HHsearch alignment for GI: 254781194 and conserved domain: cd00523

>cd00523 archeal_HJR Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain eukaryotes, however this CD includes only the archeal HJR's. The bacterial and archeal HJRs perform a similar function but differ in both sequence and structure. Structural similarity does however, exist between the archeal HJRs and type II restriction endonucleases, such as EcoRV, BglII, and Fok, and this similarity includes their active site configurations.
Probab=97.45  E-value=0.0024  Score=41.47  Aligned_cols=76  Identities=16%  Similarity=0.194  Sum_probs=58.3

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECCC--CCCCCCEEEEECCCCEEEEEEECCCCC---CCHHHHHHHHHHH-HCCCEEE
Q ss_conf             599999999999997898899971489--887662799915991999997278988---6989999999999-7898699
Q gi|254781194|r    7 SEAKLEKRLVKGSKKLDCLVFKTQFIN--QRGCPDRLIITPNGAHFWVEMKTSRGR---LSNAQKRVIATLL-LYHQKVQ   80 (98)
Q Consensus         7 ~E~~ie~~i~~~~k~~g~~~~k~~~~g--~~G~PDli~~~~~g~~~fIEvK~~~gk---ls~~Q~~~~~~l~-~~G~~~~   80 (98)
T Consensus         4 kG~~~EReL~~~l~~~GfavvR~~gSG~~~~~~pDiiA~~-~~~~~~iEvKst~~~~iYi~~e~ve~L~~Fa~~fG~~p~   82 (123)
T cd00523           4 KGSRAERELVKILEEKGFAVVRAPGSGGGPRPLPDIVAGN-GGTYLAIEVKSTKKDKIYIKKEQVEKLVEFARRFGGEPY   82 (123)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCEEEEC-CCEEEEEEEEECCCCEEEECHHHHHHHHHHHHHCCCEEE
T ss_conf             5037999999999865934998346788878899889756-985999999962698089849999999999997499389


Q ss_pred             EEC
Q ss_conf             983
Q gi|254781194|r   81 VLS   83 (98)
Q Consensus        81 Vv~   83 (98)
T Consensus        83 iav   85 (123)
T cd00523          83 LAV   85 (123)
T ss_pred             EEE
T ss_conf             999