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