HHsearch alignment for GI: 254780893 and conserved domain: cd00383

>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=99.91  E-value=7.1e-25  Score=170.16  Aligned_cols=95  Identities=32%  Similarity=0.547  Sum_probs=91.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCC
Q ss_conf             22222222222222233333222464116889998718997378999999871887777753036678999885110678
Q gi|254780893|r  127 IVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHLYDGRDEPEVKIIDVFICKLRKKLSNAAG  206 (236)
Q Consensus       127 ~~~g~~~~d~~~~~v~~~g~~i~LT~~E~~lL~~L~~~~g~vvsr~~i~~~vw~~~~~~~~~tld~~I~rLRkKL~~~~~  206 (236)
T Consensus         1 i~~g~~~~d~~~~~l~~~~~~i~Lt~~E~~lL~~L~~~~~~vvsr~~l~~~vw~~~~~~~~~~l~~~I~rLRkkl~~~~~   80 (95)
T cd00383           1 LRFGDLVLDPARREVTRDGEPVELTPKEFELLELLARNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLEDDPS   80 (95)
T ss_pred             CEEECEEEECCCCEEEECCEEEECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             97916999868899999999987799999999999877997456999999853976455745499999999999752689


Q ss_pred             CCCEEEEECCCEEEE
Q ss_conf             884388887820264
Q gi|254780893|r  207 GKNYIETVWGRGYVL  221 (236)
Q Consensus       207 ~~~~I~tvrG~GY~l  221 (236)
T Consensus        81 ~~~~I~tv~g~GY~L   95 (95)
T cd00383          81 NPRLIKTVRGVGYRL   95 (95)
T ss_pred             CCCEEEECCCCCCCC
T ss_conf             998599818855359