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Table 2 Summary of differences in DNA replication machinery of Archaea and Bacteria.

From: The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon

Function Superkingdom Protein PDB ID (if applicable) SCOP Superfamily Combination Proposed Origin in Archaea
Origin recognition Bacteria DnaA 1l8q _gap_,52540,48295  
  Archaea Cdc6/ORC (single or multiple homologues) 1fnn 52540, 46785 evolved from RuvB
Replicative helicase Bacteria DnaC 3ec2 52540 *  
  Archaea MCM 3f9v   viral transfer
Helicase loader Bacteria DnaB 1b79 (n-terminal domain) gap, 48024  
ssDNA-binding protein Archaea, Bacteria SSB (one subunit) 1o7i 50249 archaeal SSB evolved from bacterial SSB
  Archaea RPA (one or three subunits) 2b28 50249, 50249, 50249 evolved from SSB
Primase Bacteria DnaG 1dd9 56731  
  Archaea PriA (small) 1zt2:a 56747, gap viral transfer or vertically inherited
  Archaea PriB(large) 1zt2:b 140914 innovation
Replicative Polymerase Archaea, Bacteria PolB (one or multiple homologues) 1q8i gap, 56672 viral transfer
  Archaea PolD (small) none gap, 56300 innovation
  Archaea PolD (large) none gap innovation
  Bacteria PolC (DnaE) 2hqa 89550, large gap*  
DNA sliding clamp Archaea PCNA (three subunits) 3a2f 55979, 55979 evolved from β-clamp
  Bacteria β-clamp (dimer) 1ok7 55979, 55979, 55979  
Clamp loader Bacteria γ-Complex (three subunits) 1jr3:a 52540, 48019  
  Archaea RFC (two subunits) 1iqp 52540, 48019 evolved from γ-Complex
Removal of primers Archaea Fen1 1rxw 88723, 47807 viral origin
  Bacteria RNase H 1jl1 53098  
  Archaea RNase HII 1eke 53098 archaeal RNAase HII evolved from bacterial RNAase HI
  Bacteria PolA 2kfz (mssing c-terminal domain) 53098, 56672  
  Archaea, Bacteria DNA ligase(ATP-DEP) 1xn9 (human) 117018, 56091, 50249 viral origin or vertical inheritance
  Bacteria DNA ligase(NAD-DEP) 1dgs 56091, 50249, 47781  
Preinitiation complex Archaea gins 2eho(human) 158573 true innovation
  1. The list of protein functions was compiled from box 1 in [20] and table one in [129]. Italics indicate a probable horizontal transfer to a superkingdom. There are very few proteins in archaea that are true innovations. Many of their unique replication proteins could be recruited from bacterial or viral systems. A * indicates the Superfamily database was used to predict domain assignments of PDB entries not yet classified in SCOP.