HHsearch alignment for GI: 254780976 and conserved domain: cd00529

>cd00529 RuvC_resolvase 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 fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=97.51  E-value=0.0017  Score=41.75  Aligned_cols=104  Identities=12%  Similarity=0.109  Sum_probs=64.5

Q ss_pred             CEEEEECCCCEEEEEEEECCCCEEC--CCEEEECCCCC-------HHHHHHHHHHHHHCCCEEEEEECCCCCCCCCH-HH
Q ss_conf             3999986887689996307651101--21011047741-------56898999986516775899721357888884-47
Q gi|254780976|r   18 PIASIDLGTKRIGLAISDPGRRFAH--PRPFLVRKKVT-------QTALELLSFITTENIAAFIIGLPLNMNGSEGP-RV   87 (160)
Q Consensus        18 riLgiD~G~kriGiAisd~~~~~a~--Pl~~i~~~~~~-------~~~~~l~~ii~e~~i~~iVvGlP~~~~g~~~~-~~   87 (160)
T Consensus         1 RILGIDPGl~~~G~aiie~~~~~~~~l~~g~I~t~~~~~~~~RL~~I~~~l~~li~~~~P~~vaiE~~f~~~n~~tal~l   80 (154)
T cd00529           1 RILGIDPGSRNTGYGVIEQEGRKLIYLASGVIRTSSDAPLPSRLKTIYDGLNEVIDQFQPDVVAIERVFFAKNPDSALKL   80 (154)
T ss_pred             CEEEECCCCCCCEEEEEEEECCEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHCCHHHHHHH
T ss_conf             96998756687159999957997899998889669999989999999999999998349978986546560188889999


Q ss_pred             HHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHCC
Q ss_conf             999999999984048997799836716799999999869
Q gi|254780976|r   88 HSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMN  126 (160)
Q Consensus        88 ~~v~~f~~~L~~~~~~l~v~~~DEr~TS~~A~~~l~~~g  126 (160)
T Consensus        81 g~arGvi~~~~-~~~~i~v~ey----~P~~VK~~vtG~G  114 (154)
T cd00529          81 GQARGALILAL-ANRNLPVFEY----TPNQVKKAVTGYG  114 (154)
T ss_pred             HHHHHHHHHHH-HHHCCCCEEE----CHHHHHHHHHCCC
T ss_conf             99999999999-9817986168----8899889986797