HHsearch alignment for GI: 254781026 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=99.64  E-value=2.2e-16  Score=116.90  Aligned_cols=118  Identities=25%  Similarity=0.334  Sum_probs=80.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCEEECCCCCCCCCCCCCCCEEECCCCCCCHHHCCCCCCCCCHHHHHHC
Q ss_conf             97778605999999988748898978853230000002788875653111202037752100110234345682799827
Q gi|254781026|r    1 MIGPPGARKSMLASCLPSILLPLSLEESLEVSMIYSISGHSSHEYSFIQNRPFRSPHHSVTIAALIGGGLQVLPGEDSLA   80 (186)
Q Consensus         1 l~GpPG~GKS~lar~l~~iLP~l~~~e~le~~~i~s~~g~~~~~~~~~~~~p~~~~~~~~~~~~l~gg~~~~~pG~i~lA   80 (186)
T Consensus        35 L~GPPGLGKTTLA~IiA~Emg----------~~l~iTsGP-----~------------L~kPgDlaaiLt~-------L~   80 (305)
T TIGR00635        35 LYGPPGLGKTTLAHIIANEMG----------VNLKITSGP-----A------------LEKPGDLAAILTN-------LE   80 (305)
T ss_pred             EECCCCCCHHHHHHHHHHHHC----------CCCEEEECC-----C------------CCCHHHHHHHHHH-------CC
T ss_conf             317568746789999999838----------932674067-----5------------5475789999970-------56


Q ss_pred             CCCEEEEECHHHCCHHHHHHHHHHHHCCCEEEHH----CCEEEEEC-CCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             9988998038785988999999999719523010----03078984-701567522746588788988764389999999
Q gi|254781026|r   81 HNGVLFLDEIPEFSPQTLNALRQPLETGECIIAR----ANRKISYP-SRIQLIAAMNPCRCGMSNKDENVCIRGPRCATE  155 (186)
Q Consensus        81 h~GVLflDE~~e~~~~~l~~L~~~le~g~v~i~R----~g~~~~~P-a~f~Lvaa~NPcpcG~~~~~~~~c~c~~~~~~~  155 (186)
T Consensus        81 ~gDVLFIDEIHRL~p~~EE~LYpAMEDF~lDi~IG~Gp~Ar~v~ldLpPFTLvGATTR~---------------------  139 (305)
T TIGR00635        81 EGDVLFIDEIHRLSPAIEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRA---------------------  139 (305)
T ss_pred             CCCEEECCHHHHCCHHHHHHCCCCCCCEEEEEEEECCCCCCEEEECCCCCCCCCCCCCC---------------------
T ss_conf             89631012565048334531053001217877871289852576068694420000347---------------------


Q ss_pred             HHHHCCHHHHHCCCEEEECC
Q ss_conf             98512243210042599838
Q gi|254781026|r  156 YQARISGPLMDRIDIRIAVP  175 (186)
Q Consensus       156 Y~~rls~plldR~Dl~v~~~  175 (186)
T Consensus       140 --G~lt~PLrdRFG~~~rl~  157 (305)
T TIGR00635       140 --GMLTSPLRDRFGIILRLE  157 (305)
T ss_pred             --CCCCCCHHHHHHHHHHCC
T ss_conf             --741031334544745402