HHsearch alignment for GI: 254780784 and conserved domain: cd02134
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=92.14 E-value=0.14 Score=31.45 Aligned_cols=42 Identities=26% Similarity=0.377 Sum_probs=36.2
Q ss_pred CCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEE
Q ss_conf 244875799997711500003786077998999868889980
Q gi|254780784|r 547 GEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNID 588 (699)
Q Consensus 547 ~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~ 588 (699)
T Consensus 20 ~~~~~~~~~V~V~~~~~~~AIGk~G~Nvrla~~l~g~~IdI~ 61 (61)
T cd02134 20 LDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDIV 61 (61)
T ss_pred CCCCCCEEEEEECHHHHHHHHCCCCEEHHHHHHHHCCEEEEC
T ss_conf 478773799998857843876678670999999779877649