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Conserved domains on  [gi|666637946|ref|NP_001288006|]
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CCR4-NOT transcription complex subunit 8 isoform 3 [Homo sapiens]

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.-
Gene Ontology:  GO:0000175|GO:0046872|GO:0004535|GO:0003723
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 ...
 1-157 1.23e-58

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: 185.51  E-value: 1.23e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 666637946   1 MYSQDSIDLLANSGLQFQKHEEEGIDTLHFAELLMTSGVVLCDNVKWLSFHSGYDFGYMVKLLTDSRLPEEEHEFFHILN 80
Cdd:COG5228  115 MYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLH 194

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 666637946  81 LFFPSIYDVKYLMKSCKNLKGGLQEVADQLDLQRIGRQHQAGSDSLLTGMAFFRMKELFFEDSIDDAKYCgRLYGLG 157
Cdd:COG5228  195 QYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIFTTSIGQSLLM-LLSGCQ 270
 
Name Accession Description Interval E-value
POP2 COG5228
mRNA deadenylase subunit [RNA processing and modification];
1-157 1.23e-58

mRNA deadenylase subunit [RNA processing and modification];


Pssm-ID: 227553  Cd Length: 299  Bit Score: 185.51  E-value: 1.23e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 666637946   1 MYSQDSIDLLANSGLQFQKHEEEGIDTLHFAELLMTSGVVLCDNVKWLSFHSGYDFGYMVKLLTDSRLPEEEHEFFHILN 80
Cdd:COG5228  115 MYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLH 194

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 666637946  81 LFFPSIYDVKYLMKSCKNLKGGLQEVADQLDLQRIGRQHQAGSDSLLTGMAFFRMKELFFEDSIDDAKYCgRLYGLG 157
Cdd:COG5228  195 QYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIFTTSIGQSLLM-LLSGCQ 270
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
 16-132 5.33e-07

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: 48.56  E-value: 5.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 666637946   16 QFQKHEEEGIDTL----HFAELLMTSGvvlcdnvKWLSFHSG-YDFGYMVKLLtDSRLPEEEHEFFHILNLFFPSIYDVK 90
Cdd:pfam04857 235 EKKDEEEERLESAvgfrLVFDALSKSR-------KPIVGHNGlLDLLFLYQQF-YGPLPETLEEFKALIHELFPGIYDTK 306

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 666637946   91 YLMKSCKNLKGG-----LQEVADQL----------------------DLQRIGRQHQAGSDSLLTGMAF 132
Cdd:pfam04857 307 YLATTDAEFKVRlpsssLEELFEKLckenfsspsvetppfesdyhdeSSKYGGKAHEAGYDAYMTGYVF 375
 
Name Accession Description Interval E-value
POP2 COG5228
mRNA deadenylase subunit [RNA processing and modification];
1-157 1.23e-58

mRNA deadenylase subunit [RNA processing and modification];


Pssm-ID: 227553  Cd Length: 299  Bit Score: 185.51  E-value: 1.23e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 666637946   1 MYSQDSIDLLANSGLQFQKHEEEGIDTLHFAELLMTSGVVLCDNVKWLSFHSGYDFGYMVKLLTDSRLPEEEHEFFHILN 80
Cdd:COG5228  115 MYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLH 194

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 666637946  81 LFFPSIYDVKYLMKSCKNLKGGLQEVADQLDLQRIGRQHQAGSDSLLTGMAFFRMKELFFEDSIDDAKYCgRLYGLG 157
Cdd:COG5228  195 QYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIFTTSIGQSLLM-LLSGCQ 270
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
 16-132 5.33e-07

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: 48.56  E-value: 5.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 666637946   16 QFQKHEEEGIDTL----HFAELLMTSGvvlcdnvKWLSFHSG-YDFGYMVKLLtDSRLPEEEHEFFHILNLFFPSIYDVK 90
Cdd:pfam04857 235 EKKDEEEERLESAvgfrLVFDALSKSR-------KPIVGHNGlLDLLFLYQQF-YGPLPETLEEFKALIHELFPGIYDTK 306

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 666637946   91 YLMKSCKNLKGG-----LQEVADQL----------------------DLQRIGRQHQAGSDSLLTGMAF 132
Cdd:pfam04857 307 YLATTDAEFKVRlpsssLEELFEKLckenfsspsvetppfesdyhdeSSKYGGKAHEAGYDAYMTGYVF 375
 
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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