SUPERFAMILY 1.75 HMM library and genome assignments server

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PYP-like sensor domain (PAS 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 16 SUPERFAMILY models representing the PYP-like sensor domain (PAS domain) superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0048644 2836 2008-09-10 d1otda_ PYP-like
0048248 1053 2008-09-10 d1mzua_ PYP-like
0048459 1843 2008-09-10 d1nwza_ PYP-like
0050109 14509 2008-09-10 d1v9ya_ Heme-binding PAS domain
0037219 4115 2005-09-08 d1ew0a_ Heme-binding PAS domain
0046377 3718 2008-09-10 d1dp6a_ Heme-binding PAS domain
0040536 1522 2005-09-08 d1ll8a_ N-terminal PAS domain of Pas kinase
0046045 4709 2008-09-10 d1bywa_ Flavin-binding PAS domain
0046903 4689 2008-09-10 d1g28a_ Flavin-binding PAS domain
0041279 1864 2005-09-08 d1n9la_ Flavin-binding PAS domain
0048715 7560 2008-09-10 d1p97a_ Hypoxia-inducible factor Hif2a, C-terminal domain
0048579 351 2008-09-10 d1oj5a_ PAS domain of steroid receptor coactivator 1A, NCo-A1
0054714 364 2010-05-31 d2veaa3 BphP N-terminal domain-like
0054400 353 2010-05-31 d2oola2 BphP N-terminal domain-like
0054866 265 2010-05-31 d3c2wa3 BphP N-terminal domain-like
0054348 264 2010-05-31 d2o9ca2 BphP N-terminal domain-like