SUPERFAMILY 1.75 HMM library and genome assignments server

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alpha/beta knot 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 20 SUPERFAMILY models representing the alpha/beta knot superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0041137 772 2005-09-08 d1mxia_ SpoU-like RNA 2'-O ribose methyltransferase
0047409 1659 2008-09-10 d1ipaa1 SpoU-like RNA 2'-O ribose methyltransferase
0038338 933 2005-09-08 d1gz0a1 SpoU-like RNA 2'-O ribose methyltransferase
0044596 935 2005-09-08 d1v2xa_ SpoU-like RNA 2'-O ribose methyltransferase
0039893 219 2005-09-08 d1k3ra2 Hypothetical protein MTH1 (MT0001), dimerisation domain
0048501 450 2008-09-10 d1o6da_ YbeA-like
0048429 451 2008-09-10 d1ns5a_ YbeA-like
0044746 150 2005-09-08 d1vh0a_ YbeA-like
0044065 650 2005-09-08 d1to0a_ YbeA-like
0042210 210 2005-09-08 d1p9pa_ tRNA(m1G37)-methyltransferase TrmD
0044237 210 2005-09-08 d1uala_ tRNA(m1G37)-methyltransferase TrmD
0042076 210 2005-09-08 d1oy5a_ tRNA(m1G37)-methyltransferase TrmD
0044758 239 2005-09-08 d1vhka2 YggJ C-terminal domain-like
0050073 967 2008-09-10 d1v6za2 YggJ C-terminal domain-like
0041613 242 2005-09-08 d1nxza2 YggJ C-terminal domain-like
0054693 185 2010-05-31 d2v3ka1 EMG1/NEP1-like
0054822 177 2010-05-31 d3bbda1 EMG1/NEP1-like
0054635 71 2010-05-31 d2qwva1 AF1056-like
0054617 133 2010-05-31 d2qmma1 AF1056-like
0054325 72 2010-05-31 d2o3aa1 AF0751-like