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  Home > SCOP hierarchy > Positive stranded ssRNA viruses > Hidden Markov models

Positive stranded ssRNA viruses 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 90 SUPERFAMILY models representing the Positive stranded ssRNA viruses superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0046272 4729 2008-09-10 d1d4m3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0046813 4480 2008-09-10 d1fmd3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0048795 212 2008-09-10 d1pov0_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0049167 561 2008-09-10 d1rhi1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0037664 285 2005-09-08 d1fmd1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0042484 286 2005-09-08 d1pvc.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0044054 466 2005-09-08 d1tmf1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0045843 4988 2008-09-10 d1aym3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0046636 4694 2008-09-10 d1ev13_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0048329 4478 2008-09-10 d1ncq.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0049084 7635 2008-09-10 d1r1a1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0053182 6061 2008-09-10 d2mev1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0035504 516 2005-09-08 d1bev1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0037207 483 2005-09-08 d1ev11_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0041954 372 2005-09-08 d1oop.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0045603 570 2005-09-08 d4rhv3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0046192 6889 2008-09-10 d1cov1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0046506 3742 2008-09-10 d1eah.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0046844 5186 2008-09-10 d1fpn3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0049017 298 2008-09-10 d1qqp1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0049656 5007 2008-09-10 d1tme3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0035267 607 2005-09-08 d1aym1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0038482 369 2005-09-08 d1h8t.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0042486 621 2005-09-08 d1pvc3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0045357 357 2005-09-08 d2mev.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0045869 961 2008-09-10 d1b35b_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0046812 4895 2008-09-10 d1fmd.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0048616 4878 2008-09-10 d1oopc_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0049166 4468 2008-09-10 d1rhi.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0041051 476 2005-09-08 d1mqta_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0044053 365 2005-09-08 d1tmf.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0046271 6496 2008-09-10 d1d4m1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0046508 5418 2008-09-10 d1eah3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0049083 4019 2008-09-10 d1r1a.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0035503 423 2005-09-08 d1bev.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0037206 392 2005-09-08 d1ev1.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0038778 566 2005-09-08 d1hxs1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0043246 569 2005-09-08 d1rhi3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0045602 457 2005-09-08 d4rhv1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0046843 7993 2008-09-10 d1fpn1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0049655 562 2008-09-10 d1tme1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0035266 407 2005-09-08 d1aym.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0036089 375 2005-09-08 d1cov.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0037726 365 2005-09-08 d1fpn.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0042485 556 2005-09-08 d1pvc1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0045868 20 2008-09-10 d1b35a_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0049085 4797 2008-09-10 d1r1a3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0053183 5810 2008-09-10 d2mev3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0041955 471 2005-09-08 d1oopa_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0044050 387 2005-09-08 d1tme.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0045812 5124 2008-09-10 d1ar73_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0046193 5011 2008-09-10 d1cov3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0046507 691 2008-09-10 d1eah1_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0047145 6560 2008-09-10 d1h8ta_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0049018 3827 2008-09-10 d1qqp3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0035327 232 2005-09-08 d1b35.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0036267 357 2005-09-08 d1d4m.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0038484 584 2005-09-08 d1h8tc_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0042940 297 2005-09-08 d1qqp.1 Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0045944 4504 2008-09-10 d1bev3_ Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
0034903 23 2005-09-08 d1a6ca3 Comoviridae-like VP
0041619 12 2005-09-08 d1ny721 Comoviridae-like VP
0034902 159 2005-09-08 d1a6ca2 Comoviridae-like VP
0035628 18 2005-09-08 d1bmv22 Comoviridae-like VP
0045983 65 2008-09-10 d1bmv11 Comoviridae-like VP
0048466 65 2008-09-10 d1ny711 Comoviridae-like VP
0034901 22 2005-09-08 d1a6ca1 Comoviridae-like VP
0035627 14 2005-09-08 d1bmv21 Comoviridae-like VP
0041620 18 2005-09-08 d1ny722 Comoviridae-like VP
0039030 326 2005-09-08 d1ihma_ Caliciviridae-like VP
0041491 6 2005-09-08 d1novc_ Nodaviridae-like VP
0045183 6 2005-09-08 d2bbvc_ Nodaviridae-like VP
0046730 17 2008-09-10 d1f8v.1 Nodaviridae-like VP
0036176 6 2005-09-08 d1cwpa_ Bromoviridae-like VP
0047671 321 2008-09-10 d1js9c_ Bromoviridae-like VP
0037325 14 2005-09-08 d1f15b_ Bromoviridae-like VP
0040435 14 2005-09-08 d1laja_ Bromoviridae-like VP
0045827 86 2008-09-10 d1auyb_ Tymoviridae-like VP
0046307 86 2008-09-10 d1ddla_ Tymoviridae-like VP
0048972 86 2008-09-10 d1qjza_ Tymoviridae-like VP
0035877 66 2005-09-08 d1c8nc_ Tombusviridae-like VP
0041373 60 2005-09-08 d1ng0c_ Tombusviridae-like VP
0043670 67 2005-09-08 d1smvc_ Tombusviridae-like VP
0053349 417 2008-09-10 d4sbvc_ Tombusviridae-like VP
0037354 30 2005-09-08 d1f2nc_ Tombusviridae-like VP
0041965 72 2005-09-08 d1opoa_ Tombusviridae-like VP
0050118 412 2008-09-10 d1vaka_ Tombusviridae-like VP
0045464 62 2005-09-08 d2tbvc_ Tombusviridae-like VP
0041857 85 2005-09-08 d1ohfc_ Tetraviridae-like VP
0050430 971 2008-09-10 d1wcdj1 Birnaviridae-like VP


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.