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Table 1 Representatives for previous families 54 existing families (Thornton classification) representatives were selected and were validated using Jack-knifing

From: Re-visiting protein-centric two-tier classification of existing DNA-protein complexes

Group Families Representative(s)
HTH   
  Cro & repressor 1LMB
  Homeodomain 1FJL, 1HDD, 6PAX
  LacI repressor 1WET
  Endonuclease Fok1 1FOK
  Gamma Delta resolvase 1GDT
  Hin recombinase 1HCR
  RAP1 family 1IGN
  Prd paired domain 1PDN
  Tc3 transposase 1TC3
  Trp repressor 1TRR
  Diptheria tox repressor 1DDN
  Transcription factor IIB 1D3U
  Interferon regulatory 2IRF
  Catabolite gene activator protein 1RUO
  Transcription factor 1CF7, 3HTS
  Ets domain 1BC8
Zinc Co-ordinating   
  β-β-α zinc finger 1ZAA
  Harmone Nuclear Receptor 2NLL
  Loop sheet helix 1TSR
  GAL4 type 1ZME
Zipper type   
  Leucine Zipper 1YSA
  Helix loop helix 1AN2
Other-α Helix   
  Pappilomavirus 1 E2 2BOP
  Histone 1AOI
  EBNA1 nuclear protein 1B3T
  Skn-1 transcription factor 1SKN
  Cre Recombinase 1CRX
  High Mobility Group 1QRV
  MADS box 1MNM
β-Sheet   
  TATA box binding 1YTB
β-Hairpin/Ribbon   
  MetJ repressor 1CMA
  Tus replication terminator 1ECR
  Integration host factor 1IHF
  Transcription Factor T-domain 1XBR
  Hyperthermophile DNA 1AZP
  Arc repressor 1PAR
Other   
  ReI homology 1SVC
  Stat protein 1BF5
Enzyme   
  Methyltransferase 6MHT
  Endonuclease PvuII 3PVI
  Endonuclease ecorV 1RVA
  Endonuclease ecorI 1QPS
  Endonuclease BamHI 3BAM
  Enonuclease V 1VAS
  Dnase I 2DNJ
  DNA mismatch endonuclease 1CW0
  DNA polymerase β 1BPY
  DNA Polymerase I 2BDP
  DNA Polymerase T7 1T7P,1CLQ
  HIV Reverse Transcriptase 2HMI
  Uracil DNA glycosylase 1SSP
  3-Methyladenine DNA glycosylase 1BNK
  Homing endonuclease 1A73, 1BP7
  TopoisomeraseI 1A31