HHsearch alignment for GI: 254780788 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=94.02 E-value=0.19 Score=29.85 Aligned_cols=100 Identities=30% Similarity=0.570 Sum_probs=72.5
Q ss_pred EEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEE-----EECCCCHHHHHHHHCCC--CCCCEEEECCCCCEEEE
Q ss_conf 499994089988127655488621788998627782679-----95598789999976286--65424898756787999
Q gi|254780788|r 238 KLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDI-----VVWSPDSATFVINALRP--AIVTKVVLDEDVGRIEV 310 (526)
Q Consensus 238 KIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDi-----i~ws~d~~~fi~nAl~P--A~v~~v~~de~~~~~~v 310 (526)
T Consensus 10 ~ivIYt~~p~~------f~~~~~li~~iAk~ikK-RIviRpdpsil~~~e~a~~~I~~ivPeeA~i~~i~FD~~~g--EV 80 (145)
T cd02410 10 ELVVYTKNPEL------FAEDGDLVKDLAKDLRK-RIVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYFDDDTG--EV 80 (145)
T ss_pred EEEEEECCHHH------HCCCCHHHHHHHHHHHC-EEEECCCHHHCCCHHHHHHHHHHHCCCCCCCEEEEECCCCC--EE
T ss_conf 28999799799------72674099999998720-27973880341899999999998589646844689748885--79
Q ss_pred EECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCC
Q ss_conf 985342211025442789999986167457855220
Q gi|254780788|r 311 IVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE 346 (526)
Q Consensus 311 ~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~ 346 (526)
T Consensus 81 ~Iea~kPg~viGk~g~~l~eI~~~tGW~p~v~RtPp 116 (145)
T cd02410 81 IIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred EEEECCCEEEECCCCHHHHHHHHHHCCEEEEEECCC
T ss_conf 999779777972761679999997398157886599