>cd00447 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein 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. The m5C-methyltransferase Sun shares the

Probab=99.85 E-value=1.6e-20 Score=171.91 Aligned_cols=125 Identities=27% Similarity=0.293 Sum_probs=112.9 Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCHHHHH Q ss_conf 69999999999999559988999999851123216898899999999999996089999999998428-81004889999 Q gi|254780666|r 6 NARLVSSHLLSCVMRKRISLTCLLDLEYGDSAFRLLSQRDQILVRAIVNVTLRFLPRIDAVLDFVLIS-SLPRKKYSLQQ 84 (445) Q Consensus 6 ~aR~~A~~iL~~v~~~~~~~~~~l~~~~~~~~~~~L~~~Dr~~~~~Lv~gvlR~~~~ld~il~~~~~~-~~~~~~~~~~~ 84 (445) T Consensus 1 ~AR~~a~~~L~~~~~~~~~~~~~l~~~~~~~---~l~~~d~~~~~~lv~gv~~~~~~ld~~i~~~l~~~~~~~~~~i~~~ 77 (129) T cd00447 1 SAREIAFQALYQVEIRNGISLEAVLSALEKL---QLAKKDRPFALELVYGVLRNLPELDDIISPLLKKWLLDRLDKVDRA 77 (129) T ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 9899999999999820999999999999877---8977899999999999999699999999998278803110088899 Q ss_pred HHHHHHHHHHHC--CCCCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHHHHHC Q ss_conf 999999999986--89973325622587752258755444443102211001 Q gi|254780666|r 85 LLRVSVAQILYL--DVADYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSRE 134 (445) Q Consensus 85 iLr~a~~ell~~--~~p~~a~vneaVelak~~~~~~~~~~~vNAVLR~~~r~ 134 (445) T Consensus 78 iLrl~~~el~~~~~~ip~~~~InE~v~lak~~~-~~~~~~fvNavLr~i~r~ 128 (129) T cd00447 78 ILRLLLYELYQLLYDVPPPVAINEAVELAKRFG-DDDSAKFVNGVLRRIAKE 128 (129) T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHC-CCCCCCCHHHHHHHHHCC T ss_conf 999999999985058985167899999999867-886320079997798734

HHsearch alignment for GI: 254780666 and conserved domain: cd00447