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