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