HHsearch alignment for GI: 254780788 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=97.89 E-value=2.2e-05 Score=58.84 Aligned_cols=58 Identities=31% Similarity=0.487 Sum_probs=50.5
Q ss_pred HHHHHHHCCCCCCCEEEECCC--CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHC-------CEEEE
Q ss_conf 999997628665424898756--78799998534221102544278999998616-------74578
Q gi|254780788|r 284 ATFVINALRPAIVTKVVLDED--VGRIEVIVPKEQLSLAIGRRGQNVRLASQLTG-------WTIDI 341 (526)
Q Consensus 284 ~~fi~nAl~PA~v~~v~~de~--~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg-------~~idi 341 (526)
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