HHsearch alignment for GI: 254780810 and conserved domain: TIGR00635

>TIGR00635 ruvB Holliday junction DNA helicase RuvB; InterPro: IPR004605 All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.; GO: 0003677 DNA binding, 0005524 ATP binding, 0009378 Holliday junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=96.03  E-value=0.0047  Score=39.19  Aligned_cols=70  Identities=29%  Similarity=0.387  Sum_probs=46.9

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             12220487787899999999998611886469999508787899999984034278236678888999999999999999
Q gi|254780810|r  176 RSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSVQGEVISSTFDESAARHVQVAEMVIAKAKC  255 (423)
Q Consensus       176 r~~i~~~~~~gkt~ll~~ia~~~~~~~~~v~~i~~ligEr~~ev~e~~~~~~~~vv~st~d~~~~~~~~~a~~a~~~a~~  255 (423)
T Consensus        32 H~LL~GPPGLGKTTLA~IiA~Emg~~---l~iTsGP~L~kPgDlaaiLt~L-----------------------------   79 (305)
T TIGR00635        32 HLLLYGPPGLGKTTLAHIIANEMGVN---LKITSGPALEKPGDLAAILTNL-----------------------------   79 (305)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHCCC---CEEEECCCCCCHHHHHHHHHHC-----------------------------
T ss_conf             16631756874678999999983893---2674067554757899999705-----------------------------


Q ss_pred             HHHCCCCEEEEEECHHHHHHHHHCCC
Q ss_conf             99779928999816389877620013
Q gi|254780810|r  256 LVEYGLDVVILLDSITRLCRAYNVLM  281 (423)
Q Consensus       256 ~~e~G~dVll~~DslTR~ArA~~~~~  281 (423)
T Consensus        80 ---~~gD-VLFIDEIHRL~p~~EE~L  101 (305)
T TIGR00635        80 ---EEGD-VLFIDEIHRLSPAIEELL  101 (305)
T ss_pred             ---CCCC-EEECCHHHHCCHHHHHHC
T ss_conf             ---6896-310125650483345310