>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=98.44 E-value=1.7e-06 Score=56.59 Aligned_cols=63 Identities=27% Similarity=0.518 Sum_probs=42.0 Q ss_pred CCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCC--CEEEEE Q ss_conf 8987799999998199899994796036789975056643556378987999999974799--859996 Q gi|254780456|r 25 AENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSF--GEAVFS 91 (576) Q Consensus 25 ~~G~iv~G~V~~i~~~~v~vdig~k~~G~i~~~e~~~~~~~~~~kvGd~i~v~V~~~~~~~--g~i~lS 91 (576) T Consensus 2 k~geiv~G~V~r~~~~~v~vdlg-~~eailp~~eqi---p~E~~~~Gdrik~~i~~V~~~~kgp~i~lS 66 (67) T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQI---PGESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67) T ss_pred CCCCEEEEEEEEEECCCEEEEEC-CCEEECCHHHCC---CCCCCCCCCEEEEEEEEEEECCCCCEEEEE T ss_conf 87888999999980897999989-948973789957---886639999899999998746998889983

HHsearch alignment for GI: 254780456 and conserved domain: cd04455