>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.

Probab=94.98  E-value=0.086  Score=31.54  Aligned_cols=34  Identities=32%  Similarity=0.421  Sum_probs=29.7

Q ss_pred             CCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHC
Q ss_conf             4287879899783638823135327897713022213
Q gi|254780751|r   38 IKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI   74 (723)
Q Consensus        38 ~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei   74 (723)
T Consensus         2 k~geiv~G~V~r~~~--~~v~vdlg-~~eailp~~eq   35 (67)
T cd04455           2 REGEIVTGIVKRVDR--GNVIVDLG-KVEAILPKKEQ   35 (67)
T ss_pred             CCCCEEEEEEEEEEC--CCEEEEEC-CCEEECCHHHC
T ss_conf             878889999999808--97999989-94897378995