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Conserved domains on  [gi|665410276|ref|NP_001287041|]
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Pop2, isoform E [Drosophila melanogaster]

Protein Classification

CAF1 family ribonuclease( domain architecture ID 581404)

CAF1 family ribonuclease such as Xenopus laevis CCR4-NOT transcription complex subunit 7 and Arabidopsis thaliana probable CCR4-associated factor 1 homolog

CATH:  3.30.420.10
EC:  3.1.13.-
SCOP:  4001124

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CAF1 super family cl23804
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
25-257 4.52e-115

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.


The actual alignment was detected with superfamily member COG5228:

Pssm-ID: 474062  Cd Length: 299  Bit Score: 336.12  E-value: 4.52e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276  25 IRDVWKQNLEEEFRTIRKVVQKYHYVAMDTEFPGVVARPVGEFRSTADYHYQLLRCNVDLLRIIQLGLTFMDDDGKTPPG 104
Cdd:COG5228   20 IRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNG 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276 105 YSTWQFNFKFNLSEDMYAQDSIDLLQNSGIQFKKHEEDGIDPIDFAELLMSSGIVLVENIKWLCFHSGYDFGYLLKLLTD 184
Cdd:COG5228  100 PSTWQFNFEFDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTN 179
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665410276 185 QNLPPDESEFFDLLHIYFPNIFDIKYLMKSCKNLKGGLQEVADQLELRRVGPQHQAGSDALLTGMAFFKMREV 257
Cdd:COG5228  180 DPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFS 252
 
Name Accession Description Interval E-value
POP2 COG5228
mRNA deadenylase subunit [RNA processing and modification];
25-257 4.52e-115

mRNA deadenylase subunit [RNA processing and modification];


Pssm-ID: 227553  Cd Length: 299  Bit Score: 336.12  E-value: 4.52e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276  25 IRDVWKQNLEEEFRTIRKVVQKYHYVAMDTEFPGVVARPVGEFRSTADYHYQLLRCNVDLLRIIQLGLTFMDDDGKTPPG 104
Cdd:COG5228   20 IRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNG 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276 105 YSTWQFNFKFNLSEDMYAQDSIDLLQNSGIQFKKHEEDGIDPIDFAELLMSSGIVLVENIKWLCFHSGYDFGYLLKLLTD 184
Cdd:COG5228  100 PSTWQFNFEFDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTN 179
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665410276 185 QNLPPDESEFFDLLHIYFPNIFDIKYLMKSCKNLKGGLQEVADQLELRRVGPQHQAGSDALLTGMAFFKMREV 257
Cdd:COG5228  180 DPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFS 252
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
28-251 1.15e-13

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.


Pssm-ID: 461457  Cd Length: 375  Bit Score: 71.29  E-value: 1.15e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276   28 VWKQNLEEEFRTIRKVVQKYHYVAMDTEFPGVVARPVGEFRS-TADYHYQLLRCNVDLLRIIQLGLTFMDDDGKTPPgYS 106
Cdd:pfam04857   1 VTRSNFKELLPEILKAIKEADFVAIDLEFTGLGSPWRKSSLFdTPEERYLKLRDAAERFSILQFGLCCFREDEEKSK-YT 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276  107 TWQFNFK-FNLSEDMYAQD------SID-LLQN---------SGIQFKKHEE----------------DGIDPIDFAELL 153
Cdd:pfam04857  80 AKPYNFYlFPRTELDPDRDfscqasSLQfLAKHgfdfnklfyEGIPYLSRAEeeklrerleerqqaspSDIPLLDVEDKE 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276  154 MSSGIV-------------------------------------------------------------------------- 159
Cdd:pfam04857 160 FVERVRskikewldsgedkgeklnidnpvsrlllqqllkhqlvrvllvellsrgkqkvvqvvkkssedeellekeekkde 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276  160 -----------------LVENIKWLCFHSG-YDFGYLLKLLtDQNLPPDESEFFDLLHIYFPNIFDIKYLMKSCKNLKGG 221
Cdd:pfam04857 240 eeerlesavgfrlvfdaLSKSRKPIVGHNGlLDLLFLYQQF-YGPLPETLEEFKALIHELFPGIYDTKYLATTDAEFKVR 318
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 665410276  222 -----LQEVADQL----------------------ELRRVGPQHQAGSDALLTGMAF 251
Cdd:pfam04857 319 lpsssLEELFEKLckenfsspsvetppfesdyhdeSSKYGGKAHEAGYDAYMTGYVF 375
 
Name Accession Description Interval E-value
POP2 COG5228
mRNA deadenylase subunit [RNA processing and modification];
25-257 4.52e-115

mRNA deadenylase subunit [RNA processing and modification];


Pssm-ID: 227553  Cd Length: 299  Bit Score: 336.12  E-value: 4.52e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276  25 IRDVWKQNLEEEFRTIRKVVQKYHYVAMDTEFPGVVARPVGEFRSTADYHYQLLRCNVDLLRIIQLGLTFMDDDGKTPPG 104
Cdd:COG5228   20 IRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNG 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276 105 YSTWQFNFKFNLSEDMYAQDSIDLLQNSGIQFKKHEEDGIDPIDFAELLMSSGIVLVENIKWLCFHSGYDFGYLLKLLTD 184
Cdd:COG5228  100 PSTWQFNFEFDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTN 179
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665410276 185 QNLPPDESEFFDLLHIYFPNIFDIKYLMKSCKNLKGGLQEVADQLELRRVGPQHQAGSDALLTGMAFFKMREV 257
Cdd:COG5228  180 DPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFS 252
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
28-251 1.15e-13

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.


Pssm-ID: 461457  Cd Length: 375  Bit Score: 71.29  E-value: 1.15e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276   28 VWKQNLEEEFRTIRKVVQKYHYVAMDTEFPGVVARPVGEFRS-TADYHYQLLRCNVDLLRIIQLGLTFMDDDGKTPPgYS 106
Cdd:pfam04857   1 VTRSNFKELLPEILKAIKEADFVAIDLEFTGLGSPWRKSSLFdTPEERYLKLRDAAERFSILQFGLCCFREDEEKSK-YT 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276  107 TWQFNFK-FNLSEDMYAQD------SID-LLQN---------SGIQFKKHEE----------------DGIDPIDFAELL 153
Cdd:pfam04857  80 AKPYNFYlFPRTELDPDRDfscqasSLQfLAKHgfdfnklfyEGIPYLSRAEeeklrerleerqqaspSDIPLLDVEDKE 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276  154 MSSGIV-------------------------------------------------------------------------- 159
Cdd:pfam04857 160 FVERVRskikewldsgedkgeklnidnpvsrlllqqllkhqlvrvllvellsrgkqkvvqvvkkssedeellekeekkde 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276  160 -----------------LVENIKWLCFHSG-YDFGYLLKLLtDQNLPPDESEFFDLLHIYFPNIFDIKYLMKSCKNLKGG 221
Cdd:pfam04857 240 eeerlesavgfrlvfdaLSKSRKPIVGHNGlLDLLFLYQQF-YGPLPETLEEFKALIHELFPGIYDTKYLATTDAEFKVR 318
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 665410276  222 -----LQEVADQL----------------------ELRRVGPQHQAGSDALLTGMAF 251
Cdd:pfam04857 319 lpsssLEELFEKLckenfsspsvetppfesdyhdeSSKYGGKAHEAGYDAYMTGYVF 375
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
86-256 8.09e-04

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 39.78  E-value: 8.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276  86 RIIQLGLTFMDDDGKTP-------PGYSTWQFNFKFN-LSEDMYAQdsidllqnsgiqfKKHEEDGIDpiDFAELLmsSG 157
Cdd:COG0847   18 RIIEIGAVKVDDGRIVEtfhtlvnPERPIPPEATAIHgITDEDVAD-------------APPFAEVLP--ELLEFL--GG 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665410276 158 IVLVenikwlCFHSGYDFGYLLKLLTDQNLPPDESEFFDLLHIYfpnifdiKYLMKSCKNLKggLQEVADQLELRRVGPq 237
Cdd:COG0847   81 AVLV------AHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLA-------RRLLPGLPSYS--LDALCERLGIPFDER- 144
                        170
                 ....*....|....*....
gi 665410276 238 HQAGSDALLTGMAFFKMRE 256
Cdd:COG0847  145 HRALADAEATAELFLALLR 163
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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