HHsearch alignment for GI: 255764496 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=97.46  E-value=9.8e-05  Score=53.68  Aligned_cols=81  Identities=19%  Similarity=0.293  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHHHH-HH-HHHHHHHCCCCHHCCCCCCHHHHHHHHHHHC--CHHH-HHHCCHHHHHHCCCCCHHHHHHH
Q ss_conf             999887877887889-89-9864321477100488879899999999808--8898-99389888862789998999999
Q gi|255764496|r  529 FIQRLRDEAHRFAIT-TH-RKRRKKAAYSPLDEINGIGPLRKRLLLQSFG--TVKM-ISRSSPETLASIEGISKKIACKI  603 (616)
Q Consensus       529 ~Lq~iRDEaHRFAi~-~h-Rk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~-i~~As~eeL~~v~gi~~~~A~~I  603 (616)
T Consensus        55 t~~~~RedaNQi~~~LfGF~~~~Er~lF~~Li~~nGvGpk~ALaiL~~~~~~~~~~ai~~~~~~~L~k~pGvGKK~A~~l  134 (217)
T TIGR00084        55 THLVVREDANQILHLLFGFNTLEERELFKELIKVNGVGPKLALAILSNMSPEEFVQAIETEEVKALVKIPGVGKKTAERL  134 (217)
T ss_pred             EEEEEECCHHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf             87777604678999973479877899999985148802899999866788758988886410444204588573789999


Q ss_pred             H-HHHCC
Q ss_conf             9-98547
Q gi|255764496|r  604 Y-NHFHK  609 (616)
Q Consensus       604 ~-~~l~~  609 (616)
T Consensus       135 ~~leL~g  141 (217)
T TIGR00084       135 LALELKG  141 (217)
T ss_pred             HHHHHHH
T ss_conf             8777545