HHsearch alignment for GI: 254780688 and conserved domain: TIGR02480

>TIGR02480 fliN flagellar motor switch protein FliN; InterPro: IPR012826 Proteins that consist largely of this domain can be designated flagellar motor switch proteins: FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside of this family, are associated with type III secretion systems (TTSS) and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.; GO: 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0016020 membrane, 0044461 flagellin-based flagellum part.
Probab=99.95  E-value=3.3e-28  Score=180.78  Aligned_cols=77  Identities=42%  Similarity=0.826  Sum_probs=74.3

Q ss_pred             HHHHHCCCCEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCCCCEEEEEEEEEECCC
Q ss_conf             02343055138999992134429999457978899847778880699999989999999995688870558999731679
Q gi|254780688|r   68 NFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNAQ  147 (147)
Q Consensus        68 ~~~~l~dipv~i~veLG~~~i~i~dll~L~~G~Vi~Ld~~~~epV~i~vng~~ia~GElv~v~e~~~~~gvrIt~iis~~  147 (147)
T Consensus         1 ~~~~~~Dipv~l~velG~~~i~l~dll~l~~GsVieLDk~agepldI~VNG~~ia~GEvvV~~d---k~Giri~ei~~~~   77 (77)
T TIGR02480         1 NIDLILDIPVELTVELGRTRITLKDLLKLGEGSVIELDKLAGEPLDILVNGRLIARGEVVVVED---KFGIRITEIVDSS   77 (77)
T ss_pred             CCCCEEECCEEEEEEEEEEEECHHHHHCCCCCCEEEECCCCCCEEEEEECCCEEEEEEEEEECC---CEEEEEEEEECCC
T ss_conf             9784110105888888656603688843899849996477889215988892788898998679---6008989854179