HHsearch alignment for GI: 254780666 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=99.79  E-value=1.5e-18  Score=157.31  Aligned_cols=126  Identities=24%  Similarity=0.251  Sum_probs=112.7

Q ss_pred             CHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCHHHH
Q ss_conf             469999999999999559988999999851123216898899999999999996089999999998428-8100488999
Q gi|254780666|r    5 MNARLVSSHLLSCVMRKRISLTCLLDLEYGDSAFRLLSQRDQILVRAIVNVTLRFLPRIDAVLDFVLIS-SLPRKKYSLQ   83 (445)
Q Consensus         5 ~~aR~~A~~iL~~v~~~~~~~~~~l~~~~~~~~~~~L~~~Dr~~~~~Lv~gvlR~~~~ld~il~~~~~~-~~~~~~~~~~   83 (445)
T Consensus         2 ~~aRe~a~q~LYq~~~~~~~~~~i~~~~~~~---~~~~~~d~~f~~~l~~gv~~~~~~iD~~I~~~l~~w~~~rl~~i~~   78 (130)
T cd00619           2 RRARELAVQALYAWELAPEILAEVVSLLELL---QYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWSLDRLAIVER   78 (130)
T ss_pred             CHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCHHHH
T ss_conf             1999999999999670799999999999875---1133468999999999999849999999998718999676679999


Q ss_pred             HHHHHHHHHHHHCC-CCCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHHHHHC
Q ss_conf             99999999999868-9973325622587752258755444443102211001
Q gi|254780666|r   84 QLLRVSVAQILYLD-VADYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSRE  134 (445)
Q Consensus        84 ~iLr~a~~ell~~~-~p~~a~vneaVelak~~~~~~~~~~~vNAVLR~~~r~  134 (445)
T Consensus        79 ~ILr~a~~El~~~~~~p~~v~InEavelak~f~-~~~~~~fiNgVLd~i~k~  129 (130)
T cd00619          79 AILRLAVYELLFLPDVPHPVVINEAIELAKRFG-GDDSHKFVNGVLDKIAKD  129 (130)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHH
T ss_conf             999999999986867634679999999999857-786204489999998751