HHsearch alignment for GI: 254780892 and conserved domain: pfam06490

>pfam06490 FleQ Flagellar regulatory protein FleQ. This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e.g. FleQ in Pseudomonas aeruginosa. It is clearly related to pfam00072, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (pfam00072).
Probab=98.53  E-value=1.8e-06  Score=58.94  Aligned_cols=107  Identities=15%  Similarity=0.073  Sum_probs=81.4

Q ss_pred             EEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHCCCCCCCEEEEEEC
Q ss_conf             79997399899999999999889899999997999999971799948997078998773899996143488973999963
Q gi|254780892|r    3 SLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFIAHVRQMPLGTDVFVYYLLM   82 (133)
Q Consensus         3 ~ILiVDD~~~~r~~l~~~L~~~g~~v~~a~~g~eAl~~~~~~~~pdlii~D~~mP~~~~l~~~ir~~~~~~~~pii~lT~   82 (133)
T Consensus         1 kILvIddd~~r~~~L~~ILeFlGE~~~~~~~~~~~~-~~~~~~~~a~~v~~~~~~~~~~~l~~l~~--~~p~~Pvlllg~   77 (109)
T pfam06490         1 KILVIDDDAERRHDLSTILEFLGEQCEAVSSEDLSA-ALLSSRWEALAVILGSVSGLADLLKALAK--WDPHLPVLLLGE   77 (109)
T ss_pred             CEEEECCCHHHHHHHHHHHHHCCCCEEEECHHHHHH-HHHHCCCCEEEEEECCCCCHHHHHHHHHH--HCCCCCEEEECC
T ss_conf             989986888999979999986499649954889889-88637885299996785209999999996--488999999878


Q ss_pred             CCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Q ss_conf             89989999999769988997698989999999999
Q gi|254780892|r   83 EVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL  117 (133)
Q Consensus        83 ~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~~  117 (133)
T Consensus        78 ~~~~~~-----~~nvvg~Le~Pl~Y~qL~daLh~c  107 (109)
T pfam06490        78 HDSAAE-----LANVIGELEEPLNYPQLTDLLHRC  107 (109)
T ss_pred             CCCHHH-----CCCEEEEECCCCCHHHHHHHHHHH
T ss_conf             875212-----055258707889879999999875