HHsearch alignment for GI: 254780617 and conserved domain: cd01136

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.
Probab=100.00  E-value=0  Score=797.26  Aligned_cols=323  Identities=33%  Similarity=0.522  Sum_probs=311.8

Q ss_pred             EEEEECCHHHHHCCCCHHHCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCHHHHHCCHHHHHCCCCCCCCCEEEEECCCCC
Q ss_conf             78866794698300030023144664445444100101357731126600144416023310111156833655247788
Q gi|254780617|r   94 IVDVPVGLELLGRVVDALGNPIDGKGPIKCEQRSCTEADAPGIIQRQSVCEPLSTGIKAIDSLIPIGRGQRELIIGDRKT  173 (509)
Q Consensus        94 ~~~vpvG~~lLGRVvD~lG~PlDg~g~i~~~~~~~i~~~~p~~~~R~~i~~~l~TGI~~ID~l~pigrGQR~~I~g~~g~  173 (509)
T Consensus         1 Pl~vpVg~~lLGRVid~~G~PiDg~~~i~~~~~~pi~~~ap~~~~R~~v~e~l~TGI~~ID~l~pigrGQR~~Ifg~~g~   80 (326)
T cd01136           1 PLSVPVGDALLGRVLDAFGEPLDGKGPLGKEVRYPLLRTPPNPLKRRPIDEVLPTGVRAIDGLLTVGKGQRLGIFAGSGV   80 (326)
T ss_pred             CCEEECCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCHHCCCCCCCCCCEEEEECCCCC
T ss_conf             96535576651747678834157999999986152568995803307888751157704200266247987874369999


Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf             61158999999988630246678760699995167767899999851146742115899728878889999988766666
Q gi|254780617|r  174 GKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIGQKRSSVARFVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAM  253 (509)
Q Consensus       174 GKt~l~~~~I~nq~~~~~~~~~~~~v~~V~~~IGer~~ev~~~~~~l~~~~~~~~tvvv~a~a~~~~~~r~~ap~~a~ai  253 (509)
T Consensus        81 GKt~L-l~~i~~~~~---------~~v~V~~~IGer~rev~e~~~~~~~~~~l~~tvvv~atad~~~~~r~~a~~~a~~~  150 (326)
T cd01136          81 GKSTL-LGMIARGTT---------ADVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKAAYTATAI  150 (326)
T ss_pred             CCCHH-HHHHHHCCC---------CCEEEEEEECCCHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             84667-876864146---------77599996053388999999986245653222899606889989999988877777


Q ss_pred             HHHHHCCCCCEEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCC
Q ss_conf             67542046884799616478999998754530378754333752001246788887504544588735675310036766
Q gi|254780617|r  254 GEYFRDNGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGAGSLTALPVIETQVND  333 (509)
Q Consensus       254 AEyfr~~G~~VLi~~Ddltr~A~a~reisl~~~~pp~~~gyp~~vf~~~s~l~ERa~~~~~~~g~GSiT~~~~v~~~~~D  333 (509)
T Consensus       151 AEyfrd~G~dVL~~~Dsltr~A~A~rEisl~~g~~P~~~gyp~~~f~~~~~l~ERag~~~----~GSIT~i~~v~~~~dd  226 (326)
T cd01136         151 AEYFRDQGKDVLLLMDSLTRFAMAQREIGLAAGEPPTTKGYPPSVFALLPRLLERAGNSD----KGSITAFYTVLVEGDD  226 (326)
T ss_pred             HHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCC----CCCEEEEEEEECCCCC
T ss_conf             889997587337875246899999999888648998756677668888789888641799----9852444578705988


Q ss_pred             CCCCHHHHHHHHHCCEEEEECCHHHHCCCCCCCCCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC---CC
Q ss_conf             443114668854061699615012210266543344412203434389887755678887998876787987633---89
Q gi|254780617|r  334 VSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRVGSAAQVKAMKQVSGAVKGELAQYREMSSFSKFSS---DL  410 (509)
Q Consensus       334 ~~~~i~~~~~si~DG~i~l~~~l~~~g~~Paid~~~S~SRv~~~~~~~~~~~~a~~lr~~laqy~Ele~f~~fgs---dl  410 (509)
T Consensus       227 ~tdpi~~~~~~i~Dg~ivLsr~La~~g~~PAIDv~~S~SR~~~~~~~~~~~~~a~~~r~~l~~y~e~~~li~~g~y~~g~  306 (326)
T cd01136         227 LNEPIADAVRSILDGHIVLSRALAAAGHYPAIDVLKSISRLMNAVVTPEHKEAARKLRELLSAYQEVEDLIRIGAYKKGS  306 (326)
T ss_pred             CCCCCHHHHHHHCCEEEEECHHHHHCCCCCCCCCCCCHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             78862788987547389985889967999974886275336600067999999999999999899999999854976798


Q ss_pred             CHHHHHHHHHHHHHHHHHCC
Q ss_conf             98999999999999999669
Q gi|254780617|r  411 DSSTQKFLSKGERLTELLKQ  430 (509)
Q Consensus       411 D~~t~~~l~rg~ri~e~LkQ  430 (509)
T Consensus       307 d~~~d~~i~~~~~i~~fL~Q  326 (326)
T cd01136         307 DPEVDEAIKLLPKIEAFLKQ  326 (326)
T ss_pred             CHHHHHHHHHHHHHHHHHCC
T ss_conf             98999999989999998586