HHsearch alignment for GI: 254780893 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=98.02  E-value=1.1e-05  Score=54.66  Aligned_cols=104  Identities=17%  Similarity=0.156  Sum_probs=75.2

Q ss_pred             EEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCEECCCCC
Q ss_conf             59998699899999999999889899999998999999985799478831149874334311122223223310013332
Q gi|254780893|r    2 RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFEVLRALRVAKISTPVCILSGM   81 (236)
Q Consensus         2 kILivedd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~~~~~DlvIlD~~lp~~~G~~~~~~ir~~~~~~pII~ls~~   81 (236)
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             CCHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             1000001123221011122332221111122
Q gi|254780893|r   82 SSIEDKVRGLQSGADDYISKPFNKEELVARI  112 (236)
Q Consensus        82 ~~~~~~~~al~~GAddyi~KP~~~~eL~ari  112 (236)
T Consensus        79 ~~~~~~-----~nvvg~Le~Pl~Y~qL~daL  104 (109)
T pfam06490        79 DSAAEL-----ANVIGELEEPLNYPQLTDLL  104 (109)
T ss_pred             CCHHHC-----CCEEEEECCCCCHHHHHHHH
T ss_conf             752120-----55258707889879999999