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

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