HHsearch alignment for GI: 254780312 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=98.82  E-value=1.4e-07  Score=66.50  Aligned_cols=107  Identities=19%  Similarity=0.203  Sum_probs=85.4

Q ss_pred             EEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             69997599899999999999889899999997999999971899899998365599979999999985899859999437
Q gi|254780312|r    4 KILLAEDDDDMRRFLIKALGKAGYEVVSCNNGASAYDKVREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITGF   83 (122)
Q Consensus         4 rILiVDD~~~~r~~l~~~L~~~G~~v~~a~~g~~al~~~~~~~~dlii~D~~mP~~dG~el~~~ir~~~~~~pii~~s~~   83 (122)
T Consensus         1 kILvIddd~~r~~~L~~ILeFlGE~~~~~~~~~~~~~~~~~~~~a~~v~~~~~~--~~~~~l~~l~~~~p~~Pvlllg~~   78 (109)
T pfam06490         1 KILVIDDDAERRHDLSTILEFLGEQCEAVSSEDLSAALLSSRWEALAVILGSVS--GLADLLKALAKWDPHLPVLLLGEH   78 (109)
T ss_pred             CEEEECCCHHHHHHHHHHHHHCCCCEEEECHHHHHHHHHHCCCCEEEEEECCCC--CHHHHHHHHHHHCCCCCEEEECCC
T ss_conf             989986888999979999986499649954889889886378852999967852--099999999964889999998788


Q ss_pred             CCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Q ss_conf             9789999999769986997697989999999999
Q gi|254780312|r   84 AAVALNPDSNAPKNAKVLSKPFHLRDLVNEVNRL  117 (122)
Q Consensus        84 ~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~i~~~  117 (122)
T Consensus        79 ~~~~~-----~~nvvg~Le~Pl~Y~qL~daLh~c  107 (109)
T pfam06490        79 DSAAE-----LANVIGELEEPLNYPQLTDLLHRC  107 (109)
T ss_pred             CCHHH-----CCCEEEEECCCCCHHHHHHHHHHH
T ss_conf             75212-----055258707889879999999875