SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.

Restriction endonuclease-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 41 SUPERFAMILY models representing the Restriction endonuclease-like superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0036036 3 2005-09-08 d1ckqa_ Restriction endonuclease EcoRI
0037109 4 2005-09-08 d1eona_ Restriction endonuclease EcoRV
0045917 12 2008-09-10 d1bama_ Restriction endonuclease BamHI
0036506 2 2005-09-08 d1dmua_ Restriction endonuclease BglI
0046325 17 2008-09-10 d1dfma_ Restriction endonuclease BglII
0045557 3 2005-09-08 d3pvia_ Restriction endonuclease PvuII
0040166 5 2005-09-08 d1knva_ Cfr10I/Bse634I
0035965 5 2005-09-08 d1cfra_ Cfr10I/Bse634I
0036214 2 2005-09-08 d1d02a_ Restriction endonuclease MunI
0037212 4 2005-09-08 d1ev7a_ Restriction endonuclease NaeI
0037606 5 2005-09-08 d1fiua_ Restriction endonuclease NgoIV
0036344 3 2005-09-08 d1dc1a_ Restriction endonuclease BsobI
0045286 3 2005-09-08 d2foka4 Restriction endonuclease FokI, C-terminal (catalytic) domain
0035231 65 2005-09-08 d1avqa_ lambda exonuclease
0035276 44 2005-09-08 d1azoa_ DNA mismatch repair protein MutH from
0036173 53 2005-09-08 d1cw0a_ Very short patch repair (VSR) endonuclease
0037341 18 2005-09-08 d1f1za2 TnsA endonuclease, N-terminal domain
0037863 11 2005-09-08 d1fzra_ Endonuclease I (Holliday junction resolvase)
0047187 182 2008-09-10 d1hh1a_ Hjc-like
0048532 77 2008-09-10 d1ob8a_ Hjc-like
0038067 70 2005-09-08 d1gefa_ Hjc-like
0040016 2 2005-09-08 d1kc6a_ Restriction endonuclease HincII
0051967 338 2008-09-10 d2bgwa2 XPF/Rad1/Mus81 nuclease
0039325 139 2005-09-08 d1j23a_ XPF/Rad1/Mus81 nuclease
0051683 118 2008-09-10 d2a1ia1 XPF/Rad1/Mus81 nuclease
0049370 22 2008-09-10 d1sdoa_ Restriction endonuclease BstyI
0041285 12 2005-09-08 d1na6a2 Type II restriction endonuclease catalytic domain
0043536 4 2005-09-08 d1sa3a_ Restriction endonuclease MspI
0050352 496 2008-09-10 d1w36b3 Exodeoxyribonuclease V beta chain (RecB), C-terminal domain
0050355 343 2008-09-10 d1w36c3 Exodeoxyribonuclease V beta chain (RecC), C-terminal domain
0051030 88 2008-09-10 d1xmxa_ Hypothetical protein VC1899
0050442 601 2008-09-10 d1wdja_ Hypothetical protein TT1808 (TTHA1514)
0049280 158 2008-09-10 d1rzna_ RecU-like
0051182 159 2008-09-10 d1y1oa_ RecU-like
0050698 14 2008-09-10 d1wtea_ Restriction endonuclease EcoO109IR
0051238 251 2008-09-10 d1y88a2 MRR-like
0051167 15 2008-09-10 d1y0ka1 PA4535-like
0054379 93 2010-05-31 d2okfa1 XisH-like
0054150 92 2010-05-31 d2inba1 XisH-like
0054412 188 2010-05-31 d2ot9a1 YaeQ-like
0053933 192 2010-05-31 d2g3wa1 YaeQ-like