HHsearch alignment for GI: 254780383 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=94.52  E-value=0.04  Score=34.99  Aligned_cols=84  Identities=24%  Similarity=0.363  Sum_probs=53.9

Q ss_pred             HCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCH-HHHHHHHHHHHH
Q ss_conf             33320356799899873176200010126899-9999997300379999997523554442001000-014567776432
Q gi|254780383|r   59 AQSTDVNVNKATKHLFEIADTPQKMLAIGEKK-LQNYIRTIGIYRKKSENIISLSHILINEFDNKIP-QTLEGLTRLPGI  136 (227)
Q Consensus        59 ~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~e-l~~~ir~~G~~~~KAk~I~~~a~~i~~~~~g~vP-~~~~~L~~LpGV  136 (227)
T Consensus        56 ~~~~RedaNQi~~~LfG-------F~~~~Er~lF~~Li~~nGvGpk~ALaiL~~~~--~~~~~~ai~~~~~~~L~k~pGv  126 (217)
T TIGR00084        56 HLVVREDANQILHLLFG-------FNTLEERELFKELIKVNGVGPKLALAILSNMS--PEEFVQAIETEEVKALVKIPGV  126 (217)
T ss_pred             EEEEECCHHHHHHHHHC-------CCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCC--HHHHHHHHHHHHHHHHHCCCCC
T ss_conf             77776046789999734-------79877899999985148802899999866788--7589888864104442045885


Q ss_pred             HHHHHHHHH-HHHHHH
Q ss_conf             358888999-987542
Q gi|254780383|r  137 GRKGANVIL-SMAFGI  151 (227)
Q Consensus       137 G~ktA~~il-~~~~~~  151 (227)
T Consensus       127 GKK~A~~l~~leL~gk  142 (217)
T TIGR00084       127 GKKTAERLLALELKGK  142 (217)
T ss_pred             CHHHHHHHHHHHHHHH
T ss_conf             7378999987775454