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