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