HHsearch alignment for GI: 254780255 and conserved domain: cd02410
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. 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 domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=92.91 E-value=0.72 Score=24.96 Aligned_cols=83 Identities=24% Similarity=0.452 Sum_probs=56.4
Q ss_pred HHHHHHHH-HCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHHHH
Q ss_conf 99998774-22642215532588518999973741001356534899898764035870578799813755337787999
Q gi|254780255|r 41 EYLQCHLK-QAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQS 119 (227)
Q Consensus 41 ~fi~k~l~-~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA~~ 119 (227)
T Consensus 56 ~~I~~ivPeeA~i~~i~FD--~~~gEV~Iea~kPg~viGk~g~~l~eI~~~tGW~--------p~v~RtPpi~S~ti-~~ 124 (145)
T cd02410 56 KIILEIVPEEAGITDIYFD--DDTGEVIIEAEKPGLVIGKGGSTLREITRETGWA--------PKVVRTPPIQSRTV-KS 124 (145)
T ss_pred HHHHHHCCCCCCCEEEEEC--CCCCEEEEEECCCEEEECCCCHHHHHHHHHHCCE--------EEEEECCCCCHHHH-HH
T ss_conf 9999858964684468974--8885799997797779727616799999973981--------57886599961789-99
Q ss_pred HHHHHHCCCHHHHHH
Q ss_conf 999987596368999
Q gi|254780255|r 120 IAQQLERRVVFRRAM 134 (227)
Q Consensus 120 Ia~~Lekr~~fRr~~ 134 (227)
T Consensus 125 IR~~l~~~~~eRrk~ 139 (145)
T cd02410 125 IRRFLRREREERKEI 139 (145)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 999999808999999