HHsearch alignment for GI: 254780693 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=94.41 E-value=0.093 Score=31.71 Aligned_cols=49 Identities=22% Similarity=0.258 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCCC
Q ss_conf 44998999999999879----99789999949-----998899999999999807997
Q gi|254780693|r 172 RNLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAVN 220 (235)
Q Consensus 172 ~~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~n 220 (235)
T Consensus 22 i~Lt~~E~~lL~~L~~~~~~vvsr~~l~~~vw~~~~~~~~~~l~~~I~rLRkkl~~~~ 79 (95)
T cd00383 22 VELTPKEFELLELLARNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLEDDP 79 (95)
T ss_pred EECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 8779999999999987799745699999985397645574549999999999975268