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