HHsearch alignment for GI: 254781172 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=96.62  E-value=0.016  Score=38.66  Aligned_cols=138  Identities=17%  Similarity=0.233  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             46655332130123103541035555653057654045410110106777531000100013421001456899998752
Q gi|254781172|r  467 QQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRR  546 (731)
Q Consensus       467 q~~~~i~hF~SK~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK  546 (731)
T Consensus        49 ~~~~~Ft~~~~R--ed----aNQi~~~LfG------F---------~~~~Er~lF~~Li~~nGvGpk~ALaiL~~~~---  104 (217)
T TIGR00084        49 QKAQLFTHLVVR--ED----ANQILHLLFG------F---------NTLEERELFKELIKVNGVGPKLALAILSNMS---  104 (217)
T ss_pred             CCCEEEEEEEEE--CC----HHHHHHHHHC------C---------CCHHHHHHHHHHHHCCCCHHHHHHHHHCCCC---
T ss_conf             863467877776--04----6789999734------7---------9877899999985148802899999866788---


Q ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             23466677630101111689999998829989999978977612511778761388867899999999966979999999
Q gi|254781172|r  547 NISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVE  626 (731)
Q Consensus       547 ~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~  626 (731)
T Consensus       105 ------------------------------~~~~~~ai~------~~~~~~L~k~pGvGKK~A~~l~~-------leL~g  141 (217)
T TIGR00084       105 ------------------------------PEEFVQAIE------TEEVKALVKIPGVGKKTAERLLA-------LELKG  141 (217)
T ss_pred             ------------------------------HHHHHHHHH------HHHHHHHHCCCCCCHHHHHHHHH-------HHHHH
T ss_conf             ------------------------------758988886------41044420458857378999987-------77545


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCH-HHHHHHHHHCCCEEE
Q ss_conf             9997338776543224688216866999725889987-899999998298499
Q gi|254781172|r  627 ALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQR-HKAQEYVTQLGAVVS  678 (731)
Q Consensus       627 ~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R-~e~~~~ie~~Ggkv~  678 (731)
T Consensus       142 k~~~~~~~~~~~~--~~~-~~~~~~~~~~~----~~~y~E~~~aL~sLGY~~~  187 (217)
T TIGR00084       142 KLKGVKNLEMFTN--LAN-HLETDEKLTAE----AARYDELFEALVSLGYKPQ  187 (217)
T ss_pred             HHCCCCCCCCCCC--CCC-CCCCCCHHHHH----HHHHHHHHHHHHHCCCCHH
T ss_conf             4405521124554--335-33554101210----2118899999997298888