HHsearch alignment for GI: 254780661 and conserved domain: pfam04857
>pfam04857 CAF1 CAF1 family ribonuclease. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom#resolution.
Probab=98.59 E-value=5.3e-06 Score=57.34 Aligned_cols=173 Identities=19% Similarity=0.180 Sum_probs=111.8
Q ss_pred CCEEEEECCCCCCCCC---------------------CCEEEEEEEEEECCCCEECCEEEEE----EEC-CCCCCCCCH-
Q ss_conf 8379997527889877---------------------2604899999983897280400226----621-788877857-
Q gi|254780661|r 3 NHFVIYDYETFGRDVA---------------------LDRPAQFAGVRVDRQWEKIESTEVF----FCK-PADDYLPDP- 55 (471)
Q Consensus 3 ~~~v~~D~ETtG~~~~---------------------~~~iiq~~~i~~d~~~~~~~~~~~~----~~~-~~~~~~p~p- 55 (471)
T Consensus 22 ~~fVaiDtEFpG~v~~p~~~~~~t~~~~Y~~lk~nVd~l~iiQlGlt~~~~~g~~p~~~~~wqfNf~~F~~~~d-~~~~~ 100 (235)
T pfam04857 22 YDFIAIDTEFPGVVARPIGSFRSTSDYRYQALRKNVDRLKIIQLGLTLFDEKGNLPDSYYTWQFNFSLFNLEED-FYAPS 100 (235)
T ss_pred CCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCC-CCCHH
T ss_conf 99899951427524689888889878999999843001231468988874688789874378501556797322-11688
Q ss_pred --HHHHHHCCCHHHHHHCCCCHHHHHHHH--HHHHHC-CCCEEEEEECHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf --898985799889960799979999999--999511-796599950557899999999985078532132568871001
Q gi|254780661|r 56 --EAVFITGITPQKALRDGVVEAEFSRRI--HQFFSV-PNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRWSWDNGNSRWD 130 (471)
Q Consensus 56 --~a~~v~git~~~~~~~~~~~~e~~~~i--~~~~~~-~~~~~ig~N~~~FD~~~lr~~~~r~~~~~y~~~~~~~~~~~D 130 (471)
T Consensus 101 Si~fL~~~G~DF~~~~~~GI~~~~f~e~l~~S~lv~~~~~~~wv~f~g-~yD~~yl~k~l~g~~LP~---------~~~e 170 (235)
T pfam04857 101 SIEFLAKQGFDFNKHRREGIPYLRFAELLGSSGLFLNISSVTWVTFHG-LYDFGYLLKLLTGGPLPE---------TLDD 170 (235)
T ss_pred HHHHHHHCCCCHHHHHHHCCCHHHHHHHHHHHHHEECCCCCEEEEECC-HHHHHHHHHHHCCCCCCC---------CHHH
T ss_conf 999999859888999870999899998998703020579987998172-778999999974998999---------8999
Q ss_pred HHHHHHHHHHHHHHHCCCCCC------CCCCCCCCHHHHHHHHCCCC--CCCCHHHHHHHHHHHHHH
Q ss_conf 588886555653210024444------45443310898998718876--431013331899999999
Q gi|254780661|r 131 LLDVMRAIYAFSPDGIQWPSR------DDGATSFKLQDLALANGIEH--VNAHDAKADVYATLALVW 189 (471)
Q Consensus 131 ~l~~~~~~~~~~p~~~~~~~~------~~~~~~~kL~~la~~n~i~~--~~aH~A~~D~~~t~~l~k 189 (471)
T Consensus 171 F~~~l~---~~FP~vyD~K~la~~~~~~~~~~~~gL~~lA~~L~v~r~~g~~HqAGsDSllT~~~F~ 234 (235)
T pfam04857 171 FLELLR---ELFPRVYDTKYLAKFCFELDGGSNGGLQELADLLGVNRRVGRLHQAGSDSLLTALVFF 234 (235)
T ss_pred HHHHHH---HHCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 999999---9777175099999852213587557899999974997888986665529999998761