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  Home > SCOP hierarchy > PH domain-like > Hidden Markov models

PH 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 94 SUPERFAMILY models representing the PH domain-like superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0035702 161 2005-09-08 d1btka_ Pleckstrin-homology domain (PH domain)
0037469 1081 2005-09-08 d1faoa_ Pleckstrin-homology domain (PH domain)
0044633 425 2005-09-08 d1v61a_ Pleckstrin-homology domain (PH domain)
0050088 2924 2008-09-10 d1v88a_ Pleckstrin-homology domain (PH domain)
0050619 2774 2008-09-10 d1wjma_ Pleckstrin-homology domain (PH domain)
0051136 4340 2008-09-10 d1xx0a1 Pleckstrin-homology domain (PH domain)
0052196 2905 2008-09-10 d2coda1 Pleckstrin-homology domain (PH domain)
0053818 597 2010-05-31 d2dfka2 Pleckstrin-homology domain (PH domain)
0046779 2917 2008-09-10 d1fgya_ Pleckstrin-homology domain (PH domain)
0049970 3088 2008-09-10 d1upqa_ Pleckstrin-homology domain (PH domain)
0052708 2609 2008-09-10 d2fjla1 Pleckstrin-homology domain (PH domain)
0036336 629 2005-09-08 d1dbha2 Pleckstrin-homology domain (PH domain)
0037709 30 2005-09-08 d1foea2 Pleckstrin-homology domain (PH domain)
0040330 737 2005-09-08 d1kz7a2 Pleckstrin-homology domain (PH domain)
0045916 1932 2008-09-10 d1baka_ Pleckstrin-homology domain (PH domain)
0048603 1793 2008-09-10 d1omwa2 Pleckstrin-homology domain (PH domain)
0049773 2706 2008-09-10 d1u29a1 Pleckstrin-homology domain (PH domain)
0050335 375 2008-09-10 d1w1ha_ Pleckstrin-homology domain (PH domain)
0050771 815 2008-09-10 d1x1fa1 Pleckstrin-homology domain (PH domain)
0051547 720 2008-09-10 d1zc3b1 Pleckstrin-homology domain (PH domain)
0054198 2846 2010-05-31 d2j59m1 Pleckstrin-homology domain (PH domain)
0041564 546 2005-09-08 d1ntya2 Pleckstrin-homology domain (PH domain)
0044630 867 2005-09-08 d1v5ua_ Pleckstrin-homology domain (PH domain)
0050056 2878 2008-09-10 d1v5pa_ Pleckstrin-homology domain (PH domain)
0052195 1060 2008-09-10 d2coca1 Pleckstrin-homology domain (PH domain)
0036672 739 2005-09-08 d1dyna_ Pleckstrin-homology domain (PH domain)
0040866 258 2005-09-08 d1maia_ Pleckstrin-homology domain (PH domain)
0046512 5747 2008-09-10 d1eaza_ Pleckstrin-homology domain (PH domain)
0048782 3228 2008-09-10 d1plsa_ Pleckstrin-homology domain (PH domain)
0049788 938 2008-09-10 d1u5ea1 Pleckstrin-homology domain (PH domain)
0050531 3578 2008-09-10 d1wgqa_ Pleckstrin-homology domain (PH domain)
0050918 171 2008-09-10 d1xcga2 Pleckstrin-homology domain (PH domain)
0035704 1067 2005-09-08 d1btna_ Pleckstrin-homology domain (PH domain)
0037589 146 2005-09-08 d1fhoa_ Pleckstrin-homology domain (PH domain)
0040099 630 2005-09-08 d1ki1b2 Pleckstrin-homology domain (PH domain)
0050089 3099 2008-09-10 d1v89a_ Pleckstrin-homology domain (PH domain)
0052197 1055 2008-09-10 d2cofa1 Pleckstrin-homology domain (PH domain)
0053889 1435 2010-05-31 d2elba2 Pleckstrin-homology domain (PH domain)
0044152 373 2005-09-08 d1txda2 Pleckstrin-homology domain (PH domain)
0047098 2895 2008-09-10 d1h10a_ Pleckstrin-homology domain (PH domain)
0050053 335 2008-09-10 d1v5ma_ Pleckstrin-homology domain (PH domain)
0050571 2894 2008-09-10 d1wi1a_ Pleckstrin-homology domain (PH domain)
0052193 383 2008-09-10 d2coaa1 Pleckstrin-homology domain (PH domain)
0046390 1944 2008-09-10 d1droa_ Pleckstrin-homology domain (PH domain)
0048704 3258 2008-09-10 d1p6sa_ Pleckstrin-homology domain (PH domain)
0049787 4833 2008-09-10 d1u5da1 Pleckstrin-homology domain (PH domain)
0050517 3154 2008-09-10 d1wg7a_ Pleckstrin-homology domain (PH domain)
0050772 3167 2008-09-10 d1x1ga1 Pleckstrin-homology domain (PH domain)
0051750 41 2008-09-10 d2adza1 Pleckstrin-homology domain (PH domain)
0054799 148 2010-05-31 d2zkmx3 Pleckstrin-homology domain (PH domain)
0042143 201 2005-09-08 d1p3ra_ Phosphotyrosine-binding domain (PTB)
0050535 220 2008-09-10 d1wgua_ Phosphotyrosine-binding domain (PTB)
0049397 878 2008-09-10 d1shca_ Phosphotyrosine-binding domain (PTB)
0050604 1231 2008-09-10 d1wj1a_ Phosphotyrosine-binding domain (PTB)
0051073 251 2008-09-10 d1xr0b_ Phosphotyrosine-binding domain (PTB)
0042935 89 2005-09-08 d1qqga2 Phosphotyrosine-binding domain (PTB)
0052456 282 2008-09-10 d2dkqa1 Phosphotyrosine-binding domain (PTB)
0042168 122 2005-09-08 d1p5ta_ Phosphotyrosine-binding domain (PTB)
0045807 234 2008-09-10 d1aqca_ Phosphotyrosine-binding domain (PTB)
0050722 256 2008-09-10 d1wvha1 Phosphotyrosine-binding domain (PTB)
0039313 136 2005-09-08 d1j0wa_ Phosphotyrosine-binding domain (PTB)
0041561 174 2005-09-08 d1ntva_ Phosphotyrosine-binding domain (PTB)
0049013 1697 2008-09-10 d1qqga1 Phosphotyrosine-binding domain (PTB)
0036373 304 2005-09-08 d1ddma_ Phosphotyrosine-binding domain (PTB)
0052349 116 2008-09-10 d2cy4a1 Phosphotyrosine-binding domain (PTB)
0039917 607 2005-09-08 d1k5db_ Ran-binding domain
0043361 240 2005-09-08 d1rrpb_ Ran-binding domain
0050998 597 2008-09-10 d1xkea1 Ran-binding domain
0052260 637 2008-09-10 d2crfa1 Ran-binding domain
0040975 113 2005-09-08 d1mkea1 Enabled/VASP homology 1 domain (EVH1 domain)
0048923 592 2008-09-10 d1qc6a_ Enabled/VASP homology 1 domain (EVH1 domain)
0037213 132 2005-09-08 d1evha_ Enabled/VASP homology 1 domain (EVH1 domain)
0047292 181 2008-09-10 d1i2ha_ Enabled/VASP homology 1 domain (EVH1 domain)
0038905 95 2005-09-08 d1i7aa_ Enabled/VASP homology 1 domain (EVH1 domain)
0036997 454 2005-09-08 d1egxa_ Enabled/VASP homology 1 domain (EVH1 domain)
0051047 253 2008-09-10 d1xoda1 Enabled/VASP homology 1 domain (EVH1 domain)
0036787 309 2005-09-08 d1e5wa2 Third domain of FERM
0039182 310 2005-09-08 d1isna2 Third domain of FERM
0039316 319 2005-09-08 d1j19a2 Third domain of FERM
0051791 196 2008-09-10 d2al6a2 Third domain of FERM
0048169 133 2008-09-10 d1mixa2 Third domain of FERM
0038081 304 2005-09-08 d1gg3a2 Third domain of FERM
0048159 170 2008-09-10 d1mi1a2 PreBEACH PH-like domain
0049561 279 2008-09-10 d1t77a2 PreBEACH PH-like domain
0042632 49 2005-09-08 d1q67a_ Dcp1
0040694 71 2005-09-08 d1lw3a1 GRAM domain
0042287 23 2005-09-08 d1pfja_ TFIIH domain
0051204 31 2008-09-10 d1y5oa1 TFIIH domain
0052868 171 2008-09-10 d2gcla1 SSRP1-like
0049677 124 2008-09-10 d1tqza1 Necap1 N-terminal domain-like
0052133 107 2008-09-10 d2caya1 VPS36 N-terminal domain-like
0053042 54 2008-09-10 d2hthb1 VPS36 N-terminal domain-like
0054928 174 2010-05-31 d3dcxa1 BPHL domain
0054814 156 2010-05-31 d3b77a1 BPHL domain


Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.