HHsearch alignment for GI: 254780877 and conserved domain: TIGR00635

>TIGR00635 ruvB Holliday junction DNA helicase RuvB; InterPro: IPR004605 All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.; GO: 0003677 DNA binding, 0005524 ATP binding, 0009378 Holliday junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=98.91  E-value=8.9e-09  Score=90.28  Aligned_cols=160  Identities=25%  Similarity=0.380  Sum_probs=85.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCC------CEEEECCCCCCHHHHHHHHHHHHHCCCCCHHHCCCEEEEEEHHHHHCCC
Q ss_conf             8533333578999999963367778------6689528874077799999998734899844457437887313542174
Q gi|254780877|r  176 KLDPVIGRDDEMRRAIQVLSRRTKN------NPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGALIAGA  249 (853)
Q Consensus       176 kLDPVIGRe~EI~~~~~iL~r~~k~------n~~lvGe~GvGKtaive~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~  249 (853)
T Consensus         2 ~L~eFiG-Q~~vk~~L~l~I~AAk~R~e~LDH~LL~GPPGLGKTTLA~IiA~Emg~~--------l~iTsG--P~L~---   67 (305)
T TIGR00635         2 LLAEFIG-QEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVN--------LKITSG--PALE---   67 (305)
T ss_pred             CCHHCCC-CHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHCCC--------CEEEEC--CCCC---
T ss_conf             8011058-2889999999999998248973416631756874678999999983893--------267406--7554---


Q ss_pred             CCCCHHHHHHHHHHHHHHHCCCCEEEEECCHH--------------------HHCCCCCCCC--CCCHHHHHHHHHCCCC
Q ss_conf             54202454589999998607997699963627--------------------7302666554--3358888765312466
Q gi|254780877|r  250 KFRGEFEERLKSLLCEIRSEDGEIILFIDELH--------------------VLVGAGKTDG--AMDASNLLKPSLARGE  307 (853)
Q Consensus       250 ~~rg~~e~r~~~i~~~~~~~~~~~ilfide~h--------------------~~~gaG~~~g--~~Daan~LKP~LarG~  307 (853)
T Consensus        68 k-PgD----laaiLt~L~~---gDVLFIDEIHRL~p~~EE~LYpAMEDF~lDi~IG~Gp~Ar~v~ldL----------pP  129 (305)
T TIGR00635        68 K-PGD----LAAILTNLEE---GDVLFIDEIHRLSPAIEELLYPAMEDFRLDIVIGKGPSARSVRLDL----------PP  129 (305)
T ss_pred             C-HHH----HHHHHHHCCC---CCEEECCHHHHCCHHHHHHCCCCCCCEEEEEEEECCCCCCEEEECC----------CC
T ss_conf             7-578----9999970568---9631012565048334531053001217877871289852576068----------69


Q ss_pred             EEEEEEECHHHHHHHHHCCHHHHHCCCEE-ECCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             04899744899999730011132023111-1157776789999999789865414961015899999863
Q gi|254780877|r  308 LHCIGATTLDEYRKYIEKDPALARRFQSL-LVGEPTVTDTISILRGLKERYEQHHKVRISDSALVSAAVL  376 (853)
Q Consensus       308 l~~IgaTT~~Eyrk~iEkD~Al~RRFq~i-~V~Eps~~~t~~iL~gl~~~yE~~H~V~i~d~al~~av~l  376 (853)
T Consensus       130 FTLvGATTR~G~--lt---~PLrdRFG~~~rl~fY~~~EL~~Iv~R~A~~----L~~ei~~~~a~~IArr  190 (305)
T TIGR00635       130 FTLVGATTRAGM--LT---SPLRDRFGIILRLEFYTPEELAEIVSRSAGL----LNIEIEQEAALEIARR  190 (305)
T ss_pred             CCCCCCCCCCCC--CC---CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHH----CCCCCCHHHHHHHHHH
T ss_conf             442000034774--10---3133454474540268987899998753344----1430077899999875