HHsearch alignment for GI: 254780553 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=100.00  E-value=0  Score=364.65  Aligned_cols=203  Identities=29%  Similarity=0.420  Sum_probs=178.1

Q ss_pred             CCCEEEEEEEEEEC-----CEEEEEECCEEEEEECCHHHHHHCCCCC-CEEEEEEEEEECCCC----EEEEEEECHHHHH
Q ss_conf             93258999999609-----9799985883238970868898502479-849999999973884----1899970677999
Q gi|254780553|r    1 MIGKIKGNIEGLYE-----DYVLIDVQGVCYIIYCPIRTLSCLGKIG-DFCTLFVETHMRQDQ----IRLFGFLSDLDRQ   70 (207)
Q Consensus         1 MI~~i~G~i~~~~~-----~~ivi~v~GvGY~i~vs~~~~~~l~~~g-~~v~l~~~~~vrEd~----~~LyGF~~~~Er~   70 (207)
T Consensus         1 mI~~l~G~v~~v~~niqnr~~i~~e~~gv~Y~~~v~~~~~~~~~~~gP~~~~~Ft~~~~RedaNQi~~~LfGF~~~~Er~   80 (217)
T TIGR00084         1 MIGFLQGKVIEVSKNIQNRREIILEVNGVGYELQVPMTCAYELNLEGPQKAQLFTHLVVREDANQILHLLFGFNTLEERE   80 (217)
T ss_pred             CCCEEEEEEEEECCCCCCCCEEEEEEEEEEEEEECCCHHHHHCCCCCCCCCEEEEEEEEECCHHHHHHHHHCCCCHHHHH
T ss_conf             97514568888446522461788873128999878721432047871486346787777604678999973479877899


Q ss_pred             HHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHH-HHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             9999850100051011244315789999999851566875104571167999999-997422211011334432333334
Q gi|254780553|r   71 WFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIM-TELKGKAISLSSVVQQDMSCVNKE  149 (207)
Q Consensus        71 ~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi-~ELk~K~~~~~~~~~~~~~~~~~~  149 (207)
T Consensus        81 lF~~Li~~nGvGpk~ALaiL~~~~~~~~~~ai~~~~~~~L~k~pGvGKK~A~~l~~leL~gk~~~~~~~~~~~~~~~~~~  160 (217)
T TIGR00084        81 LFKELIKVNGVGPKLALAILSNMSPEEFVQAIETEEVKALVKIPGVGKKTAERLLALELKGKLKGVKNLEMFTNLANHLE  160 (217)
T ss_pred             HHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             99998514880289999986678875898888641044420458857378999987775454405521124554335335


Q ss_pred             CCCCCCCCCHH-HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf             45555653158-999999996799989999999999851688889899999999974
Q gi|254780553|r  150 QAHICSMPSFA-INAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAI  205 (207)
Q Consensus       150 ~~~~~~~~~~~-~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk~L  205 (207)
T Consensus       161 ~~~~~~~~~~~y~E~~~aL~sLGY~~~Ei~~~l~~~~--~~~~~~~~~~~~eal~~l  215 (217)
T TIGR00084       161 TDEKLTAEAARYDELFEALVSLGYKPQEIQKALKKIK--EKPDLAIEQDIKEALKQL  215 (217)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHC--CCCCCCHHHHHHHHHHHH
T ss_conf             5410121021188999999972988889999998640--467885446799999997