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  Home > SCOP hierarchy > Nucleic acid-binding proteins > Hidden Markov models

Nucleic acid-binding proteins 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 131 SUPERFAMILY models representing the Nucleic acid-binding proteins superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0046596 723 2008-09-10 d1eova1 Anticodon-binding domain
0048308 1977 2008-09-10 d1n9wa1 Anticodon-binding domain
0045922 1481 2008-09-10 d1bbua1 Anticodon-binding domain
0046050 1989 2008-09-10 d1c0aa1 Anticodon-binding domain
0036711 436 2005-09-08 d1e1oa1 Anticodon-binding domain
0045898 2347 2008-09-10 d1b8aa1 Anticodon-binding domain
0046921 1936 2008-09-10 d1g51a1 Anticodon-binding domain
0035732 201 2005-09-08 d1bvsa3 DNA helicase RuvA subunit, N-terminal domain
0036158 201 2005-09-08 d1cuka3 DNA helicase RuvA subunit, N-terminal domain
0039264 196 2005-09-08 d1ixra2 DNA helicase RuvA subunit, N-terminal domain
0040310 6 2005-09-08 d1kxla_ Single strand DNA-binding domain, SSB
0043001 135 2005-09-08 d1quqb_ Single strand DNA-binding domain, SSB
0050616 292 2008-09-10 d1wjja_ Single strand DNA-binding domain, SSB
0042019 4 2005-09-08 d1otcb_ Single strand DNA-binding domain, SSB
0048167 45 2008-09-10 d1miua5 Single strand DNA-binding domain, SSB
0048643 17 2008-09-10 d1otca3 Single strand DNA-binding domain, SSB
0050030 509 2008-09-10 d1v1qa_ Single strand DNA-binding domain, SSB
0053338 1712 2008-09-10 d3ulla_ Single strand DNA-binding domain, SSB
0037226 33 2005-09-08 d1ewia_ Single strand DNA-binding domain, SSB
0047920 269 2008-09-10 d1l1oc_ Single strand DNA-binding domain, SSB
0048514 367 2008-09-10 d1o7ia_ Single strand DNA-binding domain, SSB
0050994 78 2008-09-10 d1xjva1 Single strand DNA-binding domain, SSB
0043000 386 2005-09-08 d1quqa_ Single strand DNA-binding domain, SSB
0037576 326 2005-09-08 d1fgua1 Single strand DNA-binding domain, SSB
0039281 25 2005-09-08 d1iyjb3 Single strand DNA-binding domain, SSB
0047474 47 2008-09-10 d1iyjb5 Single strand DNA-binding domain, SSB
0048166 66 2008-09-10 d1miua4 Single strand DNA-binding domain, SSB
0048642 18 2008-09-10 d1otca2 Single strand DNA-binding domain, SSB
0049071 101 2008-09-10 d1qzga_ Single strand DNA-binding domain, SSB
0049870 1891 2008-09-10 d1ue1a_ Single strand DNA-binding domain, SSB
0046777 327 2008-09-10 d1fgua2 Single strand DNA-binding domain, SSB
0049372 1875 2008-09-10 d1se8a_ Single strand DNA-binding domain, SSB
0047473 25 2008-09-10 d1iyjb4 Single strand DNA-binding domain, SSB
0048165 84 2008-09-10 d1miua3 Single strand DNA-binding domain, SSB
0048641 86 2008-09-10 d1otca1 Single strand DNA-binding domain, SSB
0049051 1954 2008-09-10 d1qvca_ Single strand DNA-binding domain, SSB
0050995 65 2008-09-10 d1xjva2 Single strand DNA-binding domain, SSB
0038054 299 2005-09-08 d1gd7a_ Myf domain
0048841 1622 2008-09-10 d1pyba_ Myf domain
0048176 2160 2008-09-10 d1mkha_ Myf domain
0048839 2038 2008-09-10 d1pxfa_ Myf domain
0048442 2144 2008-09-10 d1ntga_ Myf domain
0048844 629 2008-09-10 d1pysb3 Myf domain
0037641 444 2005-09-08 d1fl0a_ Myf domain
0045777 972 2008-09-10 d1ah9a_ Cold shock DNA-binding domain-like
0047147 1429 2008-09-10 d1h95a_ Cold shock DNA-binding domain-like
0047805 268 2008-09-10 d1khia2 Cold shock DNA-binding domain-like
0049455 9827 2008-09-10 d1sroa_ Cold shock DNA-binding domain-like
0051771 8174 2008-09-10 d2ahob2 Cold shock DNA-binding domain-like
0054212 2205 2010-05-31 d2je6i1 Cold shock DNA-binding domain-like
0054722 424 2010-05-31 d2vnud1 Cold shock DNA-binding domain-like
0037626 325 2005-09-08 d1fjgq_ Cold shock DNA-binding domain-like
0046097 2911 2008-09-10 d1c9oa_ Cold shock DNA-binding domain-like
0047483 459 2008-09-10 d1iz6a2 Cold shock DNA-binding domain-like
0049181 1093 2008-09-10 d1ripa_ Cold shock DNA-binding domain-like
0051177 894 2008-09-10 d1y14b1 Cold shock DNA-binding domain-like
0054597 1030 2010-05-31 d2qamc2 Cold shock DNA-binding domain-like
0054772 1047 2010-05-31 d2zjra2 Cold shock DNA-binding domain-like
0038590 626 2005-09-08 d1hh2p1 Cold shock DNA-binding domain-like
0040675 896 2005-09-08 d1luza_ Cold shock DNA-binding domain-like
0044179 263 2005-09-08 d1u0la1 Cold shock DNA-binding domain-like
0046800 1388 2008-09-10 d1fjgl_ Cold shock DNA-binding domain-like
0047328 1104 2008-09-10 d1i94q_ Cold shock DNA-binding domain-like
0048887 3043 2008-09-10 d1q46a2 Cold shock DNA-binding domain-like
0054165 94 2010-05-31 d2ix0a1 Cold shock DNA-binding domain-like
0054279 543 2010-05-31 d2nn6h1 Cold shock DNA-binding domain-like
0054724 305 2010-05-31 d2vnud3 Cold shock DNA-binding domain-like
0036299 204 2005-09-08 d1d7qa_ Cold shock DNA-binding domain-like
0046451 6877 2008-09-10 d1e3pa2 Cold shock DNA-binding domain-like
0047715 1162 2008-09-10 d1k0ra1 Cold shock DNA-binding domain-like
0049427 3367 2008-09-10 d1smxa_ Cold shock DNA-binding domain-like
0050575 2574 2008-09-10 d1wi5a_ Cold shock DNA-binding domain-like
0053734 6618 2010-05-31 d2ba0a1 Cold shock DNA-binding domain-like
0054205 295 2010-05-31 d2ja9a1 Cold shock DNA-binding domain-like
0034894 444 2005-09-08 d1a62a2 Cold shock DNA-binding domain-like
0041615 59 2005-09-08 d1ny4a_ Cold shock DNA-binding domain-like
0044303 226 2005-09-08 d1ueba3 Cold shock DNA-binding domain-like
0046930 2954 2008-09-10 d1g6pa_ Cold shock DNA-binding domain-like
0051100 275 2008-09-10 d1xtda2 Cold shock DNA-binding domain-like
0052503 2958 2008-09-10 d2es2a1 Cold shock DNA-binding domain-like
0054167 449 2010-05-31 d2ix0a3 Cold shock DNA-binding domain-like
0054593 671 2010-05-31 d2qall1 Cold shock DNA-binding domain-like
0054754 3820 2010-05-31 d2z0sa1 Cold shock DNA-binding domain-like
0043292 340 2005-09-08 d1rl2a2 Cold shock DNA-binding domain-like
0047223 924 2008-09-10 d1hr0w_ Cold shock DNA-binding domain-like
0047828 7475 2008-09-10 d1kl9a2 Cold shock DNA-binding domain-like
0049576 591 2008-09-10 d1t9ha1 Cold shock DNA-binding domain-like
0052107 695 2008-09-10 d2c35b1 Cold shock DNA-binding domain-like
0053990 1041 2010-05-31 d2gy9q1 Cold shock DNA-binding domain-like
0054276 415 2010-05-31 d2nn6g1 Cold shock DNA-binding domain-like
0054723 501 2010-05-31 d2vnud2 Cold shock DNA-binding domain-like
0039578 14 2005-09-08 d1jjga_ Cold shock DNA-binding domain-like
0045011 59 2005-09-08 d1x6oa2 Cold shock DNA-binding domain-like
0047019 3071 2008-09-10 d1go3e1 Cold shock DNA-binding domain-like
0047679 688 2008-09-10 d1jt8a_ Cold shock DNA-binding domain-like
0048170 2916 2008-09-10 d1mjca_ Cold shock DNA-binding domain-like
0050502 1849 2008-09-10 d1wfqa_ Cold shock DNA-binding domain-like
0054176 1042 2010-05-31 d2j01d2 Cold shock DNA-binding domain-like
0054650 12 2010-05-31 d2r7da1 Cold shock DNA-binding domain-like
0054855 8240 2010-05-31 d3bzka4 Cold shock DNA-binding domain-like
0037529 341 2005-09-08 d1ffka2 Cold shock DNA-binding domain-like
0041327 58 2005-09-08 d1ne3a_ Cold shock DNA-binding domain-like
0044302 622 2005-09-08 d1ueba2 Cold shock DNA-binding domain-like
0045976 407 2008-09-10 d1bkba2 Cold shock DNA-binding domain-like
0052498 458 2008-09-10 d2eifa2 Cold shock DNA-binding domain-like
0054166 2151 2010-05-31 d2ix0a2 Cold shock DNA-binding domain-like
0054282 424 2010-05-31 d2nn6i1 Cold shock DNA-binding domain-like
0036423 257 2005-09-08 d1dgsa2 DNA ligase/mRNA capping enzyme postcatalytic domain
0037797 33 2005-09-08 d1fvia1 DNA ligase/mRNA capping enzyme postcatalytic domain
0045686 61 2008-09-10 d1a0ia1 DNA ligase/mRNA capping enzyme postcatalytic domain
0050885 845 2008-09-10 d1x9na2 DNA ligase/mRNA capping enzyme postcatalytic domain
0042114 49 2005-09-08 d1p16a1 DNA ligase/mRNA capping enzyme postcatalytic domain
0046163 125 2008-09-10 d1ckma1 DNA ligase/mRNA capping enzyme postcatalytic domain
0039498 15 2005-09-08 d1je5a_ Phage ssDNA-binding proteins
0047028 34 2008-09-10 d1gpca_ Phage ssDNA-binding proteins
0038296 10 2005-09-08 d1gvpa_ Phage ssDNA-binding proteins
0048748 4 2008-09-10 d1pfsa_ Phage ssDNA-binding proteins
0053683 19 2010-05-31 d2a1ka1 Phage ssDNA-binding proteins
0049722 112 2008-09-10 d1twfh_ RNA polymerase subunit RBP8
0047013 76 2008-09-10 d1gm5a2 RecG "wedge" domain
0039892 29 2005-09-08 d1k3ra1 Hypothetical protein MTH1 (MT0001), insert domain
0040655 339 2005-09-08 d1ltla_ DNA replication initiator (cdc21/cdc54) N-terminal domain
0044549 229 2005-09-08 d1uwva1 TRAM domain
0051418 919 2008-09-10 d1yvca1 TRAM domain
0051294 954 2008-09-10 d1yeza1 TRAM domain
0049790 277 2008-09-10 d1u5ka1 RecO N-terminal domain-like
0052237 260 2008-09-10 d2cqaa1 TIP49 domain
0053958 446 2010-05-31 d2gnra1 SSO2064-like
0054168 1618 2010-05-31 d2ix0a4 RNB domain-like
0054651 1638 2010-05-31 d2r7da2 RNB domain-like
0054725 1632 2010-05-31 d2vnud4 RNB domain-like


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.