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