HHsearch alignment for GI: 254780277 and conserved domain: TIGR00084

>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure . In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB.; GO: 0003678 DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=92.05  E-value=0.17  Score=29.52  Aligned_cols=111  Identities=17%  Similarity=0.216  Sum_probs=58.3

Q ss_pred             CH-HHHHHHHCCCHHH-HHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCC--CHHHHHHHHH-----HHH--HHHHHHH
Q ss_conf             89-9998884898878-7777875187435899877636024998984136--7899986454-----200--1122322
Q gi|254780277|r  164 DI-EHVIKKWGIPPEK-MVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYG--NLENILINAS-----RIK--QKKRREN  232 (976)
Q Consensus       164 ~~-~~v~~~~gv~p~~-~~d~~al~GD~sDnipGv~GiG~KtA~~ll~~~g--sle~i~~~~d-----~i~--~~k~~~~  232 (976)
T Consensus        62 daNQi~~~LfGF~~~~Er~lF~~Li--------~~nGvGpk~ALaiL~~~~~~~~~~ai~~~~~~~L~k~pGvGKK~A~~  133 (217)
T TIGR00084        62 DANQILHLLFGFNTLEERELFKELI--------KVNGVGPKLALAILSNMSPEEFVQAIETEEVKALVKIPGVGKKTAER  133 (217)
T ss_pred             CHHHHHHHHHCCCCHHHHHHHHHHH--------HCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHH
T ss_conf             4678999973479877899999985--------14880289999986678875898888641044420458857378999


Q ss_pred             HC--CCHHHHHHHHH--HHHCCCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             00--35789997655--432035642247635521267676889986532336899
Q gi|254780277|r  233 IL--EYAETARLSRK--LVMLRTDVPITIPLEHLILEDCNGPRLISFLKALEFTKL  284 (976)
Q Consensus       233 l~--~~~e~a~ls~~--L~tL~~Dvpl~~~~~~l~~~~~d~~~l~~~~~~lef~~l  284 (976)
T Consensus       134 l~~leL~gk~~~~~~~~~~~~~~~-~~~~~~-~~~~~~~~y~E~~~aL~sLGY~~~  187 (217)
T TIGR00084       134 LLALELKGKLKGVKNLEMFTNLAN-HLETDE-KLTAEAARYDELFEALVSLGYKPQ  187 (217)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCC-CCCCCC-HHHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             987775454405521124554335-335541-012102118899999997298888