HHsearch alignment for GI: 254780636 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=97.48 E-value=0.0006 Score=42.19 Aligned_cols=113 Identities=25% Similarity=0.340 Sum_probs=65.0
Q ss_pred HCCCCCCEEEECCCCCCCCCC-------------------CEEEEEEEE----ECCCC------EEEECC-----CCCCC
Q ss_conf 424898279971777898544-------------------507999984----18942------899746-----57785
Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPRR-------------------DRLCIVQLS----PGDGT------VDIIRI-----AAGQK 61 (207)
Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~~-------------------~~l~LiQl~----~~~~~------~~l~~~-----~~~~~ 61 (207)
T Consensus 18 ~i~~~~fVaiDtEFpG~v~~p~~~~~~t~~~~Y~~lk~nVd~l~iiQlGlt~~~~~g~~p~~~~~wqfNf~~F~~~~d~~ 97 (235)
T pfam04857 18 AIDSYDFIAIDTEFPGVVARPIGSFRSTSDYRYQALRKNVDRLKIIQLGLTLFDEKGNLPDSYYTWQFNFSLFNLEEDFY 97 (235)
T ss_pred HHHCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCC
T ss_conf 98319989995142752468988888987899999984300123146898887468878987437850155679732211
Q ss_pred CCH-----------------------HH------HHHHHC-CCCCEEECCCCHHHHHHHHHH-H-CC-------------
Q ss_conf 706-----------------------77------677732-364023010000168886542-0-00-------------
Q gi|254780636|r 62 NAP-----------------------NL------VGMLVD-EKREKIFHYGRFDIAVLFYTF-G-VR------------- 96 (207)
Q Consensus 62 ~~~-----------------------~L------~~ll~d-~~i~KV~Hn~~~D~~~L~~~~-g-i~------------- 96 (207)
T Consensus 98 ~~~Si~fL~~~G~DF~~~~~~GI~~~~f~e~l~~S~lv~~~~~~~wv~f~g~yD~~yl~k~l~g~~LP~~~~eF~~~l~~ 177 (235)
T pfam04857 98 APSSIEFLAKQGFDFNKHRREGIPYLRFAELLGSSGLFLNISSVTWVTFHGLYDFGYLLKLLTGGPLPETLDDFLELLRE 177 (235)
T ss_pred CHHHHHHHHHCCCCHHHHHHHCCCHHHHHHHHHHHHHEECCCCCEEEEECCHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf 68899999985988899987099989999899870302057998799817277899999997499899989999999999
Q ss_pred -CCCHHHHHHHHHHHHHH--CCCHHHHHHHHHHHCC
Q ss_conf -00004578988652110--0000088777654200
Q gi|254780636|r 97 -VRPVFCTKIASRLTRTY--TNQHGLKDNLKELLGI 129 (207)
Q Consensus 97 -~~~i~DT~ias~l~~~~--~~~~~L~~L~~~~lg~ 129 (207)
T Consensus 178 ~FP~vyD~K~la~~~~~~~~~~~~gL~~lA~~-L~v 212 (235)
T pfam04857 178 LFPRVYDTKYLAKFCFELDGGSNGGLQELADL-LGV 212 (235)
T ss_pred HCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHH-CCC
T ss_conf 77717509999985221358755789999997-499