HHsearch alignment for GI: 254780689 and conserved domain: TIGR00207

>TIGR00207 fliG flagellar motor switch protein FliG; InterPro: IPR000090 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour . The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour . CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN . Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important . Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins . This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring , . FliG is present in about 25 copies per flagellum. This structure of the C-terminal domain is known, this domain functions specifically in motor rotation .; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 flagellin-based flagellum.
Probab=100.00  E-value=0  Score=635.35  Aligned_cols=323  Identities=27%  Similarity=0.444  Sum_probs=308.3

Q ss_pred             HHCCHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHH
Q ss_conf             23686879999999838146899985199999999999986138999899999999999998510456-65348899997
Q gi|254780689|r   20 VSLTQKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQFIAGIGL-TENSKNIESIL   98 (345)
Q Consensus        20 ~~Ltg~eKAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~~~~~~~~~-~g~~~~~~~lL   98 (345)
T Consensus        14 ~~Ltg~~K~aILL~~iG~d~~a~vfkhL~~~ei~~Ls~~i~~l~~i~~~~~~~VL~EF~~~~~~~~yi~~gg~~YaR~lL   93 (346)
T TIGR00207        14 DELTGKQKAAILLISIGEDVSAEVFKHLSQEEIEELSAEIAKLEQIDKQQKDDVLEEFEEIAEAQEYINKGGLDYARELL   93 (346)
T ss_pred             HHCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_conf             42104567888877722214557864178889999999988532234888789999999999999988506378999998


Q ss_pred             HHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             61149799999975441134456756789741998999999840386478899995788899999983798999999999
Q gi|254780689|r   99 EEGLEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMKR  178 (345)
Q Consensus        99 ~~al~~d~a~~ll~~~~~~~~~~~~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~~R  178 (345)
T Consensus        94 ~kaLG~e~A~~~l~~l~-~slq~~~~f~~~~~~~P~~~~dfI~~EHPQtiAlIL~hL~~~~Aa~iLs~l~~e~~~~v~~R  172 (346)
T TIGR00207        94 EKALGEEKAKKILNKLT-SSLQTKPGFEFLRKAEPQQIADFIQQEHPQTIALILSHLDPAQAAEILSLLPEEVQAEVARR  172 (346)
T ss_pred             HHHCCHHHHHHHHHHHH-HHHCCCCCHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHCHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             86141589999999888-75316311567631586889987750586799999985183047888730685689999999


Q ss_pred             HHHCCCCCHHHHHHHHHHHHHHHCCCCC---CCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             8404899989999999999997223442---1236378999995017757799999999986599999999741578998
Q gi|254780689|r  179 TVNLPKISPYIQKTIEKCIVEMLPQSNS---NTSTGPEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPKVFLFDDL  255 (345)
Q Consensus       179 ia~l~~v~~ev~~~ie~~L~~~l~~~~~---~~~~G~~~vA~Iln~l~~~~~~~iL~~L~~~d~~la~~Ir~~mF~FeDl  255 (345)
T Consensus       173 iA~~g~~sP~vv~ev~~VLe~kL~s~~~~~~~~~GGv~~vaEi~N~~~~~~ek~~l~~~e~~D~~LA~~Ik~~MF~FEdi  252 (346)
T TIGR00207       173 IAVMGRTSPEVVKEVERVLEKKLESLTSEDYTKVGGVRAVAEIINLLDRKTEKTILESLEEVDPELAEEIKKKMFVFEDI  252 (346)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCHHHHHHHHHHCCCHHHH
T ss_conf             98507867899999999997762244212355416257899987357871599999999831847899999723640115


Q ss_pred             HCCCHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             50997899999830988899998538898999999961008999999999850058999899999999999999999986
Q gi|254780689|r  256 ITLSSHDLSIVFNNISLEVLGKALHGTSIETQNAILHCLSNRQRKIIEENIVLNDSSIAPREVAMARRSIVQEAISLLKT  335 (345)
Q Consensus       256 ~~l~~~~l~~ll~evd~~~l~~ALkga~~e~~e~il~nmS~Ra~~~l~eel~~~~g~v~~~dve~Aq~~I~~~~r~L~~~  335 (345)
T Consensus       253 V~lDdraIqr~L~~vd~~~L~~ALK~~~~~l~ek~l~NMS~Raa~~l~edm~fl-Gpvr~kdVe~~Q~~I~~iVr~L~E~  331 (346)
T TIGR00207       253 VKLDDRAIQRVLREVDKEDLLLALKTAEKPLREKFLNNMSQRAAEILKEDMEFL-GPVRLKDVEEAQKKIVSIVRKLEEK  331 (346)
T ss_pred             HHHCCHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             430308999999984335567785126624788986315489999999988726-8844024589999999999866117


Q ss_pred             CCEECCCCC
Q ss_conf             979518888
Q gi|254780689|r  336 NKIELSNPI  344 (345)
Q Consensus       336 G~I~l~~~~  344 (345)
T Consensus       332 GEiVI~~Gg  340 (346)
T TIGR00207       332 GEIVIQRGG  340 (346)
T ss_pred             CCEEEECCC
T ss_conf             605760478