>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=98.23 E-value=1.1e-05 Score=51.73 Aligned_cols=56 Identities=20% Similarity=0.364 Sum_probs=24.4 Q ss_pred CCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCC Q ss_conf 89879999999708908999617798499999747182121042011068987999999970576 Q gi|254780456|r 458 KNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKD 522 (576) Q Consensus 458 ~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~ 522 (576) T Consensus 3 ~geiv~G~V~r~~~~~v~vdl---g~~eailp~~eqi------p~E~~~~Gdrik~~i~~V~~~~ 58 (67) T cd04455 3 EGEIVTGIVKRVDRGNVIVDL---GKVEAILPKKEQI------PGESYRPGDRIKAYVLEVRKTS 58 (67) T ss_pred CCCEEEEEEEEEECCCEEEEE---CCCEEECCHHHCC------CCCCCCCCCEEEEEEEEEEECC T ss_conf 788899999998089799998---9948973789957------8866399998999999987469

HHsearch alignment for GI: 254780456 and conserved domain: cd04455