HHsearch alignment for GI: 254780701 and conserved domain: cd00082

>cd00082 HisKA Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes.
Probab=98.81  E-value=1.3e-08  Score=92.66  Aligned_cols=64  Identities=52%  Similarity=0.789  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9988999997764201389999999998503368789378999999999999999999999999987
Q gi|254780701|r  247 LAKSRFLASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDIHRSGQHLLNLINEILDLSR  313 (495)
Q Consensus       247 ~~Ks~FlA~~SHELRTPL~aI~g~~elL~~~~~~~~~~~~~~~~l~~i~~s~~~L~~Li~~lLdlsr  313 (495)
T Consensus         2 ~~~~~~~a~iaHelrtPL~~i~~~~~~l~~~~~---~~~~~~~~~~~i~~~~~~l~~lv~~~l~~~~   65 (65)
T cd00082           2 QAKGEFLANVSHELRTPLTAIRGALELLEEELL---DDEEQREYLERIREEAERLLRLINDLLDLSR   65 (65)
T ss_pred             CHHHHHHHHHHHHHCCHHHHHHCCHHHHHHCCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             359999998729870488888601489885668---8699999999999999999999999998609