>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=98.82 E-value=7.5e-08 Score=73.11 Aligned_cols=107 Identities=13% Similarity=0.053 Sum_probs=78.6 Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-----------HH- Q ss_conf 689999999999999569978999999998685889557999999999999758999997056896-----------79- Q gi|254780634|r 4 GGQIAAAIEILKDIRTHKKPITNSLKDWGMSHRFAGSSDRASISNIVHDVLRKYLSSAYIMDSDDP-----------ES- 71 (429) Q Consensus 4 ~aR~~AA~eiL~~v~~~~~~ad~~L~~~~~~~r~lgs~DR~~i~~lvyg~lR~~~~ld~il~~~~~-----------r~- 71 (429) T Consensus 1 ~AR~-~a~~~L~~~~~~~~~~~~~l~~~~~~~~-l~~~d~~~~~~lv~gv~~~~~~ld~~i~~~l~~~~~~~~~~i~~~i 78 (129) T cd00447 1 SARE-IAFQALYQVEIRNGISLEAVLSALEKLQ-LAKKDRPFALELVYGVLRNLPELDDIISPLLKKWLLDRLDKVDRAI 78 (129) T ss_pred CHHH-HHHHHHHHHHHHCCCHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 9899-9999999998209999999999998778-9778999999999999996999999999982788031100888999 Q ss_pred ---HHHHHHHHHCCCCHHHHHHHHHHHHHCC-CCCHHHHHHHHHC Q ss_conf ---9999999743889899999885433034-3320467754420 Q gi|254780634|r 72 ---LVYAVIMKDWDIPWEKMLSMLKEDLFSP-PLPKESVIKSFHS 112 (429) Q Consensus 72 ---~~~~~l~~~~~~~~~~~v~~~~~~~~~~-~~~~~~~~~~~~~ 112 (429) T Consensus 79 Lrl~~~el~~~~~~ip~~~~InE~v~lak~~~~~~~~~fvNavLr 123 (129) T cd00447 79 LRLLLYELYQLLYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLR 123 (129) T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHH T ss_conf 999999999850589851678999999998678863200799977

HHsearch alignment for GI: 254780634 and conserved domain: cd00447