SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from Please contact us if you experience any problems.

DNA-binding domain superfamily models

A superfamily is represented by one or more models; usually there is more than one model representing the superfamily. Since each model is built to capture the whole superfamily, they are likely to be overlapping and sometimes are mostly overlapping or even redundant to each other. Also models often do not score their own seed sequence more highly than other sequences in the superfamily, so it is a mistake to think that the model represents the seed sequence.

All models are available for immediate download after obtaining a license by filling in a short online registration form. Licenses are free for academic and commercial purposes.

Plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be viewed for each model by following the model ID link.

All 5 SUPERFAMILY models representing the DNA-binding domain superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0035437 6 2005-09-08 d1bb8a_ DNA-binding domain from tn916 integrase
0038039 550 2005-09-08 d1gcca_ GCC-box binding domain
0049847 350 2008-09-10 d1ub1a_ Methyl-CpG-binding domain, MBD
0036316 124 2005-09-08 d1d9na_ Methyl-CpG-binding domain, MBD
0040114 5 2005-09-08 d1kjka_ lambda integrase N-terminal domain