HHsearch alignment for GI: 254780916 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=98.48  E-value=1.1e-06  Score=66.92  Aligned_cols=106  Identities=18%  Similarity=0.183  Sum_probs=81.5

Q ss_pred             CEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHH-HCC-CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             3899869989999999999988988999893799998-608-99899997854698889999999985789839999268
Q gi|254780916|r   12 RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTI-SKI-QVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQ   89 (482)
Q Consensus        12 rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~al~~l-~~~-~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~~   89 (482)
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             CCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99999998885057432222222222222222222
Q gi|254780916|r   90 DNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL  124 (482)
Q Consensus        90 ~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al  124 (482)
T Consensus        79 ~~~~~-----~~nvvg~Le~Pl~Y~qL~daLh~cQ  108 (109)
T pfam06490        79 DSAAE-----LANVIGELEEPLNYPQLTDLLHRCQ  108 (109)
T ss_pred             CCHHH-----CCCEEEEECCCCCHHHHHHHHHHHC
T ss_conf             75212-----0552587078898799999998752