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Conserved domains on  [gi|388453443|ref|NP_001253776|]
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CCR4-NOT transcription complex subunit 7 [Macaca mulatta]

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 ...
1-279 1.09e-118

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: 342.28  E-value: 1.09e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443   1 MPAATVD--HSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDLLKIIQLG 78
Cdd:COG5228    7 MPPIFLDgpNYLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLG 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443  79 LTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHS 158
Cdd:COG5228   87 LSLSDENGNKPNGPSTWQFNFEFDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHS 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443 159 GYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAF 238
Cdd:COG5228  167 AYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEF 246
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 388453443 239 FKMREMFFEDHIDDAKYCgHLYGLG-SGSSYVQNGTGNAYEE 279
Cdd:COG5228  247 FLPRFSIFTTSIGQSLLM-LLSGCQlSKLSLHKFPNGTDFAK 287
 
Name Accession Description Interval E-value
POP2 COG5228
mRNA deadenylase subunit [RNA processing and modification];
1-279 1.09e-118

mRNA deadenylase subunit [RNA processing and modification];


Pssm-ID: 227553  Cd Length: 299  Bit Score: 342.28  E-value: 1.09e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443   1 MPAATVD--HSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDLLKIIQLG 78
Cdd:COG5228    7 MPPIFLDgpNYLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLG 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443  79 LTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHS 158
Cdd:COG5228   87 LSLSDENGNKPNGPSTWQFNFEFDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHS 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443 159 GYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAF 238
Cdd:COG5228  167 AYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEF 246
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 388453443 239 FKMREMFFEDHIDDAKYCgHLYGLG-SGSSYVQNGTGNAYEE 279
Cdd:COG5228  247 FLPRFSIFTTSIGQSLLM-LLSGCQlSKLSLHKFPNGTDFAK 287
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
18-238 3.85e-10

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: 59.73  E-value: 3.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443   18 CNLDEEMKKIRQVIRKYNYVAM--------DTEFPGVVARPIGEFRSNA-DYQYQLLRCNVDLLKIIQLGLTFMNEQGEY 88
Cdd:pfam04857 127 LSRAEEEKLRERLEERQQASPSdiplldveDKEFVERVRSKIKEWLDSGeDKGEKLNIDNPVSRLLLQQLLKHQLVRVLL 206
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443   89 PPGTSTWQFNFKFNLTEDMYAQDSIELlttsgIQFKKHEEEGIETQ----YFAELLMTSGvvlcegvKWLSFHSG-YDFG 163
Cdd:pfam04857 207 VELLSRGKQKVVQVVKKSSEDEELLEK-----EEKKDEEEERLESAvgfrLVFDALSKSR-------KPIVGHNGlLDLL 274
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443  164 YLIKILtNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGG-----LQEVAEQLELER------------------ 220
Cdd:pfam04857 275 FLYQQF-YGPLPETLEEFKALIHELFPGIYDTKYLATTDAEFKVRlpsssLEELFEKLCKENfsspsvetppfesdyhde 353
                         250       260
                  ....*....|....*....|..
gi 388453443  221 ----IGPQHQAGSDSLLTGMAF 238
Cdd:pfam04857 354 sskyGGKAHEAGYDAYMTGYVF 375
 
Name Accession Description Interval E-value
POP2 COG5228
mRNA deadenylase subunit [RNA processing and modification];
1-279 1.09e-118

mRNA deadenylase subunit [RNA processing and modification];


Pssm-ID: 227553  Cd Length: 299  Bit Score: 342.28  E-value: 1.09e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443   1 MPAATVD--HSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDLLKIIQLG 78
Cdd:COG5228    7 MPPIFLDgpNYLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLG 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443  79 LTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHS 158
Cdd:COG5228   87 LSLSDENGNKPNGPSTWQFNFEFDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHS 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443 159 GYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAF 238
Cdd:COG5228  167 AYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEF 246
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 388453443 239 FKMREMFFEDHIDDAKYCgHLYGLG-SGSSYVQNGTGNAYEE 279
Cdd:COG5228  247 FLPRFSIFTTSIGQSLLM-LLSGCQlSKLSLHKFPNGTDFAK 287
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
18-238 3.85e-10

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: 59.73  E-value: 3.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443   18 CNLDEEMKKIRQVIRKYNYVAM--------DTEFPGVVARPIGEFRSNA-DYQYQLLRCNVDLLKIIQLGLTFMNEQGEY 88
Cdd:pfam04857 127 LSRAEEEKLRERLEERQQASPSdiplldveDKEFVERVRSKIKEWLDSGeDKGEKLNIDNPVSRLLLQQLLKHQLVRVLL 206
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443   89 PPGTSTWQFNFKFNLTEDMYAQDSIELlttsgIQFKKHEEEGIETQ----YFAELLMTSGvvlcegvKWLSFHSG-YDFG 163
Cdd:pfam04857 207 VELLSRGKQKVVQVVKKSSEDEELLEK-----EEKKDEEEERLESAvgfrLVFDALSKSR-------KPIVGHNGlLDLL 274
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443  164 YLIKILtNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGG-----LQEVAEQLELER------------------ 220
Cdd:pfam04857 275 FLYQQF-YGPLPETLEEFKALIHELFPGIYDTKYLATTDAEFKVRlpsssLEELFEKLCKENfsspsvetppfesdyhde 353
                         250       260
                  ....*....|....*....|..
gi 388453443  221 ----IGPQHQAGSDSLLTGMAF 238
Cdd:pfam04857 354 sskyGGKAHEAGYDAYMTGYVF 375
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
15-129 1.01e-09

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: 58.58  E-value: 1.01e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388453443   15 VWACNLDEEMKKIRQVIRKYNYVAMDTEFPGV--VARPIGEFRSNADYqYQLLRCNVDLLKIIQLGLTFMneqgEYPPGT 92
Cdd:pfam04857   1 VTRSNFKELLPEILKAIKEADFVAIDLEFTGLgsPWRKSSLFDTPEER-YLKLRDAAERFSILQFGLCCF----REDEEK 75
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 388453443   93 STWQ---FNFK-FNLTEDMYAQD------SIELLT----------TSGIQFKKHEEE 129
Cdd:pfam04857  76 SKYTakpYNFYlFPRTELDPDRDfscqasSLQFLAkhgfdfnklfYEGIPYLSRAEE 132
 
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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