SUPERFAMILY 1.75 HMM library and genome assignments server

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Retroviral matrix 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 9 SUPERFAMILY models representing the Retroviral matrix proteins superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0036911 844 2005-09-08 d1ed1a_ Immunodeficiency virus matrix proteins
0047937 11726 2008-09-10 d1l6na1 Immunodeficiency virus matrix proteins
0049585 11635 2008-09-10 d1tama_ Immunodeficiency virus matrix proteins
0039783 12 2005-09-08 d1jvra_ HTLV-II matrix protein
0052612 170 2008-09-10 d2f76x1 Mason-Pfizer monkey virus matrix protein
0034915 42 2005-09-08 d1a6sa_ GAG polyprotein M-domain
0038565 4 2005-09-08 d1heka_ EIAV matrix antigen
0044370 47 2005-09-08 d1uhua_ MMLV matrix protein-like
0041011 48 2005-09-08 d1mn8a_ MMLV matrix protein-like