HHsearch alignment for GI: 254780784 and conserved domain: cd02395
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. 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=97.54 E-value=0.00064 Score=50.58 Aligned_cols=58 Identities=21% Similarity=0.313 Sum_probs=50.0
Q ss_pred CCCEEEEECCCCHHHHHHHHHHCCEEEEEC-----------------------CEEEEEEECC--HHHHHHHHHHHHHHC
Q ss_conf 115000037860779989998688899808-----------------------8089999689--899999999999852
Q gi|254780784|r 560 PDQIRNVIGMGGKVIRGIVEQTGAKVNIDD-----------------------DGTVKIASSS--LAEIEAAREMIRSIT 614 (699)
Q Consensus 560 ~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d-----------------------~g~v~i~~~~--~~~~~~a~~~i~~~~ 614 (699)
T Consensus 14 ~Nfvg~ilGprG~t~k~l~~~t~~~i~irG~GS~Kd~~~e~~~~~~~~~hl~epLHVlI~a~~~~~e~~~~a~~~i~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCEEEEEECCCCCHHHHHHHHHCCEEEEEECCCCCCCCCHHHCCCCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHH
T ss_conf 88567887798506999999879879997178766765354436899855689977999953988999999999999981
Q ss_pred CCC
Q ss_conf 475
Q gi|254780784|r 615 DVP 617 (699)
Q Consensus 615 ~~~ 617 (699)
T Consensus 94 ~p~ 96 (120)
T cd02395 94 KPA 96 (120)
T ss_pred CCC
T ss_conf 789