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Conserved domains on  [gi|1958672650|ref|XP_038946753|]
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protein angel homolog 2 isoform X4 [Rattus norvegicus]

Protein Classification

exonuclease/endonuclease/phosphatase family protein( domain architecture ID 662)

exonuclease/endonuclease/phosphatase (EEP) family protein may cleave phosphodiester bonds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EEP super family cl00490
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 8-298 1.88e-36

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


The actual alignment was detected with superfamily member cd09097:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 329  Bit Score: 132.81  E-value: 1.88e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650   8 DGCAICFKHSKFSLLSVNPVEF----CRRDIP---------LLDRDNIGLVLLLQPKIPRAASPS---ICIANTHLLYNP 71
Cdd:cd09097    91 DGCAIFFKTSKFKLVEKHLIEFnqlaMANADAegsedmlnrVMTKDNIALIVVLEARETSYEGNKgqlLIVANTHIHWDP 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650  72 RRGDIKLTQLAMLLAEISNVAHQ------KDGSFCPIVMCGDFNSVPGSPLYSFikegklnyegLAIGKVSGQEqssrgq 145
Cdd:cd09097   171 EFSDVKLVQTMMLLEELEKIAEKfsrypyEDSADIPLVVCGDFNSLPDSGVYEL----------LSNGSVSPNH------ 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 146 rilsipiwpPNLGISQNCVYEAqqvpkvektdsdvtqaqqekaevpvpadkvSSHLQHGFSLSSVYSH--------YVPD 217
Cdd:cd09097   235 ---------PDFKEDPYGEYLT------------------------------ASGLTHSFKLKSAYANlgelpftnYTPD 275

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 218 -TGVpevttchsrsaitVDYIFYSAekdDTARgpgaEVALVGGLKLlarlslltEQDLWTVNGLPNEHNSSDHLPLLAKF 296
Cdd:cd09097   276 fKGV-------------IDYIFYSA---DTLS----VLGLLGPPDE--------DWYLNKVVGLPNPHFPSDHIALLAEF 327


                  ..
gi 1958672650 297 RL 298
Cdd:cd09097   328 RI 329
 
Name Accession Description Interval E-value
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 8-298 1.88e-36

C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the C-terminal catalytic domain of the deadenylases, Saccharomyces cerevisiae Ccr4p and two vertebrate homologs (CCR4a and CCR4b), and related domains. CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1 (called Pop2 in yeast), is a DEDD-type protein and does not belong in this superfamily. Saccharomyces cerevisiae CCR4 (or Ccr4p) is a 3'-5' poly(A) RNA and ssDNA exonuclease. It is the catalytic subunit of the yeast mRNA deadenylase (Ccr4p/Pop2p/Not complex). This complex participates in various ways in mRNA metabolism, including transcription initiation and elongation, and mRNA degradation. Ccr4p degrades both poly(A) and single-stranded DNA. There are two vertebrate homologs of Ccr4p, CCR4a (also called CCR4-NOT transcription complex subunit 6 or CNOT6) and CCR4b (also called CNOT6-like or CNOT6L), which independently associate with other components to form distinct CCR4-NOT multisubunit complexes. The nuclease domain of CNOT6 and CNOT6L exhibits Mg2+-dependent deadenylase activity, with specificity for poly (A) RNA as substrate. CCR4a is a component of P-bodies and is necessary for foci formation. CCR4b regulates p27/Kip1 mRNA levels, thereby influencing cell cycle progression. They both contribute to the prevention of cell death by regulating insulin-like growth factor-binding protein 5.


Pssm-ID: 197331 [Multi-domain]  Cd Length: 329  Bit Score: 132.81  E-value: 1.88e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650   8 DGCAICFKHSKFSLLSVNPVEF----CRRDIP---------LLDRDNIGLVLLLQPKIPRAASPS---ICIANTHLLYNP 71
Cdd:cd09097    91 DGCAIFFKTSKFKLVEKHLIEFnqlaMANADAegsedmlnrVMTKDNIALIVVLEARETSYEGNKgqlLIVANTHIHWDP 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650  72 RRGDIKLTQLAMLLAEISNVAHQ------KDGSFCPIVMCGDFNSVPGSPLYSFikegklnyegLAIGKVSGQEqssrgq 145
Cdd:cd09097   171 EFSDVKLVQTMMLLEELEKIAEKfsrypyEDSADIPLVVCGDFNSLPDSGVYEL----------LSNGSVSPNH------ 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 146 rilsipiwpPNLGISQNCVYEAqqvpkvektdsdvtqaqqekaevpvpadkvSSHLQHGFSLSSVYSH--------YVPD 217
Cdd:cd09097   235 ---------PDFKEDPYGEYLT------------------------------ASGLTHSFKLKSAYANlgelpftnYTPD 275

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 218 -TGVpevttchsrsaitVDYIFYSAekdDTARgpgaEVALVGGLKLlarlslltEQDLWTVNGLPNEHNSSDHLPLLAKF 296
Cdd:cd09097   276 fKGV-------------IDYIFYSA---DTLS----VLGLLGPPDE--------DWYLNKVVGLPNPHFPSDHIALLAEF 327


                  ..
gi 1958672650 297 RL 298
Cdd:cd09097   328 RI 329
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 8-297 1.85e-26

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 109.05  E-value: 1.85e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650   8 DGCAICFKHSKFSLLSVNPVEFCRRDIPLLD----------------RDNIGLVLLLQPKI-PRAASPS-----ICIANT 65
Cdd:PLN03144  345 DGCATFFRRDRFSLVKKYEVEFNKAAQSLTEalipsaqkkaalnrllKDNVALIVVLEAKFgNQGADNGgkrqlLCVANT 424

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650  66 HLLYNPRRGDIKLTQLAMLLAEISNVAHQKDgsfCPIVMCGDFNSVPGSPLYSFikegklnyegLAIGKVSGQEqssrgq 145
Cdd:PLN03144  425 HIHANQELKDVKLWQVHTLLKGLEKIAASAD---IPMLVCGDFNSVPGSAPHCL----------LATGKVDPLH------ 485

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 146 rilsipiwpPNLGISqncvyeaqqvpkvektdsdvtqaqqekaevPVPADKVSSHLQHGFSLSSVYSHYV---------- 215
Cdd:PLN03144  486 ---------PDLAVD------------------------------PLGILRPASKLTHQLPLVSAYSSFArmpgsgsgle 526

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 216 -------PDTGVPEVTTChSRSAI-TVDYIFYSAekddTARGPGAEVALVgglkllarlsllTEQDLWTVNGLPNEHNSS 287
Cdd:PLN03144  527 qqrrrmdPATNEPLFTNC-TRDFIgTLDYIFYTA----DSLTVESLLELL------------DEESLRKDTALPSPEWSS 589

                         330
                  ....*....|
gi 1958672650 288 DHLPLLAKFR 297
Cdd:PLN03144  590 DHIALLAEFR 599
CCR4 COG5239
mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];
39-296 9.14e-09

mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];


Pssm-ID: 227564 [Multi-domain]  Cd Length: 378  Bit Score: 55.93  E-value: 9.14e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650  39 RDNIGLVLLLQpkipRAASPSIC---IANTHLLYNP--RRGDIKLTQLAmllaeiSNVAHQKDGSFCPIVMCGDFNSVPG 113
Cdd:COG5239   120 TKVDGCAIFLK----RFIDSSKLgliLAVTHLFWHPygYYERFRQTYIL------LNRIGEKDNIAWVCLFVGLFNKEPG 189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 114 SPLYSFIKEGKLNYEGLA------------IGKVSGQE-------QSSRGQRILSIPIWP-PNLGISQNcVYEAQQVPKV 173
Cdd:COG5239   190 DTPYVANTHLPWDPKYRDvkliqcsllyreLKKVLKEElnddkeeGDIKSYPEVDILITGdFNSLRASL-VYKFLVTSQI 268

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 174 EKTDSDVTQAQQEKAevpvpadkVSSHLQHGFSLSSVYSHyvpdtGVPEVTTCHSRSAITVDYIFYSAEKDDTARGPGAE 253
Cdd:COG5239   269 QLHESLNGRDFSLYS--------VGYKFVHPENLKSDNSK-----GELGFTNWTPGFKGVIDYIFYHGGLLTRQTGLLGV 335

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1958672650 254 ValvgglkllarlsllteQDLWTVN--GLPNEHNSSDHLPLLAKF 296
Cdd:COG5239   336 V-----------------EGEYASKviGLPNMPFPSDHIPLLAEF 363
 
Name Accession Description Interval E-value
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 8-298 1.88e-36

C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the C-terminal catalytic domain of the deadenylases, Saccharomyces cerevisiae Ccr4p and two vertebrate homologs (CCR4a and CCR4b), and related domains. CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1 (called Pop2 in yeast), is a DEDD-type protein and does not belong in this superfamily. Saccharomyces cerevisiae CCR4 (or Ccr4p) is a 3'-5' poly(A) RNA and ssDNA exonuclease. It is the catalytic subunit of the yeast mRNA deadenylase (Ccr4p/Pop2p/Not complex). This complex participates in various ways in mRNA metabolism, including transcription initiation and elongation, and mRNA degradation. Ccr4p degrades both poly(A) and single-stranded DNA. There are two vertebrate homologs of Ccr4p, CCR4a (also called CCR4-NOT transcription complex subunit 6 or CNOT6) and CCR4b (also called CNOT6-like or CNOT6L), which independently associate with other components to form distinct CCR4-NOT multisubunit complexes. The nuclease domain of CNOT6 and CNOT6L exhibits Mg2+-dependent deadenylase activity, with specificity for poly (A) RNA as substrate. CCR4a is a component of P-bodies and is necessary for foci formation. CCR4b regulates p27/Kip1 mRNA levels, thereby influencing cell cycle progression. They both contribute to the prevention of cell death by regulating insulin-like growth factor-binding protein 5.


Pssm-ID: 197331 [Multi-domain]  Cd Length: 329  Bit Score: 132.81  E-value: 1.88e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650   8 DGCAICFKHSKFSLLSVNPVEF----CRRDIP---------LLDRDNIGLVLLLQPKIPRAASPS---ICIANTHLLYNP 71
Cdd:cd09097    91 DGCAIFFKTSKFKLVEKHLIEFnqlaMANADAegsedmlnrVMTKDNIALIVVLEARETSYEGNKgqlLIVANTHIHWDP 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650  72 RRGDIKLTQLAMLLAEISNVAHQ------KDGSFCPIVMCGDFNSVPGSPLYSFikegklnyegLAIGKVSGQEqssrgq 145
Cdd:cd09097   171 EFSDVKLVQTMMLLEELEKIAEKfsrypyEDSADIPLVVCGDFNSLPDSGVYEL----------LSNGSVSPNH------ 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 146 rilsipiwpPNLGISQNCVYEAqqvpkvektdsdvtqaqqekaevpvpadkvSSHLQHGFSLSSVYSH--------YVPD 217
Cdd:cd09097   235 ---------PDFKEDPYGEYLT------------------------------ASGLTHSFKLKSAYANlgelpftnYTPD 275

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 218 -TGVpevttchsrsaitVDYIFYSAekdDTARgpgaEVALVGGLKLlarlslltEQDLWTVNGLPNEHNSSDHLPLLAKF 296
Cdd:cd09097   276 fKGV-------------IDYIFYSA---DTLS----VLGLLGPPDE--------DWYLNKVVGLPNPHFPSDHIALLAEF 327


                  ..
gi 1958672650 297 RL 298
Cdd:cd09097   328 RI 329
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 8-297 1.85e-26

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 109.05  E-value: 1.85e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650   8 DGCAICFKHSKFSLLSVNPVEFCRRDIPLLD----------------RDNIGLVLLLQPKI-PRAASPS-----ICIANT 65
Cdd:PLN03144  345 DGCATFFRRDRFSLVKKYEVEFNKAAQSLTEalipsaqkkaalnrllKDNVALIVVLEAKFgNQGADNGgkrqlLCVANT 424

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650  66 HLLYNPRRGDIKLTQLAMLLAEISNVAHQKDgsfCPIVMCGDFNSVPGSPLYSFikegklnyegLAIGKVSGQEqssrgq 145
Cdd:PLN03144  425 HIHANQELKDVKLWQVHTLLKGLEKIAASAD---IPMLVCGDFNSVPGSAPHCL----------LATGKVDPLH------ 485

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 146 rilsipiwpPNLGISqncvyeaqqvpkvektdsdvtqaqqekaevPVPADKVSSHLQHGFSLSSVYSHYV---------- 215
Cdd:PLN03144  486 ---------PDLAVD------------------------------PLGILRPASKLTHQLPLVSAYSSFArmpgsgsgle 526

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 216 -------PDTGVPEVTTChSRSAI-TVDYIFYSAekddTARGPGAEVALVgglkllarlsllTEQDLWTVNGLPNEHNSS 287
Cdd:PLN03144  527 qqrrrmdPATNEPLFTNC-TRDFIgTLDYIFYTA----DSLTVESLLELL------------DEESLRKDTALPSPEWSS 589

                         330
                  ....*....|
gi 1958672650 288 DHLPLLAKFR 297
Cdd:PLN03144  590 DHIALLAEFR 599
Deadenylase_CCR4b cd10312
C-terminal deadenylase domain of CCR4b, also known as CCR4-NOT transcription complex subunit ...
 8-298 4.40e-17

C-terminal deadenylase domain of CCR4b, also known as CCR4-NOT transcription complex subunit 6-like; This subfamily contains the C-terminal catalytic domain of the deadenylase, CCR4b, also known as CCR4-NOT transcription complex subunit 6-like (CNOT6L). CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1, is a DEDD-type protein and does not belong in this superfamily. There are two vertebrate CCR4 proteins, CCR4a (also called CCR4-NOT transcription complex subunit 6 or CNOT6) and CCR4b. CCR4b associates with other components, such as CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit complex, which regulates transcription and mRNA degradation. The nuclease domain of CCR4b exhibits Mg2+-dependent deadenylase activity with strict specificity for poly (A) RNA as substrate. CCR4b is mainly localized in the cytoplasm. It regulates cell growth and influences cell cycle progression by regulating p27/Kip1 mRNA levels. It contributes to the prevention of cell death by regulating insulin-like growth factor-binding protein 5.


Pssm-ID: 197339  Cd Length: 348  Bit Score: 80.45  E-value: 4.40e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650   8 DGCAICFKHSKFSLLSVNPVEFCRRDIP-------LLDR----DNIGLVLLLQPK----------IPRAASPSICIANTH 66
Cdd:cd10312    91 DGCAIFFKTEKFSLVQKHTVEFNQVAMAnsegseaMLNRvmtkDNIGVAVVLEVHkelfgagmkpIHAADKQLLIVANAH 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650  67 LLYNPRRGDIKLTQLAMLLAEISNVAHQ---------KDGSFCPIVMCGDFNSVPGSplysfikeGKLNYegLAIGKVSG 137
Cdd:cd10312   171 MHWDPEYSDVKLIQTMMFVSELKNILEKassrpgsptADPNSIPLVLCADLNSLPDS--------GVVEY--LSNGGVAD 240

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 138 QEQSSRGQRIlsipiwppnlgisQNCVYEAQQVPKVEKTDSDVTqaqqekaevpvpadkvsshlqHGFSLSSVYSHYVpd 217
Cdd:cd10312   241 NHKDFKELRY-------------NECLMNFSCNGKNGSSEGRIT---------------------HGFQLKSAYENNL-- 284

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 218 tgVPEVTTCHSRSAItVDYIFYSAEKDDT--ARGPGAEVALVGGlkllarlsllteqdlwTVNGLPNEHNSSDHLPLLAK 295
Cdd:cd10312   285 --MPYTNYTFDFKGV-IDYIFYSKTHMNVlgVLGPLDPQWLVEN----------------NITGCPHPHIPSDHFSLLTQ 345


                  ...
gi 1958672650 296 FRL 298
Cdd:cd10312   346 LEL 348
Deadenylase_CCR4a cd10313
C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6; ...
 8-123 1.07e-14

C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6; This subfamily contains the C-terminal catalytic domain of the deadenylase, CCR4a, also known as CCR4-NOT transcription complex subunit 6 (CNOT6). CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1, is a DEDD-type protein and does not belong in this superfamily. There are two vertebrate CCR4 proteins, CCR4a and CCR4b (also called CNOT6-like or CNOT6L). CCR4a associates with other components, such as CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit complex, which regulates transcription and mRNA degradation. The nuclease domain of CCR4a exhibits Mg2+-dependent deadenylase activity with specificity for poly (A) RNA as substrate. CCR4a is a component of P-bodies and is necessary for foci formation of various P-body components. It also plays a role in cellular responses to DNA damage, by regulating Chk2 activity.


Pssm-ID: 197340  Cd Length: 350  Bit Score: 73.54  E-value: 1.07e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650   8 DGCAICFKHSKFSLLSVNPVEFCRRDIP-----------LLDRDNIGLVLLLQPKIPRAASPS-----------ICIANT 65
Cdd:cd10313    91 DGCAIFFKTEKFTLVQKHTVEFNQLAMAnsegseamlnrVMTKDNIGVAVLLELRKELIEMSSgkphlgmekqlILVANA 170

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958672650  66 HLLYNPRRGDIKLTQLAMLLAEISNVAHQKDGSF----------CPIVMCGDFNSVPGSPLYSFIKEG 123
Cdd:cd10313   171 HMHWDPEYSDVKLVQTMMFLSEVKNIIDKASRSLkssvlgetgtIPLVLCADLNSLPDSGVVEYLSTG 238
Deadenylase_nocturnin cd09096
C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the ...
 7-126 1.02e-11

C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the C-terminal catalytic domain of the deadenylase, nocturnin, and related domains. Nocturnin is a poly(A)-specific 3' exonuclease that specifically degrades the 3' poly(A) tail of RNA in a process known as deadenylation. This nuclease activity is manganese dependent. Nocturnin is expressed in the cytoplasm of Xenopus laevis retinal photoreceptor cells in a rhythmic fashion, and it has been proposed that it participates in posttranscriptional regulation of the circadian clock or its outputs, and that the mRNA target(s) of this deadenylase are circadian clock-related. In mouse, the nocturnin gene, mNoc, is expressed in a circadian pattern in a range of tissues including retina, spleen, heart, kidney, and liver. It is highly expressed in bone-marrow stromal cells, adipocytes and hepatocytes. In mammals, nocturnin plays a role in regulating mesenchymal stem-cell lineage allocation, perhaps through regulating PPAR-gamma (peroxisome proliferator-activated receptor-gamma) nuclear translocation. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197330 [Multi-domain]  Cd Length: 280  Bit Score: 63.98  E-value: 1.02e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650   7 PDGCAICFKHSKFSLLSVnpvEFCRRDIPLLDRDNIGLVLLLQPKiprAASPSICIANTHLlyNPRRG--DIKLTQLAML 84
Cdd:cd09096    90 PDGCALFFRKDRFELVNT---EKIRLSAMTLKTNQVAIACTLRCK---ETGREICLAVTHL--KARTGweRLRSEQGKDL 161

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1958672650  85 LAEISNVAHQKdgsFCPIVMCGDFNSVPGSPLYSFIKEGKLN 126
Cdd:cd09096   162 LQNLQSFIEGA---KIPLIICGDFNAEPTEPVYKTFSNSSLN 200
CCR4 COG5239
mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];
39-296 9.14e-09

mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];


Pssm-ID: 227564 [Multi-domain]  Cd Length: 378  Bit Score: 55.93  E-value: 9.14e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650  39 RDNIGLVLLLQpkipRAASPSIC---IANTHLLYNP--RRGDIKLTQLAmllaeiSNVAHQKDGSFCPIVMCGDFNSVPG 113
Cdd:COG5239   120 TKVDGCAIFLK----RFIDSSKLgliLAVTHLFWHPygYYERFRQTYIL------LNRIGEKDNIAWVCLFVGLFNKEPG 189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 114 SPLYSFIKEGKLNYEGLA------------IGKVSGQE-------QSSRGQRILSIPIWP-PNLGISQNcVYEAQQVPKV 173
Cdd:COG5239   190 DTPYVANTHLPWDPKYRDvkliqcsllyreLKKVLKEElnddkeeGDIKSYPEVDILITGdFNSLRASL-VYKFLVTSQI 268

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650 174 EKTDSDVTQAQQEKAevpvpadkVSSHLQHGFSLSSVYSHyvpdtGVPEVTTCHSRSAITVDYIFYSAEKDDTARGPGAE 253
Cdd:COG5239   269 QLHESLNGRDFSLYS--------VGYKFVHPENLKSDNSK-----GELGFTNWTPGFKGVIDYIFYHGGLLTRQTGLLGV 335

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1958672650 254 ValvgglkllarlsllteQDLWTVN--GLPNEHNSSDHLPLLAKF 296
Cdd:COG5239   336 V-----------------EGEYASKviGLPNMPFPSDHIPLLAEF 363
Deadenylase cd09082
C-terminal deadenylase domain of CCR4, nocturnin, and related domains; This family contains ...
 7-126 2.21e-04

C-terminal deadenylase domain of CCR4, nocturnin, and related domains; This family contains the C-terminal catalytic domains of the deadenylases, CCR4 and nocturnin, and related domains. Nocturnin is a poly(A)-specific 3' exonuclease that specifically degrades the 3' poly(A) tail of RNA in a process known as deadenylation. This nuclease activity is manganese dependent. Nocturnin is expressed in the cytoplasm of the Xenopus laevis retinal photoreceptor cells in a rhythmic fashion, and it has been proposed that it participates in posttranscriptional regulation of the circadian clock or its outputs, and that the mRNA target(s) of this deadenylase are circadian clock-related. Saccharomyces cerevisiae CCR4p is a 3'-5' poly(A) RNA and ssDNA exonuclease. It is the catalytic subunit of the yeast mRNA deadenylase (Ccr4p/Pop2p/Not complex). This complex participates in various ways in mRNA metabolism, including transcription initiation and elongation, and mRNA degradation. The deadenylase activities of Ccr4p and nocturnin differ: nocturnin degrades poly(A), Ccr4p degrades both poly(A) and single-stranded DNA, and in contrast to Ccr4p, nocturnin appears to function in a highly processive manner. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197316 [Multi-domain]  Cd Length: 348  Bit Score: 42.34  E-value: 2.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650   7 PDGCAICFKHSKFSLLSVNPVEFCRRDIPL------------LDRDNIGLVLLLQ---------PKIPRAASPSICIANT 65
Cdd:cd09082    90 VDGCAIFFKTEKFTLVQKHTVEFNQVAMANsdgseamlnrvmTKDNIGVAVVLEVhkelfgagmKPIHAADKQLLIVANA 169

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650  66 HLLYNPRRGDIKLTQLAMLLAEISNVAH---------QKDGSFCPIVMCGDFNSVPGSPLYSFIKEGKLN 126
Cdd:cd09082   170 HMHWDPEYSDVKLIQTMMFVSEVKNILEkassrpgspTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVA 239
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 59-125 4.80e-04

Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.


Pssm-ID: 197317 [Multi-domain]  Cd Length: 252  Bit Score: 40.66  E-value: 4.80e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958672650  59 SICIANTHLLYnprRGDI-KLTQLAMLLAEISNVAHQkdgsfCPIVMCGDFNSVPGSPLYSFIKEGKL 125
Cdd:cd09083   127 EFYVFNTHLDH---VGEEaREESAKLILERIKEIAGD-----LPVILTGDFNAEPDSEPYKTLTSGGL 186
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 60-110 9.47e-04

Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only];


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 39.12  E-value: 9.47e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958672650  60 ICIANTHLLYNPRRgdIKLTQLAMLLAEISNVAHQkdgsfCPIVMCGDFNS 110
Cdd:COG3568    85 LRVVNTHLDLRSAA--ARRRQARALAELLAELPAG-----APVILAGDFND 128
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 8-114 2.11e-03

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


Pssm-ID: 197306 [Multi-domain]  Cd Length: 241  Bit Score: 39.00  E-value: 2.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958672650   8 DGCAICFKHSKFSLLSVNPVEFCRRDipllDRDNIGLVLllqpKIPRAASpSICIANTHLLYNPRRGDIKLTQLAMLLAE 87
Cdd:cd08372    67 EGVAILSKTPKFKIVEKHQYKFGEGD----SGERRAVVV----KFDVHDK-ELCVVNAHLQAGGTRADVRDAQLKEVLEF 137

                          90       100
                  ....*....|....*....|....*..
gi 1958672650  88 ISNVAHQKDGsfcPIVMCGDFNSVPGS 114
Cdd:cd08372   138 LKRLRQPNSA---PVVICGDFNVRPSE 161
 
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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