HHsearch alignment for GI: 254780255 and conserved domain: cd02411
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. 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 general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.79 E-value=6.4e-19 Score=129.27 Aligned_cols=83 Identities=28% Similarity=0.458 Sum_probs=79.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCC-CEEEEEEE
Q ss_conf 31257999989999999998774226422155325885189999737410013565348998987640358-70578799
Q gi|254780255|r 26 GSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN-SEIHLSVN 104 (227)
Q Consensus 26 ~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~-~~v~i~v~ 104 (227)
T Consensus 2 kK~Fi~~~~~~~~ireyl~k~l~~Ag~s~ieIeRtp~~~~I~I~t~rPG~VIGr~G~~I~~L~~~L~~~~g~~~~~I~V~ 81 (85)
T cd02411 2 ERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGLENPQIDVQ 81 (85)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEE
T ss_conf 41698855689999999999888678655999988996699999789984777886659999999999968998659999
Q ss_pred EECC
Q ss_conf 8137
Q gi|254780255|r 105 EVPK 108 (227)
Q Consensus 105 ei~~ 108 (227)
T Consensus 82 EV~n 85 (85)
T cd02411 82 EVEN 85 (85)
T ss_pred ECCC
T ss_conf 6689