the two subunits of integration host factor, a specific DNA-binding protein LHK_00870 L. nitroferrum 82.35 2.00E-39
  dnaA Chromosomal replication initiator protein DnaA Initiates and regulates chromosomal replication LHK_03240 L. nitroferrum 76.72 0
  dnaB Replicative DNA helicase Initiation and elongation, DNA-dependent ATPase LHK_01738 C. violaceum 76.48 0
     LHK_01506 N. gonorrhoeae 40.73 3.00E-76
  dnaG DNA primase Polymerase synthesizes small RNA primers for the Okazaki fragments on both template strands at replication forks LHK_00463 C. violaceum 65.42 2.00E-155
  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
  fis DNA-binding protein Fis Nucleoid-associated protein LHK_03207 C. violaceum 73.68 1.00E-25
  hvrA H-NS like protein Binds tightly to dsDNA, increases thermal stability and inhibits transcription LHK_00853 C. violaceum 58.82 4.00E-28
     LHK_00959 C. violaceum 53.47 2.00E-18
  iciA Chromosome initiation inhibitor In vitro inhibitor of chromosomal replication initiation LHK_00797 Acinetobacter baumannii 43.24 1.00E-63
Elongation factors 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 polymerse III subunit epsilon Subunit of DNA polymerase, a 3'-5' exonuclease possesses 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 polymerse 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
  rnhA Ribonuclease HI Endonuclease degrades RNA of RNA-DNA hybrids, specifies the origin of replication by suppressing initiation at origins other than the oriC locus, removes RNA primers from the Okazaki fragments of lagging strands LHK_00880 L. nitroferrum 77.3 2.00E-59
  rnhB Ribonuclease HII Endonuclease degrades RNA of RNA-DNA hybrids LHK_00722 L. nitroferrum 71.88 1.00E-68
  polA DNA polymerase I DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity LHK_02983 C. violaceum 68.03 0
  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 C. taiwanensis 65.83 0
Termination factors dam DNA adenine methylase Methylates DNA within the sequence GATC and protects the 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
  hda DnaA-homolog protein hda Mediates interactions of DnaA with beta subunit sliding clamp, controls initiation of DNA replication by inhibiting reinitiation of replication LHK_00510 C. violaceum 66.82 1.00E-77
Topoisomerases gyrA DNA gyrase subunit A Negatively supercoils closed circular double-stranded DNA, catalyzes interconversion of topological isomers of double-stranded DNA rings, including catenanes and knotted rings. Consists of subunit A and B. Responsible for DNA breakage and rejoining, forms A2B2 tetramer LHK_01836 L. nitroferrum 82.09 0
  gyrB DNA gyrase subunit B Negatively supercoils closed circular double-stranded DNA, catalyzes interconversion of topological isomers of double-stranded DNA rings, including catenanes and knotted rings. Consists of subunit A and B. Catalyzes ATP hydrolysis, forms A2B2 tetramer LHK_03242 L. nitroferrum 83.06 0
  parC DNA topoisomerse 4 subunit A Essential for chromosome segregation, relaxation of supercoiled DNA. Performs decatenation during replication of circular DNA molecule. Composed of subunits ParC and ParE LHK_00093 L. nitroferrum 74.47 0
  parE DNA topoisomerase 4 subunit B Essential for chromosome segregation, relaxation of supercoiled DNA. Performs decatenation during replication of circular DNA molecule. Composed of subunits ParC and ParE LHK_00606 L. nitroferrum 82.01 0
  topA DNA topoisomerase 1 Conversion of one DNA topological isomer to another LHK_03143 C. violaceum 80.13 0