HHsearch alignment for GI: 254780788 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=99.65 E-value=9.6e-17 Score=142.31 Aligned_cols=60 Identities=55% Similarity=0.783 Sum_probs=56.0
Q ss_pred HHHHHHHHCCCCCCCEEEECC-CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf 899999762866542489875-678799998534221102544278999998616745785
Q gi|254780788|r 283 SATFVINALRPAIVTKVVLDE-DVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII 342 (526)
Q Consensus 283 ~~~fi~nAl~PA~v~~v~~de-~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~ 342 (526)
T Consensus 1 p~~fi~nal~Pa~v~~V~i~~~~~~~~~V~V~~~~~~~AIGk~G~Nvrla~~l~g~~IdI~ 61 (61)
T cd02134 1 PAEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDIV 61 (61)
T ss_pred CHHHHHHHCCCCEEEEEEECCCCCCEEEEEECHHHHHHHHCCCCEEHHHHHHHHCCEEEEC
T ss_conf 9789986369875579884478773799998857843876678670999999779877649