HHsearch alignment for GI: 254780255 and conserved domain: cd02409
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. 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. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=98.34 E-value=1.2e-06 Score=58.43 Aligned_cols=64 Identities=41% Similarity=0.701 Sum_probs=56.7
Q ss_pred HHHHHHHHHHCCCCCEEEEECCCCCEEEEEECC--CCCCCCCCCHHHHHHHHHHHCCC-CCEEEEEE
Q ss_conf 999998774226422155325885189999737--41001356534899898764035-87057879
Q gi|254780255|r 40 REYLQCHLKQAGVAKILIERTHKNCRIIVYSAR--PGLIIGKKGTDIEKIRKKLSNMT-NSEIHLSV 103 (227)
Q Consensus 40 R~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~k--P~~iiGkkg~~i~~l~~~L~~~~-~~~v~i~v 103 (227)
T Consensus 1 ~~~l~~~l~~~~~~~V~i~~~~~~~~~~i~~~~~~~g~~IGk~G~~l~~l~~ll~~~~~~~~~~i~v 67 (68)
T cd02409 1 REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRKKRVKIDV 67 (68)
T ss_pred CHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCCCEEECCCCHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 9578745565685569999779967999998777996489888363999999999982899843853