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Conserved domains on  [gi|966922006|ref|XP_014972567|]
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protein angel homolog 2 isoform X3 [Macaca mulatta]

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 ...
 43-416 1.86e-59

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: 196.76  E-value: 1.86e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  43 VMSYNILSQdlLEDNSHLYRHCRRPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGYHCEYKMRTG 122
Cdd:cd09097    1 VMCYNVLCD--KYATRQQYGYCPSWALNWDYRKQNILKEILSYNADILCLQEVETDQYEDFFLPELKQHGYDGVFKPKSR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 123 RKP---------DGCAICFKHSKFSLLSVNPVEFF-----RPDIS--------LLDRDNVGLVLLLQPKIACAASPA--- 177
Cdd:cd09097   79 AKTmseaerkhvDGCAIFFKTSKFKLVEKHLIEFNqlamaNADAEgsedmlnrVMTKDNIALIVVLEARETSYEGNKgql 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 178 ICVANTHLLYNPRRGDIKLTQLAMLLAEISSVAHQ------KDGSFCPIVMCGDFNSVPGSPLYSFIKEGKLnyeglpig 251
Cdd:cd09097  159 LIVANTHIHWDPEFSDVKLVQTMMLLEELEKIAEKfsrypyEDSADIPLVVCGDFNSLPDSGVYELLSNGSV-------- 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 252 kvsgqeqssrgqrilsipiwPPNLgisqncvyevqqvpkvektdSDLTQTQLKqteVLVTAEKLSsnlqHHFSLSSVYSH 331
Cdd:cd09097  231 --------------------SPNH--------------------PDFKEDPYG---EYLTASGLT----HSFKLKSAYAN 263

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 332 yfpdTGIPEVTTCHSRSAITVDYIFYSAEKEDVAGHPGaevalvgglkllarlSLLTEQDLWTVNGLPNENNSSDHLPLL 411
Cdd:cd09097  264 ----LGELPFTNYTPDFKGVIDYIFYSADTLSVLGLLG---------------PPDEDWYLNKVVGLPNPHFPSDHIALL 324


                 ....*
gi 966922006 412 AKFRL 416
Cdd:cd09097  325 AEFRI 329
ANGEL2_N super family cl44769
Protein angel homolog 2 N-terminal; This family represents the N-terminal unstructured domain ...
 3-33 2.92e-08

Protein angel homolog 2 N-terminal; This family represents the N-terminal unstructured domain of the protein angel homolog 2 (ANGEL2). This protein is a member of the CCR4 nocturin family and 2',3'-cyclic phosphatase activity involved in RNA processing and modification.


The actual alignment was detected with superfamily member pfam19339:

Pssm-ID: 466047  Cd Length: 172  Bit Score: 53.01  E-value: 2.92e-08
                          10        20        30
                  ....*....|....*....|....*....|.
gi 966922006    3 GVIKRNWEYICSHDKeKTKILGDKNVDPKCE 33
Cdd:pfam19339 143 GTIKRHWEYFCQHSK-TMKILEDKETDQSNT 172
 
Name Accession Description Interval E-value
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 43-416 1.86e-59

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: 196.76  E-value: 1.86e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  43 VMSYNILSQdlLEDNSHLYRHCRRPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGYHCEYKMRTG 122
Cdd:cd09097    1 VMCYNVLCD--KYATRQQYGYCPSWALNWDYRKQNILKEILSYNADILCLQEVETDQYEDFFLPELKQHGYDGVFKPKSR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 123 RKP---------DGCAICFKHSKFSLLSVNPVEFF-----RPDIS--------LLDRDNVGLVLLLQPKIACAASPA--- 177
Cdd:cd09097   79 AKTmseaerkhvDGCAIFFKTSKFKLVEKHLIEFNqlamaNADAEgsedmlnrVMTKDNIALIVVLEARETSYEGNKgql 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 178 ICVANTHLLYNPRRGDIKLTQLAMLLAEISSVAHQ------KDGSFCPIVMCGDFNSVPGSPLYSFIKEGKLnyeglpig 251
Cdd:cd09097  159 LIVANTHIHWDPEFSDVKLVQTMMLLEELEKIAEKfsrypyEDSADIPLVVCGDFNSLPDSGVYELLSNGSV-------- 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 252 kvsgqeqssrgqrilsipiwPPNLgisqncvyevqqvpkvektdSDLTQTQLKqteVLVTAEKLSsnlqHHFSLSSVYSH 331
Cdd:cd09097  231 --------------------SPNH--------------------PDFKEDPYG---EYLTASGLT----HSFKLKSAYAN 263

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 332 yfpdTGIPEVTTCHSRSAITVDYIFYSAEKEDVAGHPGaevalvgglkllarlSLLTEQDLWTVNGLPNENNSSDHLPLL 411
Cdd:cd09097  264 ----LGELPFTNYTPDFKGVIDYIFYSADTLSVLGLLG---------------PPDEDWYLNKVVGLPNPHFPSDHIALL 324


                 ....*
gi 966922006 412 AKFRL 416
Cdd:cd09097  325 AEFRI 329
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 41-415 2.60e-53

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 187.24  E-value: 2.60e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  41 FSVMSYNILSqDLLEdNSHLYRHCRRPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGYHCEYKMR 120
Cdd:PLN03144 255 FTVLSYNILS-DLYA-TSDMYSYCPPWALSWTYRRQNLLREIVGYRADILCLQEVQSDHFEEFFAPELDKHGYQALYKKK 332

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 121 TGR-------KPDGCAICFKHSKFSLLSVNPVEFFRPDISLLD----------------RDNVGLVLLLQPKIACAASPA 177
Cdd:PLN03144 333 TTEvytgntyVIDGCATFFRRDRFSLVKKYEVEFNKAAQSLTEalipsaqkkaalnrllKDNVALIVVLEAKFGNQGADN 412

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 178 ------ICVANTHLLYNPRRGDIKLTQLAMLLAEISSVAHQKDgsfCPIVMCGDFNSVPGSPLYSFIKEGklnyeglpig 251
Cdd:PLN03144 413 ggkrqlLCVANTHIHANQELKDVKLWQVHTLLKGLEKIAASAD---IPMLVCGDFNSVPGSAPHCLLATG---------- 479

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 252 kvsgqeqssrgqrilsipiwppnlgisqncvyevqqvpKVEKTDSDLTQTQLKqteVLvtaeKLSSNLQHHFSLSSVYSH 331
Cdd:PLN03144 480 --------------------------------------KVDPLHPDLAVDPLG---IL----RPASKLTHQLPLVSAYSS 514

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 332 YF-----------------PDTGIPEVTTChSRSAI-TVDYIFYSAEKEDVAGhpgaevalvgglkllaRLSLLTEQDLW 393
Cdd:PLN03144 515 FArmpgsgsgleqqrrrmdPATNEPLFTNC-TRDFIgTLDYIFYTADSLTVES----------------LLELLDEESLR 577

                        410       420
                 ....*....|....*....|..
gi 966922006 394 TVNGLPNENNSSDHLPLLAKFR 415
Cdd:PLN03144 578 KDTALPSPEWSSDHIALLAEFR 599
CCR4 COG5239
mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];
34-414 1.98e-28

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


Pssm-ID: 227564 [Multi-domain]  Cd Length: 378  Bit Score: 114.87  E-value: 1.98e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  34 DSENKFDFSVMSYNILSQDLLedNSHLYRHCRrPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGY 113
Cdd:COG5239   24 YAEKDTDFTIMTYNVLAQTYA--TRKMYPYSG-WALKWSYRSRLLLQELLYYNADILCLQEVDAEDFEDFWKDQLGKLGY 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 114 HCEYKMRTG----------RKPDGCAICFK----HSKFSLLSVNPVEFFRPDISLLD-RDNVGLVLLLQPKIACAASPAI 178
Cdd:COG5239  101 DGIFIPKERkvkwmidydtTKVDGCAIFLKrfidSSKLGLILAVTHLFWHPYGYYERfRQTYILLNRIGEKDNIAWVCLF 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 179 C------------VANTHLLYNPRRGDIKLTQLAMLLAEISSVAHQK---DGSFC--------PIVMCGDFNSVPGSPLY 235
Cdd:COG5239  181 VglfnkepgdtpyVANTHLPWDPKYRDVKLIQCSLLYRELKKVLKEElndDKEEGdiksypevDILITGDFNSLRASLVY 260

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 236 SFIkegklnyeglpigkVSGQEQSSRGQRILSIPIWPPNLGISQNCVYEvqqvpkvektdsdltqtqlkqtevlvtaekl 315
Cdd:COG5239  261 KFL--------------VTSQIQLHESLNGRDFSLYSVGYKFVHPENLK------------------------------- 295

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 316 SSNLQHHFSLSSvYSHYFpdTGIpevttchsrsaitVDYIFYSaekedvaGHPGAEVALVGGLKllarlsllteQDLWTV 395
Cdd:COG5239  296 SDNSKGELGFTN-WTPGF--KGV-------------IDYIFYH-------GGLLTRQTGLLGVV----------EGEYAS 342

                        410       420
                 ....*....|....*....|.
gi 966922006 396 N--GLPNENNSSDHLPLLAKF 414
Cdd:COG5239  343 KviGLPNMPFPSDHIPLLAEF 363
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 44-228 2.38e-13

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 68.02  E-value: 2.38e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006   44 MSYNILSQdllednshlyrhcRRPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGYHCEYKMRTGR 123
Cdd:pfam03372   1 LTWNVNGG-------------NADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  124 KPDGCAICFKHSKFSLLSVNPVEFFRPDISLLDRDNVGLVLllqpkiaCAASPAICVANTHLLYNPRRGDIKLTQLAMLL 203
Cdd:pfam03372  68 GGGGVAILSRYPLSSVILVDLGEFGDPALRGAIAPFAGVLV-------VPLVLTLAPHASPRLARDEQRADLLLLLLALL 140

                         170       180
                  ....*....|....*....|....*
gi 966922006  204 AEISSvahqkdgsfcPIVMCGDFNS 228
Cdd:pfam03372 141 APRSE----------PVILAGDFNA 155
ANGEL2_N pfam19339
Protein angel homolog 2 N-terminal; This family represents the N-terminal unstructured domain ...
 3-33 2.92e-08

Protein angel homolog 2 N-terminal; This family represents the N-terminal unstructured domain of the protein angel homolog 2 (ANGEL2). This protein is a member of the CCR4 nocturin family and 2',3'-cyclic phosphatase activity involved in RNA processing and modification.


Pssm-ID: 466047  Cd Length: 172  Bit Score: 53.01  E-value: 2.92e-08
                          10        20        30
                  ....*....|....*....|....*....|.
gi 966922006    3 GVIKRNWEYICSHDKeKTKILGDKNVDPKCE 33
Cdd:pfam19339 143 GTIKRHWEYFCQHSK-TMKILEDKETDQSNT 172
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 78-230 5.64e-05

exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 272954 [Multi-domain]  Cd Length: 254  Bit Score: 44.30  E-value: 5.64e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006   78 ILKEIKHFDADVLCLQE--VQEDHYGAEIRpslESLGYHCEYKMRTGRkpDGCAIcfkHSKFSLLSVnpveffRPDISLL 155
Cdd:TIGR00195  18 GLAWLKENQPDVLCLQEtkVQDEQFPLEPF---HKEGYHVFFSGQKGY--SGVAI---FSKEEPISV------RRGFGVE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 966922006  156 DRDNVGLVLllqpkIACAASpaICVANTHLLYNPRRGDIKLTQLAMLLAEISSVAHQKDGSFCPIVMCGDFNSVP 230
Cdd:TIGR00195  84 EEDAEGRII-----MAEFDS--FLVINGYFPNGSRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAP 151
 
Name Accession Description Interval E-value
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 43-416 1.86e-59

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: 196.76  E-value: 1.86e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  43 VMSYNILSQdlLEDNSHLYRHCRRPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGYHCEYKMRTG 122
Cdd:cd09097    1 VMCYNVLCD--KYATRQQYGYCPSWALNWDYRKQNILKEILSYNADILCLQEVETDQYEDFFLPELKQHGYDGVFKPKSR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 123 RKP---------DGCAICFKHSKFSLLSVNPVEFF-----RPDIS--------LLDRDNVGLVLLLQPKIACAASPA--- 177
Cdd:cd09097   79 AKTmseaerkhvDGCAIFFKTSKFKLVEKHLIEFNqlamaNADAEgsedmlnrVMTKDNIALIVVLEARETSYEGNKgql 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 178 ICVANTHLLYNPRRGDIKLTQLAMLLAEISSVAHQ------KDGSFCPIVMCGDFNSVPGSPLYSFIKEGKLnyeglpig 251
Cdd:cd09097  159 LIVANTHIHWDPEFSDVKLVQTMMLLEELEKIAEKfsrypyEDSADIPLVVCGDFNSLPDSGVYELLSNGSV-------- 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 252 kvsgqeqssrgqrilsipiwPPNLgisqncvyevqqvpkvektdSDLTQTQLKqteVLVTAEKLSsnlqHHFSLSSVYSH 331
Cdd:cd09097  231 --------------------SPNH--------------------PDFKEDPYG---EYLTASGLT----HSFKLKSAYAN 263

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 332 yfpdTGIPEVTTCHSRSAITVDYIFYSAEKEDVAGHPGaevalvgglkllarlSLLTEQDLWTVNGLPNENNSSDHLPLL 411
Cdd:cd09097  264 ----LGELPFTNYTPDFKGVIDYIFYSADTLSVLGLLG---------------PPDEDWYLNKVVGLPNPHFPSDHIALL 324


                 ....*
gi 966922006 412 AKFRL 416
Cdd:cd09097  325 AEFRI 329
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 41-415 2.60e-53

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 187.24  E-value: 2.60e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  41 FSVMSYNILSqDLLEdNSHLYRHCRRPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGYHCEYKMR 120
Cdd:PLN03144 255 FTVLSYNILS-DLYA-TSDMYSYCPPWALSWTYRRQNLLREIVGYRADILCLQEVQSDHFEEFFAPELDKHGYQALYKKK 332

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 121 TGR-------KPDGCAICFKHSKFSLLSVNPVEFFRPDISLLD----------------RDNVGLVLLLQPKIACAASPA 177
Cdd:PLN03144 333 TTEvytgntyVIDGCATFFRRDRFSLVKKYEVEFNKAAQSLTEalipsaqkkaalnrllKDNVALIVVLEAKFGNQGADN 412

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 178 ------ICVANTHLLYNPRRGDIKLTQLAMLLAEISSVAHQKDgsfCPIVMCGDFNSVPGSPLYSFIKEGklnyeglpig 251
Cdd:PLN03144 413 ggkrqlLCVANTHIHANQELKDVKLWQVHTLLKGLEKIAASAD---IPMLVCGDFNSVPGSAPHCLLATG---------- 479

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 252 kvsgqeqssrgqrilsipiwppnlgisqncvyevqqvpKVEKTDSDLTQTQLKqteVLvtaeKLSSNLQHHFSLSSVYSH 331
Cdd:PLN03144 480 --------------------------------------KVDPLHPDLAVDPLG---IL----RPASKLTHQLPLVSAYSS 514

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 332 YF-----------------PDTGIPEVTTChSRSAI-TVDYIFYSAEKEDVAGhpgaevalvgglkllaRLSLLTEQDLW 393
Cdd:PLN03144 515 FArmpgsgsgleqqrrrmdPATNEPLFTNC-TRDFIgTLDYIFYTADSLTVES----------------LLELLDEESLR 577

                        410       420
                 ....*....|....*....|..
gi 966922006 394 TVNGLPNENNSSDHLPLLAKFR 415
Cdd:PLN03144 578 KDTALPSPEWSSDHIALLAEFR 599
Deadenylase_nocturnin cd09096
C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the ...
 43-244 4.63e-30

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: 117.14  E-value: 4.63e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  43 VMSYNILSQDLLEDNSHlYRHCRRPVLHWSFRFPNILKEIKHFDADVLCLQEVqeDHYGAEIRPSLESLGYHCEY----- 117
Cdd:cd09096    2 VMQWNILAQALGEGKDG-FVRCPCEALKWEERKYLILEEILTYDPDILCLQEV--DHYKDTLQPLLSRLGYQGTFfpkpd 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 118 ----KMRTGRKPDGCAICFKHSKFSLLSvnpVEFFRPDISLLDRDNVGLVLLLQPKiacAASPAICVANTHLlyNPRRG- 192
Cdd:cd09096   79 spclYIENNNGPDGCALFFRKDRFELVN---TEKIRLSAMTLKTNQVAIACTLRCK---ETGREICLAVTHL--KARTGw 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 966922006 193 -DIKLTQLAMLLAEISSVAHQKdgsFCPIVMCGDFNSVPGSPLYSFIKEGKLN 244
Cdd:cd09096  151 eRLRSEQGKDLLQNLQSFIEGA---KIPLIICGDFNAEPTEPVYKTFSNSSLN 200
Deadenylase_CCR4b cd10312
C-terminal deadenylase domain of CCR4b, also known as CCR4-NOT transcription complex subunit ...
 43-241 1.08e-29

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: 117.81  E-value: 1.08e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  43 VMSYNILSQDLLedNSHLYRHCRRPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGYHCEYKMRTG 122
Cdd:cd10312    1 VMCYNVLCDKYA--TRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 123 RK---------PDGCAICFKHSKFSLLSVNPVEFFRPDIS-------LLDR----DNVGLVLLLQPK----------IAC 172
Cdd:cd10312   79 AKimseqerkhVDGCAIFFKTEKFSLVQKHTVEFNQVAMAnsegseaMLNRvmtkDNIGVAVVLEVHkelfgagmkpIHA 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 966922006 173 AASPAICVANTHLLYNPRRGDIKLTQLAMLLAEISSVAHQ---------KDGSFCPIVMCGDFNSVPGSPLYSFIKEG 241
Cdd:cd10312  159 ADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSELKNILEKassrpgsptADPNSIPLVLCADLNSLPDSGVVEYLSNG 236
CCR4 COG5239
mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];
34-414 1.98e-28

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


Pssm-ID: 227564 [Multi-domain]  Cd Length: 378  Bit Score: 114.87  E-value: 1.98e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  34 DSENKFDFSVMSYNILSQDLLedNSHLYRHCRrPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGY 113
Cdd:COG5239   24 YAEKDTDFTIMTYNVLAQTYA--TRKMYPYSG-WALKWSYRSRLLLQELLYYNADILCLQEVDAEDFEDFWKDQLGKLGY 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 114 HCEYKMRTG----------RKPDGCAICFK----HSKFSLLSVNPVEFFRPDISLLD-RDNVGLVLLLQPKIACAASPAI 178
Cdd:COG5239  101 DGIFIPKERkvkwmidydtTKVDGCAIFLKrfidSSKLGLILAVTHLFWHPYGYYERfRQTYILLNRIGEKDNIAWVCLF 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 179 C------------VANTHLLYNPRRGDIKLTQLAMLLAEISSVAHQK---DGSFC--------PIVMCGDFNSVPGSPLY 235
Cdd:COG5239  181 VglfnkepgdtpyVANTHLPWDPKYRDVKLIQCSLLYRELKKVLKEElndDKEEGdiksypevDILITGDFNSLRASLVY 260

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 236 SFIkegklnyeglpigkVSGQEQSSRGQRILSIPIWPPNLGISQNCVYEvqqvpkvektdsdltqtqlkqtevlvtaekl 315
Cdd:COG5239  261 KFL--------------VTSQIQLHESLNGRDFSLYSVGYKFVHPENLK------------------------------- 295

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 316 SSNLQHHFSLSSvYSHYFpdTGIpevttchsrsaitVDYIFYSaekedvaGHPGAEVALVGGLKllarlsllteQDLWTV 395
Cdd:COG5239  296 SDNSKGELGFTN-WTPGF--KGV-------------IDYIFYH-------GGLLTRQTGLLGVV----------EGEYAS 342

                        410       420
                 ....*....|....*....|.
gi 966922006 396 N--GLPNENNSSDHLPLLAKF 414
Cdd:COG5239  343 KviGLPNMPFPSDHIPLLAEF 363
Deadenylase_CCR4a cd10313
C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6; ...
 43-241 1.93e-23

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: 100.50  E-value: 1.93e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  43 VMSYNILSQDLLedNSHLYRHCRRPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGYHCEY----K 118
Cdd:cd10313    1 VMCYNVLCDKYA--TRQLYGYCPSWALNWDYRKKAIMQEILSCNADIISLQEVETEQYYSFFLVELKERGYNGFFspksR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 119 MRT-----GRKPDGCAICFKHSKFSLLSVNPVEFFRPDIS-----------LLDRDNVGLVLLLQPKIACAASPA----- 177
Cdd:cd10313   79 ARTmseqeRKHVDGCAIFFKTEKFTLVQKHTVEFNQLAMAnsegseamlnrVMTKDNIGVAVLLELRKELIEMSSgkphl 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 178 ------ICVANTHLLYNPRRGDIKLTQLAMLLAEISSVAHQKDGSF----------CPIVMCGDFNSVPGSPLYSFIKEG 241
Cdd:cd10313  159 gmekqlILVANAHMHWDPEYSDVKLVQTMMFLSEVKNIIDKASRSLkssvlgetgtIPLVLCADLNSLPDSGVVEYLSTG 238
Deadenylase cd09082
C-terminal deadenylase domain of CCR4, nocturnin, and related domains; This family contains ...
 43-244 4.64e-18

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: 84.71  E-value: 4.64e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  43 VMSYNILSQDLLEDNSHLYrhCRRPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGYHCEY----- 117
Cdd:cd09082    1 VMCYNVLCDKYATRQLYGY--CPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFspksr 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 118 ----KMRTGRKPDGCAICFKHSKFSLLS------------VNPVEFFRPDISLLDRDNVGLVLLLQ---------PKIAC 172
Cdd:cd09082   79 akimSEQERKHVDGCAIFFKTEKFTLVQkhtvefnqvamaNSDGSEAMLNRVMTKDNIGVAVVLEVhkelfgagmKPIHA 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 173 AASPAICVANTHLLYNPRRGDIKLTQLAMLLAEISSVAH---------QKDGSFCPIVMCGDFNSVPGSPLYSFIKEGKL 243
Cdd:cd09082  159 ADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEkassrpgspTADPNSIPLVLCADLNSLPDSGVVEYLSNGGV 238


                 .
gi 966922006 244 N 244
Cdd:cd09082  239 A 239
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 44-228 2.38e-13

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 68.02  E-value: 2.38e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006   44 MSYNILSQdllednshlyrhcRRPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGYHCEYKMRTGR 123
Cdd:pfam03372   1 LTWNVNGG-------------NADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  124 KPDGCAICFKHSKFSLLSVNPVEFFRPDISLLDRDNVGLVLllqpkiaCAASPAICVANTHLLYNPRRGDIKLTQLAMLL 203
Cdd:pfam03372  68 GGGGVAILSRYPLSSVILVDLGEFGDPALRGAIAPFAGVLV-------VPLVLTLAPHASPRLARDEQRADLLLLLLALL 140

                         170       180
                  ....*....|....*....|....*
gi 966922006  204 AEISSvahqkdgsfcPIVMCGDFNS 228
Cdd:pfam03372 141 APRSE----------PVILAGDFNA 155
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 42-243 6.22e-13

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: 68.40  E-value: 6.22e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  42 SVMSYNIlSQDLLEDNSHlyrhcrrpvlHWSFRFPNILKEIKHFDADVLCLQEVQeDHYGAEIRPSLEslgyhcEYKM-- 119
Cdd:cd09083    1 RVMTFNI-RYDNPSDGEN----------SWENRKDLVAELIKFYDPDIIGTQEAL-PHQLADLEELLP------EYDWig 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 120 --RTGRKPDG--CAICFKHSKFSLLSVNpvEFFrpdislldrdnvglvLLLQPKIAC-----AASPAIC----------- 179
Cdd:cd09083   63 vgRDDGKEKGefSAIFYRKDRFELLDSG--TFW---------------LSETPDVVGskgwdAALPRICtwarfkdkktg 125

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 966922006 180 ----VANTHLLYnprRGDI-KLTQLAMLLAEISSVAHQkdgsfCPIVMCGDFNSVPGSPLYSFIKEGKL 243
Cdd:cd09083  126 kefyVFNTHLDH---VGEEaREESAKLILERIKEIAGD-----LPVILTGDFNAEPDSEPYKTLTSGGL 186
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 41-227 8.67e-10

Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. 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: 197314 [Multi-domain]  Cd Length: 248  Bit Score: 58.89  E-value: 8.67e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  41 FSVMSYNILSqdlLEDNshlyrhcrRPVLhwsfRFPNILKEIKHFDADVLCLQEVqedhygaeIRPSLESL--------G 112
Cdd:cd09080    1 LKVLTWNVDF---LDDV--------NLAE----RMRAILKLLEELDPDVIFLQEV--------TPPFLAYLlsqpwvrkN 57

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 113 YHC-EYKMRTGRKPDGCAICFKhsKFSLLSVNPVeffrPDISlLDRDnvglvlLLQPKIACAASPAICVANTHLLYNPRR 191
Cdd:cd09080   58 YYFsEGPPSPAVDPYGVLILSK--KSLVVRRVPF----TSTR-MGRN------LLAAEINLGSGEPLRLATTHLESLKSH 124

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 966922006 192 GDIKLTQLAMLLAEISSVAHQKDgsfcpIVMCGDFN 227
Cdd:cd09080  125 SSERTAQLEEIAKKLKKPPGAAN-----VILGGDFN 155
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 40-228 1.53e-09

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 56.46  E-value: 1.53e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  40 DFSVMSYNIlsqdllednshlyRHCRRPvlHWSFRFPNILKEIKHFDADVLCLQEVqedhygaeirpsleslgyhceykm 119
Cdd:COG3568    7 TLRVMTYNI-------------RYGLGT--DGRADLERIARVIRALDPDVVALQEN------------------------ 47

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 120 rtgrkpdgcAIcfkHSKFSLLSVNPVEFFRPDISlldrDNVGLVLLLQpkiacAASPAICVANTHLLYNPRRgdIKLTQL 199
Cdd:COG3568   48 ---------AI---LSRYPIVSSGTFDLPDPGGE----PRGALWADVD-----VPGKPLRVVNTHLDLRSAA--ARRRQA 104

                        170       180
                 ....*....|....*....|....*....
gi 966922006 200 AMLLAEISSVAHQkdgsfCPIVMCGDFNS 228
Cdd:COG3568  105 RALAELLAELPAG-----APVILAGDFND 128
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 43-232 8.98e-09

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: 55.57  E-value: 8.98e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  43 VMSYNIlsqDLLEDNSHLyrhcrrpvlhwsfrfPNILKEIKHFDADVLCLQEVQEDHYGAEIRPSLESLGYHCEYKMRTG 122
Cdd:cd08372    1 VASYNV---NGLNAATRA---------------SGIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGYHQYQSGPSR 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 123 RK-PDGCAICFKHSKFSLLSVNPVEFFRPDISllDRDNVGLVLLLQPKIacaaspaICVANTHLLYNPRRGDIKLTQLAM 201
Cdd:cd08372   63 KEgYEGVAILSKTPKFKIVEKHQYKFGEGDSG--ERRAVVVKFDVHDKE-------LCVVNAHLQAGGTRADVRDAQLKE 133

                        170       180       190
                 ....*....|....*....|....*....|...
gi 966922006 202 LLAEIssvahQKDGSFC--PIVMCGDFNSVPGS 232
Cdd:cd08372  134 VLEFL-----KRLRQPNsaPVVICGDFNVRPSE 161
ANGEL2_N pfam19339
Protein angel homolog 2 N-terminal; This family represents the N-terminal unstructured domain ...
 3-33 2.92e-08

Protein angel homolog 2 N-terminal; This family represents the N-terminal unstructured domain of the protein angel homolog 2 (ANGEL2). This protein is a member of the CCR4 nocturin family and 2',3'-cyclic phosphatase activity involved in RNA processing and modification.


Pssm-ID: 466047  Cd Length: 172  Bit Score: 53.01  E-value: 2.92e-08
                          10        20        30
                  ....*....|....*....|....*....|.
gi 966922006    3 GVIKRNWEYICSHDKeKTKILGDKNVDPKCE 33
Cdd:pfam19339 143 GTIKRHWEYFCQHSK-TMKILEDKETDQSNT 172
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 74-230 5.29e-08

Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and 3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197320 [Multi-domain]  Cd Length: 254  Bit Score: 53.67  E-value: 5.29e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  74 RFPNILKEIKHFDADVLCLQE--VQEDHYGAEIrpsLESLGYHCEYKmrtGRKP-DGCAICfkhSKFSLLSVnpveffrp 150
Cdd:cd09086   14 RLEQVLDWLKEEDPDVLCLQEtkVEDDQFPADA---FEALGYHVAVH---GQKAyNGVAIL---SRLPLEDV-------- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 151 disllDRDNVGLVLLLQPKIACAASPAICVANthlLYNPRRGDI-------KLTQLAMLLAEISSVAHQKDgsfcPIVMC 223
Cdd:cd09086   77 -----RTGFPGDPDDDQARLIAARVGGVRVIN---LYVPNGGDIgspkfayKLDWLDRLIRYLQKLLKPDD----PLVLV 144


                 ....*..
gi 966922006 224 GDFNSVP 230
Cdd:cd09086  145 GDFNIAP 151
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 43-241 2.87e-07

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; 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: 197318 [Multi-domain]  Cd Length: 246  Bit Score: 51.14  E-value: 2.87e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  43 VMSYNIlsqdllednSHLYRHcrrpvlHWSFRFPNILKEIKHFDADVLCLQEV--QEDHYGAEIRPSLESLGYHCeYKMR 120
Cdd:cd09084    1 VMSYNV---------RSFNRY------KWKDDPDKILDFIKKQDPDILCLQEYygSEGDKDDDLRLLLKGYPYYY-VVYK 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 121 TGRKPDGCAIcFkhSKFSLLSVNPVEF-------FRPDIsLLDRDNVGLV-LLLQpkiacaaSPAIcvaNTHLLYNPRRG 192
Cdd:cd09084   65 SDSGGTGLAI-F--SKYPILNSGSIDFpntnnnaIFADI-RVGGDTIRVYnVHLE-------SFRI---TPSDKELYKEE 130

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 193 DIKLTQLAMLL-----------AEISSVAHQKDGSFCPIVMCGDFNSVPGSPLYSFIKEG 241
Cdd:cd09084  131 KKAKELSRNLLrklaeafkrraAQADLLAADIAASPYPVIVCGDFNDTPASYVYRTLKKG 190
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 40-243 1.70e-06

Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily [General function prediction only];


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 49.61  E-value: 1.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  40 DFSVMSYNILSqdlleDNSHLYRhcrrpvlhwsfrfpnILKEIKHFDADVLCLQEVQEDHygaeiRPSLESLGYHCEYKM 119
Cdd:COG3021   94 DLRVLTANVLF-----GNADAEA---------------LAALVREEDPDVLVLQETTPAW-----EEALAALEADYPYRV 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 120 RTGRkPDGCAICFkHSKFSLLSVNPVEFFRPDISLLdrdnvglVLLLQPkiacaASPAICVANTHL---LYNPRRGDIKL 196
Cdd:COG3021  149 LCPL-DNAYGMAL-LSRLPLTEAEVVYLVGDDIPSI-------RATVEL-----PGGPVRLVAVHPappVGGSAERDAEL 214

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 966922006 197 TQLAMLLAEISSvahqkdgsfcPIVMCGDFNSVPGSPLY-SFIKEGKL 243
Cdd:COG3021  215 AALAKAVAALDG----------PVIVAGDFNATPWSPTLrRLLRASGL 252
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 78-230 5.64e-05

exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 272954 [Multi-domain]  Cd Length: 254  Bit Score: 44.30  E-value: 5.64e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006   78 ILKEIKHFDADVLCLQE--VQEDHYGAEIRpslESLGYHCEYKMRTGRkpDGCAIcfkHSKFSLLSVnpveffRPDISLL 155
Cdd:TIGR00195  18 GLAWLKENQPDVLCLQEtkVQDEQFPLEPF---HKEGYHVFFSGQKGY--SGVAI---FSKEEPISV------RRGFGVE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 966922006  156 DRDNVGLVLllqpkIACAASpaICVANTHLLYNPRRGDIKLTQLAMLLAEISSVAHQKDGSFCPIVMCGDFNSVP 230
Cdd:TIGR00195  84 EEDAEGRII-----MAEFDS--FLVINGYFPNGSRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAP 151
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 73-244 8.88e-04

Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. 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: 197310 [Multi-domain]  Cd Length: 236  Bit Score: 40.80  E-value: 8.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  73 FRFPNILKEIKHFDADVLCLQEVqedHYGAEIRPSLESLGYHCEYKMRTGRKPDGCAICFKHS-KFSLLSVNPVEFFRpd 151
Cdd:cd09076   13 GKRAQLLEELKRKKLDILGLQET---HWTGEGELKKKREGGTILYSGSDSGKSRGVAILLSKTaANKLLEYTKVVSGR-- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 152 ISLLDRDNVGLVLLLqpkiacaaspaICVanthllY--NPRRGDIKLTQLAMLLAEISSVAhQKDgsfcPIVMCGDFNSV 229
Cdd:cd09076   88 IIMVRFKIKGKRLTI-----------INV------YapTARDEEEKEEFYDQLQDVLDKVP-RHD----TLIIGGDFNAV 145

                        170
                 ....*....|....*
gi 966922006 230 PGSPLYSFIKEGKLN 244
Cdd:cd09076  146 LGPKDDGRKGLDKRN 160
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
40-233 1.15e-03

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 40.77  E-value: 1.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006  40 DFSVMSYNILS-QDLLEDNSHLYRHCRRPVlhwsfRF----PNILKEIKHFDADVLCLQEVqEDHYGAeirpsLESL--- 111
Cdd:COG2374   68 DLRVATFNVENlFDTDDDDDDFGRGADTPE-----EYerklAKIAAAIAALDADIVGLQEV-ENNGSA-----LQDLvaa 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966922006 112 --------GYHCEYKMRTGRKPDgCAICFKHSKFSLLSVNPVEFFRPDISLLD---RDnvglvlLLQPKIACAASPAICV 180
Cdd:COG2374  137 lnlaggtyAFVHPPDGPDGDGIR-VALLYRPDRVTLVGSATIADLPDSPGNPDrfsRP------PLAVTFELANGEPFTV 209

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 966922006 181 ANTHL-------------LYNPRRgdiklTQLAMLLAE-ISSVAHQKDGSfcPIVMCGDFNSVPGSP 233
Cdd:COG2374  210 IVNHFkskgsddpgdgqgASEAKR-----TAQAEALRAfVDSLLAADPDA--PVIVLGDFNDYPFED 269
XthA COG0708
Exonuclease III [Replication, recombination and repair];
74-117 2.73e-03

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 39.29  E-value: 2.73e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 966922006  74 RFPNILKEIKHFDADVLCLQE--VQEDHYGAEIrpsLESLGYHCEY 117
Cdd:COG0708   14 RLPKLLDWLAEEDPDVLCLQEtkAQDEQFPLEA---FEAAGYHVYF 56
 
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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