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=95.90 E-value=0.0067 Score=40.57 Aligned_cols=58 Identities=31% Similarity=0.446 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHHHHCCEEEEEEEECCCC--CEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEE
Q ss_conf 899999999766777558087856631677--5034999940899881276554886217889986277826799
Q gi|254780788|r 205 PQFMVKLFHMEVPEIYNGIVQVKAVSRDPG--SRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIV 277 (526)
Q Consensus 205 p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG--~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii 277 (526)
T Consensus 2 ~~fi~nal~Pa---------~v~~V~i~~~~~~~~~V~V~~-----~~~~~AIGk~G~Nvrla~~l~g-~~IdI~ 61 (61)
T cd02134 2 AEFIRNALSPA---------KVTSVTVLDDEEKRARVVVPD-----DQLGLAIGKGGQNVRLASKLLG-EKIDIV 61 (61)
T ss_pred HHHHHHHCCCC---------EEEEEEECCCCCCEEEEEECH-----HHHHHHHCCCCEEHHHHHHHHC-CEEEEC
T ss_conf 78998636987---------557988447877379999885-----7843876678670999999779-877649