HHsearch alignment for GI: 254780617 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=96.13  E-value=0.0086  Score=39.33  Aligned_cols=210  Identities=20%  Similarity=0.236  Sum_probs=107.1

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHH
Q ss_conf             36552477886115899999998863024667876069999516776789999985114674211589972887888999
Q gi|254780617|r  164 RELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIGQKRSSVARFVKALEDRGALSYSIVVVASASDPAPMQ  243 (509)
Q Consensus       164 R~~I~g~~g~GKt~l~~~~I~nq~~~~~~~~~~~~v~~V~~~IGer~~ev~~~~~~l~~~~~~~~tvvv~a~a~~~~~~r  243 (509)
T Consensus        32 H~LL~GPPGLGKTTLA~-IiA~Emg~~l~i--------TsGP~L~kPgDlaaiLt~L~~g--------------------   82 (305)
T TIGR00635        32 HLLLYGPPGLGKTTLAH-IIANEMGVNLKI--------TSGPALEKPGDLAAILTNLEEG--------------------   82 (305)
T ss_pred             CEEEECCCCCCHHHHHH-HHHHHHCCCCEE--------EECCCCCCHHHHHHHHHHCCCC--------------------
T ss_conf             16631756874678999-999983893267--------4067554757899999705689--------------------


Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCC---
Q ss_conf             99887666666754204688479961647899999875453037875433375200124678888750454458873---
Q gi|254780617|r  244 LLAPFAGCAMGEYFRDNGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGAGS---  320 (509)
Q Consensus       244 ~~ap~~a~aiAEyfr~~G~~VLi~~Ddltr~A~a~reisl~~~~pp~~~gyp~~vf~~~s~l~ERa~~~~~~~g~GS---  320 (509)
T Consensus        83 -------------------DVL-FIDEIHRL~p~~EE~-----LYpAMEDF~lDi~I---------G~Gp~---Ar~v~l  125 (305)
T TIGR00635        83 -------------------DVL-FIDEIHRLSPAIEEL-----LYPAMEDFRLDIVI---------GKGPS---ARSVRL  125 (305)
T ss_pred             -------------------CEE-ECCHHHHCCHHHHHH-----CCCCCCCEEEEEEE---------ECCCC---CCEEEE
T ss_conf             -------------------631-012565048334531-----05300121787787---------12898---525760


Q ss_pred             ----EEEEEEEECCCCCCCCCHHHHHHHHHCCEEEEECCHHHHCCCCCCCCCCCHHHCC---CC-CCCHHH---------
Q ss_conf             ----5675310036766443114668854061699615012210266543344412203---43-438988---------
Q gi|254780617|r  321 ----LTALPVIETQVNDVSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRVG---SA-AQVKAM---------  383 (509)
Q Consensus       321 ----iT~~~~v~~~~~D~~~~i~~~~~si~DG~i~l~~~l~~~g~~Paid~~~S~SRv~---~~-~~~~~~---------  383 (509)
T Consensus       126 dLpPFTLvG-ATTR~G~lt~PLrdRFG~~~rl~fY~~~EL~~I-----------v~R~A~~L~~ei~~~~a~~IArrSRG  193 (305)
T TIGR00635       126 DLPPFTLVG-ATTRAGMLTSPLRDRFGIILRLEFYTPEELAEI-----------VSRSAGLLNIEIEQEAALEIARRSRG  193 (305)
T ss_pred             CCCCCCCCC-CCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHH-----------HHHHHHHCCCCCCHHHHHHHHHHCCC
T ss_conf             686944200-003477410313345447454026898789999-----------87533441430077899999875478


Q ss_pred             -HHHHHHHHH---HHHHHHHH---------HHHHHHH---CCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH--
Q ss_conf             -775567888---79988767---------8798763---38998999999999999999669998874889999999--
Q gi|254780617|r  384 -KQVSGAVKG---ELAQYREM---------SSFSKFS---SDLDSSTQKFLSKGERLTELLKQPQFSPLAMEEQVVMI--  445 (509)
Q Consensus       384 -~~~a~~lr~---~laqy~El---------e~f~~fg---sdlD~~t~~~l~rg~ri~e~LkQ~~~~p~~~~~qv~~l--  445 (509)
T Consensus       194 TPRIAnRLLRRVRDfA~V~~~~~I~~~i~~~AL~~L~iD~~GLd~~D~~~L------~~li~~f~GGPVGl~tlA~a~GE  267 (305)
T TIGR00635       194 TPRIANRLLRRVRDFAQVRGQGVITRDIALKALEMLDIDELGLDEIDRKLL------SVLIEKFQGGPVGLDTLAAALGE  267 (305)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHH------HHHHHHCCCCCHHHHHHHHHHCC
T ss_conf             637888776766448887267873889999998862533300579989999------99998628985238989988557


Q ss_pred             -----------HHHHCCCCCCCC
Q ss_conf             -----------998669806679
Q gi|254780617|r  446 -----------FAGISGCLDEVA  457 (509)
Q Consensus       446 -----------~a~~~G~ld~i~  457 (509)
T Consensus       268 d~~TiEdv~EPyLl~~G~~~RT~  290 (305)
T TIGR00635       268 DADTIEDVYEPYLLQQGFLQRTP  290 (305)
T ss_pred             CHHHHHCCCCHHHHHHHHHHCCC
T ss_conf             51114203465899876650067