HHsearch alignment for GI: 254780345 and conserved domain: cd00619
>cd00619 Terminator_NusB Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation.
Probab=100.00 E-value=1e-34 Score=228.87 Aligned_cols=130 Identities=35% Similarity=0.459 Sum_probs=121.1
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 46999999999999995699989999999985310013221120144343999999999999989999999997410357
Q gi|254780345|r 16 RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKW 95 (170)
Q Consensus 16 r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~w 95 (170)
T Consensus 1 R~~aRe~a~q~LYq~~~~~~~~~~i~~~~~~-----------~~~~~~~d~~f~~~l~~gv~~~~~~iD~~I~~~l-~~w 68 (130)
T cd00619 1 RRRARELAVQALYAWELAPEILAEVVSLLEL-----------LQYKSKKVLPFALKLVRGVLENIEEIDELIEKHL-RNW 68 (130)
T ss_pred CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH-----------HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCC
T ss_conf 9199999999999967079999999999987-----------5113346899999999999984999999999871-899
Q ss_pred CHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 63323534899999999998643557810339889999998338772314999999999523
Q gi|254780345|r 96 SFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKE 157 (170)
Q Consensus 96 ~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~ 157 (170)
T Consensus 69 ~~~rl~~i~~~ILr~a~~El~~~~~~p~~v~InEavelak~f~~~~~~~fiNgVLd~i~k~l 130 (130)
T cd00619 69 SLDRLAIVERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKDL 130 (130)
T ss_pred CHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHC
T ss_conf 96766799999999999999868676346799999999998577862044899999987519