SUPERFAMILY 1.75 HMM library and genome assignments server

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

GAF domain-like 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 15 SUPERFAMILY models representing the GAF domain-like superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0054864 1406 2010-05-31 d3c2wa1 GAF domain
0048135 1096 2008-09-10 d1mc0a1 GAF domain
0054399 1411 2010-05-31 d2oola1 GAF domain
0050183 1714 2008-09-10 d1vhma_ GAF domain
0046710 1256 2008-09-10 d1f5ma_ GAF domain
0054347 1457 2010-05-31 d2o9ca1 GAF domain
0048136 4582 2008-09-10 d1mc0a2 GAF domain
0054712 1419 2010-05-31 d2veaa1 GAF domain
0054249 3695 2010-05-31 d2k2na1 GAF domain
0049595 2342 2008-09-10 d1td5a_ IclR ligand-binding domain-like
0048178 2427 2008-09-10 d1mkma2 IclR ligand-binding domain-like
0049608 2402 2008-09-10 d1tf1a_ IclR ligand-binding domain-like
0043759 119 2005-09-08 d1stza2 HrcA C-terminal domain-like
0054713 688 2010-05-31 d2veaa2 Phytochrome-specific domain
0054865 586 2010-05-31 d3c2wa2 Phytochrome-specific domain