SUPERFAMILY 1.75 HMM library and genome assignments server

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Ribonuclease H-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 58 SUPERFAMILY models representing the Ribonuclease H-like superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0047295 1258 2008-09-10 d1i39a_ Ribonuclease H
0041082 512 2005-09-08 d1mu2a1 Ribonuclease H
0047617 2366 2008-09-10 d1jl2a_ Ribonuclease H
0049179 1552 2008-09-10 d1rila_ Ribonuclease H
0037052 287 2005-09-08 d1ekea_ Ribonuclease H
0049844 1265 2008-09-10 d1uaxa_ Ribonuclease H
0047398 1261 2008-09-10 d1io2a_ Ribonuclease H
0052515 1243 2008-09-10 d2etja1 Ribonuclease H
0041666 525 2005-09-08 d1o1wa_ Ribonuclease H
0046687 4502 2008-09-10 d1f21a_ Ribonuclease H
0051538 823 2008-09-10 d1zbfa1 Ribonuclease H
0035416 750 2005-09-08 d1b9da_ Retroviral integrase, catalytic domain
0045815 10680 2008-09-10 d1asua_ Retroviral integrase, catalytic domain
0046649 334 2008-09-10 d1exqa_ Retroviral integrase, catalytic domain
0046055 7685 2008-09-10 d1c0ma2 Retroviral integrase, catalytic domain
0046085 10076 2008-09-10 d1c6va_ Retroviral integrase, catalytic domain
0045929 137 2008-09-10 d1bcoa2 mu transposase, core domain
0048225 684 2008-09-10 d1musa_ Transposase inhibitor (Tn5 transposase)
0048406 983 2008-09-10 d1noya_ DnaQ-like 3'-5' exonuclease
0049624 829 2008-09-10 d1tgoa1 DnaQ-like 3'-5' exonuclease
0050668 853 2008-09-10 d1wnsa1 DnaQ-like 3'-5' exonuclease
0050330 3037 2008-09-10 d1w0ha_ DnaQ-like 3'-5' exonuclease
0048905 784 2008-09-10 d1q8ia1 DnaQ-like 3'-5' exonuclease
0051245 740 2008-09-10 d1y97a1 DnaQ-like 3'-5' exonuclease
0052620 1824 2008-09-10 d2f96a1 DnaQ-like 3'-5' exonuclease
0044818 62 2005-09-08 d1vk0a_ DnaQ-like 3'-5' exonuclease
0046881 2745 2008-09-10 d1fxxa_ DnaQ-like 3'-5' exonuclease
0049562 167 2008-09-10 d1t7pa1 DnaQ-like 3'-5' exonuclease
0050648 2927 2008-09-10 d1wlja_ DnaQ-like 3'-5' exonuclease
0046173 972 2008-09-10 d1clqa1 DnaQ-like 3'-5' exonuclease
0047541 1809 2008-09-10 d1j9aa_ DnaQ-like 3'-5' exonuclease
0049035 93 2008-09-10 d1qtma1 DnaQ-like 3'-5' exonuclease
0051402 1821 2008-09-10 d1ytaa1 DnaQ-like 3'-5' exonuclease
0053015 708 2008-09-10 d2hhva1 DnaQ-like 3'-5' exonuclease
0036277 398 2005-09-08 d1d5aa1 DnaQ-like 3'-5' exonuclease
0050971 44 2008-09-10 d1xhxa1 DnaQ-like 3'-5' exonuclease
0047793 1726 2008-09-10 d1kfsa1 DnaQ-like 3'-5' exonuclease
0049323 1037 2008-09-10 d1s5ja1 DnaQ-like 3'-5' exonuclease
0054813 681 2010-05-31 d3b6oa1 DnaQ-like 3'-5' exonuclease
0047514 2118 2008-09-10 d1j54a_ DnaQ-like 3'-5' exonuclease
0048960 814 2008-09-10 d1qhta1 DnaQ-like 3'-5' exonuclease
0051397 1192 2008-09-10 d1yt3a3 DnaQ-like 3'-5' exonuclease
0053000 1077 2008-09-10 d2hbja2 DnaQ-like 3'-5' exonuclease
0038606 168 2005-09-08 d1hjra_ RuvC resolvase
0040018 25 2005-09-08 d1kcfa2 Mitochondrial resolvase ydc2 catalytic domain
0047446 777 2008-09-10 d1iv0a_ Putative Holliday junction resolvase RuvX
0050187 817 2008-09-10 d1vhxa_ Putative Holliday junction resolvase RuvX
0048444 813 2008-09-10 d1nu0a_ Putative Holliday junction resolvase RuvX
0053802 471 2010-05-31 d2d5ra1 CAF1-like ribonuclease
0049961 230 2008-09-10 d1uoca_ CAF1-like ribonuclease
0051425 227 2008-09-10 d1yvua2 PIWI domain
0049752 81 2008-09-10 d1u04a2 PIWI domain
0050411 359 2008-09-10 d1w9ha1 PIWI domain
0051650 18 2008-09-10 d1zupa1 TM1739-like
0052065 33 2008-09-10 d2bw3a2 Hermes transposase-like
0054856 920 2010-05-31 d3bzka5 Tex RuvX-like domain-like
0054948 204 2010-05-31 d3e9la1 Prp8 beta-finger domain-like
0054949 115 2010-05-31 d3e9oa1 Prp8 beta-finger domain-like