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Conserved domains on  [gi|1375569202|gb|AVW17716|]
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endonuclease [Listeria monocytogenes]

Protein Classification

endonuclease/exonuclease/phosphatase family protein( domain architecture ID 10173375)

endonuclease/exonuclease/phosphatase (EEP) family protein is among a diverse set of enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins

CATH:  3.60.10.10
EC:  3.1.-.-
Gene Ontology:  GO:0046872|GO:0016787|GO:0003677
PubMed:  10838565
SCOP:  4002213

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 3-253 2.46e-111

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: 320.70  E-value: 2.46e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202   3 SVTTFNIRFDDTSERKKSWELRKTLTKSLLDKYQWDFMGVEEPLLPQMLDMKAML-DWDYFGVGRDDGFEKGEFTAVFYN 81
Cdd:cd09083     1 RVMTFNIRYDNPSDGENSWENRKDLVAELIKFYDPDIIGTQEALPHQLADLEELLpEYDWIGVGRDDGKEKGEFSAIFYR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  82 STRFTLLQEGHFWLSETPDV-PSIHSTAMFPRICVWGKFADLD-GKQFYIFNTHLDHISEEARLFASQLLLKKAATIAEN 159
Cdd:cd09083    81 KDRFELLDSGTFWLSETPDVvGSKGWDAALPRICTWARFKDKKtGKEFYVFNTHLDHVGEEAREESAKLILERIKEIAGD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 160 SPVIILGDFNTEPDTPTYNFITK-KYQDAQLISQKRAKGPIGSFHDFrplRPINELEKIDYIFVSKEFQVCTYETIVDEV 238
Cdd:cd09083   161 LPVILTGDFNAEPDSEPYKTLTSgGLKDARDTAATTDGGPEGTFHGF---KGPPGGSRIDYIFVSPGVKVLSYEILTDRY 237

                         250
                  ....*....|....*
gi 1375569202 239 DGFSASDHFPVTANL 253
Cdd:cd09083   238 DGRYPSDHFPVVADL 252
 
Name Accession Description Interval E-value
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 3-253 2.46e-111

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: 320.70  E-value: 2.46e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202   3 SVTTFNIRFDDTSERKKSWELRKTLTKSLLDKYQWDFMGVEEPLLPQMLDMKAML-DWDYFGVGRDDGFEKGEFTAVFYN 81
Cdd:cd09083     1 RVMTFNIRYDNPSDGENSWENRKDLVAELIKFYDPDIIGTQEALPHQLADLEELLpEYDWIGVGRDDGKEKGEFSAIFYR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  82 STRFTLLQEGHFWLSETPDV-PSIHSTAMFPRICVWGKFADLD-GKQFYIFNTHLDHISEEARLFASQLLLKKAATIAEN 159
Cdd:cd09083    81 KDRFELLDSGTFWLSETPDVvGSKGWDAALPRICTWARFKDKKtGKEFYVFNTHLDHVGEEAREESAKLILERIKEIAGD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 160 SPVIILGDFNTEPDTPTYNFITK-KYQDAQLISQKRAKGPIGSFHDFrplRPINELEKIDYIFVSKEFQVCTYETIVDEV 238
Cdd:cd09083   161 LPVILTGDFNAEPDSEPYKTLTSgGLKDARDTAATTDGGPEGTFHGF---KGPPGGSRIDYIFVSPGVKVLSYEILTDRY 237

                         250
                  ....*....|....*
gi 1375569202 239 DGFSASDHFPVTANL 253
Cdd:cd09083   238 DGRYPSDHFPVVADL 252
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-256 6.38e-31

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 112.69  E-value: 6.38e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202   1 MFSVTTFNIRFDDTSERKKSWELrktlTKSLLDKYQWDFMGVEEpllpqmldmkamldwdyfgvgrddgfekgefTAVFy 80
Cdd:COG3568     7 TLRVMTYNIRYGLGTDGRADLER----IARVIRALDPDVVALQE-------------------------------NAIL- 50

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  81 nsTRFTLLQEGHFWLSETPDVPsihstamfpRICVWGKFaDLDGKQFYIFNTHLDHISEEARLFASQLLLKKAATIAENS 160
Cdd:COG3568    51 --SRYPIVSSGTFDLPDPGGEP---------RGALWADV-DVPGKPLRVVNTHLDLRSAAARRRQARALAELLAELPAGA 118

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 161 PVIILGDFNTepdtptynfitkkyqdaqlisqkrakgpigsfhdfrplrpinelekIDYIFVSKEFQVCTYEtIVDEVDG 240
Cdd:COG3568   119 PVILAGDFND----------------------------------------------IDYILVSPGLRVLSAE-VLDSPLG 151

                         250
                  ....*....|....*.
gi 1375569202 241 FSASDHFPVTANLDWK 256
Cdd:COG3568   152 RAASDHLPVVADLELP 167
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 6-246 6.09e-09

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: 54.15  E-value: 6.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202   6 TFNIRFDDTSERKksWELRKTLTKSLLDKYQWDFMGVEEPLLP--QMLDMKAMLDWDYFGVGRDDGFEKGEFTAVFYnst 83
Cdd:pfam03372   2 TWNVNGGNADAAG--DDRKLDALAALIRAYDPDVVALQETDDDdaSRLLLALLAYGGFLSYGGPGGGGGGGGVAILS--- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  84 RFTLLQEGHFWLSETPDVPSIHSTAMFPRICVwgkfadldGKQFYIFNTHLDHISEEARLFASQLLLKKAATIAENSPVI 163
Cdd:pfam03372  77 RYPLSSVILVDLGEFGDPALRGAIAPFAGVLV--------VPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVI 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 164 ILGDFNtepdtptynfitkkyqdaqlisqkrakgpigsfhdfrplrpinelekIDYIFVSKEFQVCTYETiVDEVDGFSA 243
Cdd:pfam03372 149 LAGDFN-----------------------------------------------ADYILVSGGLTVLSVGV-LPDLGPRTG 180


                  ...
gi 1375569202 244 SDH 246
Cdd:pfam03372 181 SDH 183
PRK08068 PRK08068
transaminase; Reviewed
 144-228 4.86e-03

transaminase; Reviewed


Pssm-ID: 181219  Cd Length: 389  Bit Score: 37.60  E-value: 4.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 144 FASqLLLKKAATIAENSPVIILGDFNtePDTPTYNFITKKYQDAqlisqkrAKGPigSFHDFRPLRPINELEKIDYIFVS 223
Cdd:PRK08068   17 FAS-LVAKVNKKVAEGHDVINLGQGN--PDQPTPEHIVEALQEA-------AENP--ANHKYSPFRGYPFLKEAAADFYK 84


                  ....*
gi 1375569202 224 KEFQV 228
Cdd:PRK08068   85 REYGV 89
 
Name Accession Description Interval E-value
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 3-253 2.46e-111

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: 320.70  E-value: 2.46e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202   3 SVTTFNIRFDDTSERKKSWELRKTLTKSLLDKYQWDFMGVEEPLLPQMLDMKAML-DWDYFGVGRDDGFEKGEFTAVFYN 81
Cdd:cd09083     1 RVMTFNIRYDNPSDGENSWENRKDLVAELIKFYDPDIIGTQEALPHQLADLEELLpEYDWIGVGRDDGKEKGEFSAIFYR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  82 STRFTLLQEGHFWLSETPDV-PSIHSTAMFPRICVWGKFADLD-GKQFYIFNTHLDHISEEARLFASQLLLKKAATIAEN 159
Cdd:cd09083    81 KDRFELLDSGTFWLSETPDVvGSKGWDAALPRICTWARFKDKKtGKEFYVFNTHLDHVGEEAREESAKLILERIKEIAGD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 160 SPVIILGDFNTEPDTPTYNFITK-KYQDAQLISQKRAKGPIGSFHDFrplRPINELEKIDYIFVSKEFQVCTYETIVDEV 238
Cdd:cd09083   161 LPVILTGDFNAEPDSEPYKTLTSgGLKDARDTAATTDGGPEGTFHGF---KGPPGGSRIDYIFVSPGVKVLSYEILTDRY 237

                         250
                  ....*....|....*
gi 1375569202 239 DGFSASDHFPVTANL 253
Cdd:cd09083   238 DGRYPSDHFPVVADL 252
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-256 6.38e-31

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 112.69  E-value: 6.38e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202   1 MFSVTTFNIRFDDTSERKKSWELrktlTKSLLDKYQWDFMGVEEpllpqmldmkamldwdyfgvgrddgfekgefTAVFy 80
Cdd:COG3568     7 TLRVMTYNIRYGLGTDGRADLER----IARVIRALDPDVVALQE-------------------------------NAIL- 50

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  81 nsTRFTLLQEGHFWLSETPDVPsihstamfpRICVWGKFaDLDGKQFYIFNTHLDHISEEARLFASQLLLKKAATIAENS 160
Cdd:COG3568    51 --SRYPIVSSGTFDLPDPGGEP---------RGALWADV-DVPGKPLRVVNTHLDLRSAAARRRQARALAELLAELPAGA 118

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 161 PVIILGDFNTepdtptynfitkkyqdaqlisqkrakgpigsfhdfrplrpinelekIDYIFVSKEFQVCTYEtIVDEVDG 240
Cdd:COG3568   119 PVILAGDFND----------------------------------------------IDYILVSPGLRVLSAE-VLDSPLG 151

                         250
                  ....*....|....*.
gi 1375569202 241 FSASDHFPVTANLDWK 256
Cdd:COG3568   152 RAASDHLPVVADLELP 167
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 4-253 8.83e-18

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: 79.83  E-value: 8.83e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202   4 VTTFNIRFDDTSERKKSWelrktltKSLLDKYQWDFMGVEEPLLPQMLDMKAMLD----WDYFGVGRDDgFEKGEFTAVF 79
Cdd:cd08372     1 VASYNVNGLNAATRASGI-------ARWVRELDPDIVCLQEVKDSQYSAVALNQLlpegYHQYQSGPSR-KEGYEGVAIL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  80 YNSTRFTLLQEGHFWLSETPDvpsihstamFPRICVWGKFaDLDGKQFYIFNTHLDHIS-------EEARLFASQLLLKK 152
Cdd:cd08372    73 SKTPKFKIVEKHQYKFGEGDS---------GERRAVVVKF-DVHDKELCVVNAHLQAGGtradvrdAQLKEVLEFLKRLR 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 153 aatIAENSPVIILGDFNTEPDTPTYN----FITKKYQdAQLISQKRAKGPIGSFHDFRPLRPinelEKIDYIFVSKEFQ- 227
Cdd:cd08372   143 ---QPNSAPVVICGDFNVRPSEVDSEnpssMLRLFVA-LNLVDSFETLPHAYTFDTYMHNVK----SRLDYIFVSKSLLp 214

                         250       260
                  ....*....|....*....|....*..
gi 1375569202 228 -VCTYETIVDEVDGFSASDHFPVTANL 253
Cdd:cd08372   215 sVKSSKILSDAARARIPSDHYPIEVTL 241
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
76-256 7.19e-16

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 75.83  E-value: 7.19e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  76 TAVFYNSTRFTLL-QEGHFWLSETPDVPSIHStamfpRICVWGKFADLDGKQFYIFNTHL-----------DHISEEARL 143
Cdd:COG2374   160 VALLYRPDRVTLVgSATIADLPDSPGNPDRFS-----RPPLAVTFELANGEPFTVIVNHFkskgsddpgdgQGASEAKRT 234

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 144 FASQLLLKKAATIAE---NSPVIILGDFNTEPDTPTYNFITKKYQDAQLISQKRAKGPiGSFHdFRplrpiNELEKIDYI 220
Cdd:COG2374   235 AQAEALRAFVDSLLAadpDAPVIVLGDFNDYPFEDPLRALLGAGGLTNLAEKLPAAER-YSYV-YD-----GNSGLLDHI 307

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1375569202 221 FVSKEFQvcTYETIVDEV--------------------DGFSASDHFPVTANLDWK 256
Cdd:COG2374   308 LVSPALA--ARVTGADIWhinadiynddfkpdfrtyadDPGRASDHDPVVVGLRLP 361
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 2-256 1.96e-12

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 65.79  E-value: 1.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202   2 FSVTTFNIRFDDTSERKkswelrktlTKSLLDKYQWDFMGVEE---PLLPQMLDMKAMLDWDYFgVGRDDGFEkgefTAV 78
Cdd:COG3021    95 LRVLTANVLFGNADAEA---------LAALVREEDPDVLVLQEttpAWEEALAALEADYPYRVL-CPLDNAYG----MAL 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  79 FynsTRFTLLQEGHFWLSETpDVPSIHSTAmfpricvwgkfaDLDGKQFYIFNTHLDHISEEARLFASQLLLKKAATIAE 158
Cdd:COG3021   161 L---SRLPLTEAEVVYLVGD-DIPSIRATV------------ELPGGPVRLVAVHPAPPVGGSAERDAELAALAKAVAAL 224

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 159 NSPVIILGDFNTEPDTPTYNFITK--KYQDAQlisqkRAKGPIGSFHDFRPLRPINelekIDYIFVSKEFQVCTYETIvd 236
Cdd:COG3021   225 DGPVIVAGDFNATPWSPTLRRLLRasGLRDAR-----AGRGLGPTWPANLPFLRLP----IDHVLVSRGLTVVDVRVL-- 293

                         250       260
                  ....*....|....*....|
gi 1375569202 237 EVDGfsaSDHFPVTANLDWK 256
Cdd:COG3021   294 PVIG---SDHRPLLAELALP 310
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 153-253 1.28e-11

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: 62.70  E-value: 1.28e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 153 AATIAENS-PVIILGDFNTEPDTPTYNFITKKYQDAqliSQKRAKGPIGSFH-DFRPLRpinelekIDYIFVSKEFQVCT 230
Cdd:cd09084   159 AADIAASPyPVIVCGDFNDTPASYVYRTLKKGLTDA---FVEAGSGFGYTFNgLFFPLR-------IDYILTSKGFKVLR 228

                          90       100
                  ....*....|....*....|...
gi 1375569202 231 YETIVDevdgfSASDHFPVTANL 253
Cdd:cd09084   229 YRVDPG-----KYSDHYPIVATL 246
RgfB-like cd09079
Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, ...
 123-253 2.19e-10

Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, and related proteins; This family includes Streptococcus agalactiae RgfB (for regulator of fibrinogen binding) and related proteins. The function of RgfB is unknown. It is part of a putative two component signal transduction system designated rgfBDAC (the rgf locus was identified in a screen for mutants of Streptococcus agalactiae with altered binding to fibrinogen). RgfA,-C,and -D do not belong to this superfamily: rgfA encodes a putative response regulator, and rgfC, a putative histidine kinase. All four genes are co-transcribed, and may be involved in regulating expression of bacterial cell surface components. 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: 197313 [Multi-domain]  Cd Length: 259  Bit Score: 59.20  E-value: 2.19e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 123 DGKQFYIFNTHLDHISEEARLFASQLL-LKKAATIAENsPVIILGDFNTEPDTPTYNFITKKY---QDAQLISQKRAKGP 198
Cdd:cd09079   127 NGQPIDVYSCHLGWWYDEEEPFAYEWSkLEKALAEAGR-PVLLMGDFNNPAGSRGEGYDLISSlglQDTYDLAEEKDGGV 205

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1375569202 199 IGSFH--DFRPlrpiNELEK-IDYIFVSKEFQVCTYETIVDEVDGFSASDHFPVTANL 253
Cdd:cd09079   206 TVEKAidGWRG----NKEAKrIDYIFVNRKVKVKSSRVIFNGKNPPIVSDHFGVEVEL 259
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 6-246 6.09e-09

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: 54.15  E-value: 6.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202   6 TFNIRFDDTSERKksWELRKTLTKSLLDKYQWDFMGVEEPLLP--QMLDMKAMLDWDYFGVGRDDGFEKGEFTAVFYnst 83
Cdd:pfam03372   2 TWNVNGGNADAAG--DDRKLDALAALIRAYDPDVVALQETDDDdaSRLLLALLAYGGFLSYGGPGGGGGGGGVAILS--- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  84 RFTLLQEGHFWLSETPDVPSIHSTAMFPRICVwgkfadldGKQFYIFNTHLDHISEEARLFASQLLLKKAATIAENSPVI 163
Cdd:pfam03372  77 RYPLSSVILVDLGEFGDPALRGAIAPFAGVLV--------VPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVI 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 164 ILGDFNtepdtptynfitkkyqdaqlisqkrakgpigsfhdfrplrpinelekIDYIFVSKEFQVCTYETiVDEVDGFSA 243
Cdd:pfam03372 149 LAGDFN-----------------------------------------------ADYILVSGGLTVLSVGV-LPDLGPRTG 180


                  ...
gi 1375569202 244 SDH 246
Cdd:pfam03372 181 SDH 183
nSMase cd09078
Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological ...
 121-253 9.40e-08

Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine; Sphingomyelinases (SMase) are phosphodiesterases that catalyze the hydrolysis of sphingomyelin to ceramide and phosphorylcholine. Eukaryotic SMases have been classified according to their pH optima and are known as acid SMase, alkaline SMase, and neutral SMase (nSMase). Eukaryotic proteins in this family are nSMases, and are activated by a variety of stress-inducing agents such as cytokines or UV radiation. Ceramides and other metabolic derivatives, including sphingosine, are lipid "second messenger" molecules that participate in the regulation of stress-induced cellular responses, including cell death, adhesion, differentiation, and proliferation. Bacterial neutral SMases, which also belong to this domain family, are secreted proteins that act as membrane-damaging virulence factors. They promote colonization of the host tissue. 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: 197312 [Multi-domain]  Cd Length: 280  Bit Score: 51.57  E-value: 9.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 121 DLDGKQFY-IFNTHL-----DHISEEARLfaSQL-LLKK---AATIAENSPVIILGDFNTEPDTPTYNFITK-KYQDAQL 189
Cdd:cd09078   121 NKGGTKVYhVFGTHLqasdgSCLDRAVRQ--KQLdELRAfieEKNIPDNEPVIIAGDFNVDKRSSRDEYDDMlEQLHDYN 198

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 190 ISQKRAKG------PIGSFHDFRPLRPINELEKIDYIFVSKEFQVCTYETivDEVDGFSA--------------SDHFPV 249
Cdd:cd09078   199 APEPITAGetpltwDPGTNLLAKYNYPGGGGERLDYILYSNDHLQPSSWS--NEVEVPKSptwsvtngytfadlSDHYPV 276


                  ....
gi 1375569202 250 TANL 253
Cdd:cd09078   277 SATF 280
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 2-187 2.17e-06

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: 47.34  E-value: 2.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202   2 FSVTTFNIRFDDTSERKKswelRKTLTKSLLDKYQWDFMG---VEEPLLPQMLDMKAMLDWDYFGVGRDDGFEKGEFTAV 78
Cdd:cd09080     1 LKVLTWNVDFLDDVNLAE----RMRAILKLLEELDPDVIFlqeVTPPFLAYLLSQPWVRKNYYFSEGPPSPAVDPYGVLI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  79 FynsTRFTLLQEGHFWlsetpdvpsihSTAMFPRICVWGKFADLDGKQFYIFNTHLDHISEEARLFASQL--LLKKAATI 156
Cdd:cd09080    77 L---SKKSLVVRRVPF-----------TSTRMGRNLLAAEINLGSGEPLRLATTHLESLKSHSSERTAQLeeIAKKLKKP 142

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1375569202 157 AENSPVIILGDFNTEPDTPTYNFITKKYQDA 187
Cdd:cd09080   143 PGAANVILGGDFNLRDKEDDTGGLPNGFVDA 173
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 77-255 6.95e-06

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: 46.53  E-value: 6.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  77 AVFYNSTRFTLLQEgH---FWLSETPDVPSIHSTAMFPR---------ICVW----GKFADLDGKQFYIFNTHL--DHIS 138
Cdd:cd09097    94 AIFFKTSKFKLVEK-HlieFNQLAMANADAEGSEDMLNRvmtkdnialIVVLeareTSYEGNKGQLLIVANTHIhwDPEF 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 139 EEARLFASQLLLKKAATIAE-----------NSPVIILGDFNTEPDTPTYNFITKkyqdaQLISQKRAKGPIGSFHDFR- 206
Cdd:cd09097   173 SDVKLVQTMMLLEELEKIAEkfsrypyedsaDIPLVVCGDFNSLPDSGVYELLSN-----GSVSPNHPDFKEDPYGEYLt 247

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 207 --------PLRP----INEL----------EKIDYIFVSKE-FQVCTYETIVDE------VDGFS----ASDHFPVTANL 253
Cdd:cd09097   248 asglthsfKLKSayanLGELpftnytpdfkGVIDYIFYSADtLSVLGLLGPPDEdwylnkVVGLPnphfPSDHIALLAEF 327


                  ..
gi 1375569202 254 DW 255
Cdd:cd09097   328 RI 329
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 122-253 1.25e-05

Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like 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 efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197322 [Multi-domain]  Cd Length: 309  Bit Score: 45.39  E-value: 1.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 122 LDGKQFYIFNT---HLDHISEEA---RLFASQLLLKKA-ATIAENSPVIILGDFNT--------EPDTPTYNFIT----- 181
Cdd:cd09088   139 TDHGTFVLINVycpRADPEKEERlefKLDFYRLLEERVeALLKAGRRVILVGDVNVshrpidhcDPDDSEDFGGEsfedn 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 182 --KKYQDAQLI-SQKRAKGPIGSFHD----FRP--------------LRPINELEKIDYIFVSKEFQVCTYE-TIVDEVD 239
Cdd:cd09088   219 psRQWLDQLLGdSGEGGGSPGGLLIDsfryFHPtrkgaytcwntltgARPTNYGTRIDYILADRGLLPWVKAaDILPEVE 298

                         170
                  ....*....|....
gi 1375569202 240 GfsaSDHFPVTANL 253
Cdd:cd09088   299 G---SDHCPVYADL 309
MnuA_DNase1-like cd10283
Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a ...
 2-253 2.44e-05

Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a membrane-associated nuclease related to Deoxyribonuclease 1 (DNase1 or DNase I, EC 3.1.21.1). The in vivo role of MnuA is as yet undetermined. 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: 197338 [Multi-domain]  Cd Length: 266  Bit Score: 44.31  E-value: 2.44e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202   2 FSVTTFNIRFDDTSERKKSWE-LRKTLTKSLLDkyqwdFMGVEE-----PLLPQMLDM-----KAMLDWDY--FGVGRDD 68
Cdd:cd10283     1 LRIASWNILNFGNSKGKEKNPaIAEIISAFDLD-----LIALQEvmdngGGLDALAKLvnelnKPGGTWKYivSDKTGGS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  69 GfEKGEFTAVFYNSTRFtllqeghfWLSETPDVPSIHSTAMFPRICVWGKFADL-DGKQFYIFNTHLD------HISEEA 141
Cdd:cd10283    76 S-GDKERYAFLYKSSKV--------RKVGKAVLEKDSNTDGFARPPYAAKFKSGgTGFDFTLVNVHLKsggsskSGQGAK 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 142 RL-FASQLL--LKKAATIAENSPVIILGDFNTEPDTPTYNFITKK-YQDAQLISQK---RAKGPIGSFhD---FRPLRPI 211
Cdd:cd10283   147 RVaEAQALAeyLKELADEDPDDDVILLGDFNIPADEDAFKALTKAgFKSLLPDSTNlstSFKGYANSY-DnifVSGNLKE 225

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1375569202 212 NELEK--IDYIFVSKEFQVctyETIVDEVDGFSASDHFPVTANL 253
Cdd:cd10283   226 KFSNSgvFDFNILVDEAGE---EDLDYSKWRKQISDHDPVWVEF 266
Deadenylase_nocturnin cd09096
C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the ...
 77-224 2.72e-05

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: 44.34  E-value: 2.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202  77 AVFYNSTRFTLLQEGHFWLSETPDVPSIHSTAMFPRICvwgkfadLDGKQFYIFNTHLDHIS--EEARLFASQLLLKKAA 154
Cdd:cd09096    94 ALFFRKDRFELVNTEKIRLSAMTLKTNQVAIACTLRCK-------ETGREICLAVTHLKARTgwERLRSEQGKDLLQNLQ 166

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1375569202 155 TIAENS--PVIILGDFNTEPDTPTY----NFITKKYQDAQLISQKRAKGPIGSFHDFRPLRPINELekIDYIFVSK 224
Cdd:cd09096   167 SFIEGAkiPLIICGDFNAEPTEPVYktfsNSSLNLNSAYKLLSADGQSEPPYTTWKIRTSGECRHT--LDYIFYSK 240
PRK08068 PRK08068
transaminase; Reviewed
 144-228 4.86e-03

transaminase; Reviewed


Pssm-ID: 181219  Cd Length: 389  Bit Score: 37.60  E-value: 4.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1375569202 144 FASqLLLKKAATIAENSPVIILGDFNtePDTPTYNFITKKYQDAqlisqkrAKGPigSFHDFRPLRPINELEKIDYIFVS 223
Cdd:PRK08068   17 FAS-LVAKVNKKVAEGHDVINLGQGN--PDQPTPEHIVEALQEA-------AENP--ANHKYSPFRGYPFLKEAAADFYK 84


                  ....*
gi 1375569202 224 KEFQV 228
Cdd:PRK08068   85 REYGV 89
 
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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