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Conserved domains on  [gi|493530444|ref|WP_006484455|]
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endonuclease/exonuclease/phosphatase family protein [Burkholderia cenocepacia]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-283 6.13e-26

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


:

Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 100.37  E-value: 6.13e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   1 MRLIDWNIQWGRDADGVVDLPRTVAAIRELgDFDVLCLQEvtrgfdalpgrpgpdqfgelaallpgytvvdaigadlpai 80
Cdd:COG3568    8 LRVMTYNIRYGLGTDGRADLERIARVIRAL-DPDVVALQE---------------------------------------- 46

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  81 rpgaprrqfgNAIATRLPVGRVLRQSLPWPADAgapsmPRVALDIELQAPFGPLRVVTTHLEYYSARQRLAQVDALRDRH 160
Cdd:COG3568   47 ----------NAILSRYPIVSSGTFDLPDPGGE-----PRGALWADVDVPGKPLRVVNTHLDLRSAAARRRQARALAELL 111

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 161 REacahathparaetaegpfSATGQPrdAIVCGDFNsafgsdayrrflapladapdfidawvarhpgrtppptagvydtv 240
Cdd:COG3568  112 AE------------------LPAGAP--VILAGDFN-------------------------------------------- 127

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 493530444 241 qwsdgplACDFVFVTDTLlpRVTRCEI---DGNVRASDHQPVLLDL 283
Cdd:COG3568  128 -------DIDYILVSPGL--RVLSAEVldsPLGRAASDHLPVVADL 164
EEP super family cl00490
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 190-283 1.33e-04

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 cd09087:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 253  Bit Score: 42.54  E-value: 1.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 190 IVCGDFNSAF------------GS--------DAYRRFLAPladapDFIDAWVARHPGRTP------PPTAGVYDTVQWS 243
Cdd:cd09087  144 IWCGDLNVAHeeidlanpktnkKSagftpeerESFTELLEA-----GFVDTFRHLHPDKEGaytfwsYRGNARAKNVGWR 218

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 493530444 244 dgplaCDFVFVTDTLLPRVTRCEIDGNVRASDHQPVLLDL 283
Cdd:cd09087  219 -----LDYFLVSERLKDRVVDSFIRSDIMGSDHCPIGLEL 253
 
Name Accession Description Interval E-value
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-283 6.13e-26

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 100.37  E-value: 6.13e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   1 MRLIDWNIQWGRDADGVVDLPRTVAAIRELgDFDVLCLQEvtrgfdalpgrpgpdqfgelaallpgytvvdaigadlpai 80
Cdd:COG3568    8 LRVMTYNIRYGLGTDGRADLERIARVIRAL-DPDVVALQE---------------------------------------- 46

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  81 rpgaprrqfgNAIATRLPVGRVLRQSLPWPADAgapsmPRVALDIELQAPFGPLRVVTTHLEYYSARQRLAQVDALRDRH 160
Cdd:COG3568   47 ----------NAILSRYPIVSSGTFDLPDPGGE-----PRGALWADVDVPGKPLRVVNTHLDLRSAAARRRQARALAELL 111

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 161 REacahathparaetaegpfSATGQPrdAIVCGDFNsafgsdayrrflapladapdfidawvarhpgrtppptagvydtv 240
Cdd:COG3568  112 AE------------------LPAGAP--VILAGDFN-------------------------------------------- 127

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 493530444 241 qwsdgplACDFVFVTDTLlpRVTRCEI---DGNVRASDHQPVLLDL 283
Cdd:COG3568  128 -------DIDYILVSPGL--RVLSAEVldsPLGRAASDHLPVVADL 164
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 1-226 2.72e-17

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: 78.92  E-value: 2.72e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   1 MRLIDWNIQWGRDadgVVDLPRTVAAIR--ELGDFDVLCLQEVTRGF-DALPGRPgpdqfgelaALLPGYTVVDaigadl 77
Cdd:cd09080    1 LKVLTWNVDFLDD---VNLAERMRAILKllEELDPDVIFLQEVTPPFlAYLLSQP---------WVRKNYYFSE------ 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  78 paIRPGAPRRQFGNAIATRLPvgrVLRQSLPWPADagapSMPR--VALDIELQAPfGPLRVVTTHLE--YYSARQRLAQV 153
Cdd:cd09080   63 --GPPSPAVDPYGVLILSKKS---LVVRRVPFTST----RMGRnlLAAEINLGSG-EPLRLATTHLEslKSHSSERTAQL 132

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493530444 154 DALRDRhreacahathparaetaegpFSATGQPRDAIVCGDFNsaFGSDAYRRFLAPladaPDFIDAWVARHP 226
Cdd:cd09080  133 EEIAKK--------------------LKKPPGAANVILGGDFN--LRDKEDDTGGLP----NGFVDAWEELGP 179
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-283 1.49e-10

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 59.99  E-value: 1.49e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444    1 MRLIDWNIqwgrdaDGVVDLPRTVA-AIRELGDFDVLCLQEVtrgfdalpgRPGPDQFGELAALLPGYTVVDAigadlpa 79
Cdd:TIGR00633   1 MKIISWNV------NGLRARLHKLFlDWLKEEQPDVLCLQET---------KVADEQFPAELFEELGYHVFFH------- 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   80 irpGAPRRQFGNAIATRLPVGRVlRQSLPW-PADAGAPsmprvaldiELQAPFGPLRVVTT-----------HLEYysar 147
Cdd:TIGR00633  59 ---GAKKGYSGVAILSKVEPLDV-RYGFGGePHDEEGR---------VITAEFDGFTVVNVyvpnggsrdleRLEY---- 121

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  148 qRLAQVDALRDRH-REACAhathparaetaegpfsatGQPrdAIVCGDFNSA-----------------FgSDAYRRFLA 209
Cdd:TIGR00633 122 -KLQFWDALFQYLeKELDA------------------GKP--VVICGDMNVAhteidlgnpkenkgnagF-TPEEREWFD 179

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 493530444  210 PLADApDFIDAWVARHPGRTPPPTAGVYDTVQWSDGP-LACDFVFVTDTLLPRVTRCEIDGNVRASDHQPVLLDL 283
Cdd:TIGR00633 180 ELLEA-GFVDTFRHFNPDTGDAYTWWDYRSGARDRNRgWRIDYFLVSEPLAERVVDSYIDSEIRGSDHCPIVLEL 253
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 6-197 4.79e-08

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: 51.84  E-value: 4.79e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444    6 WNIQWGR-DADGVVDLPRTVAAIRELGDFDVLCLQEVTrgfdalpgrpgPDQFGELAALLPGYtvvdaiGADLPAIRPGA 84
Cdd:pfam03372   3 WNVNGGNaDAAGDDRKLDALAALIRAYDPDVVALQETD-----------DDDASRLLLALLAY------GGFLSYGGPGG 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   85 PRRQFGNAIATRLPVGRVLRQSLPwpaDAGAPSMPRVALDIELQAPFGPLRVVTTHLEYYSARQRlaQVDALRDRHREAC 164
Cdd:pfam03372  66 GGGGGGVAILSRYPLSSVILVDLG---EFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDE--QRADLLLLLLALL 140

                         170       180       190
                  ....*....|....*....|....*....|...
gi 493530444  165 AHATHParaetaegpfsatgqprdAIVCGDFNS 197
Cdd:pfam03372 141 APRSEP------------------VILAGDFNA 155
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 190-283 1.33e-04

Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) 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 example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase 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: 197321 [Multi-domain]  Cd Length: 253  Bit Score: 42.54  E-value: 1.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 190 IVCGDFNSAF------------GS--------DAYRRFLAPladapDFIDAWVARHPGRTP------PPTAGVYDTVQWS 243
Cdd:cd09087  144 IWCGDLNVAHeeidlanpktnkKSagftpeerESFTELLEA-----GFVDTFRHLHPDKEGaytfwsYRGNARAKNVGWR 218

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 493530444 244 dgplaCDFVFVTDTLLPRVTRCEIDGNVRASDHQPVLLDL 283
Cdd:cd09087  219 -----LDYFLVSERLKDRVVDSFIRSDIMGSDHCPIGLEL 253
 
Name Accession Description Interval E-value
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-283 6.13e-26

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 100.37  E-value: 6.13e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   1 MRLIDWNIQWGRDADGVVDLPRTVAAIRELgDFDVLCLQEvtrgfdalpgrpgpdqfgelaallpgytvvdaigadlpai 80
Cdd:COG3568    8 LRVMTYNIRYGLGTDGRADLERIARVIRAL-DPDVVALQE---------------------------------------- 46

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  81 rpgaprrqfgNAIATRLPVGRVLRQSLPWPADAgapsmPRVALDIELQAPFGPLRVVTTHLEYYSARQRLAQVDALRDRH 160
Cdd:COG3568   47 ----------NAILSRYPIVSSGTFDLPDPGGE-----PRGALWADVDVPGKPLRVVNTHLDLRSAAARRRQARALAELL 111

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 161 REacahathparaetaegpfSATGQPrdAIVCGDFNsafgsdayrrflapladapdfidawvarhpgrtppptagvydtv 240
Cdd:COG3568  112 AE------------------LPAGAP--VILAGDFN-------------------------------------------- 127

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 493530444 241 qwsdgplACDFVFVTDTLlpRVTRCEI---DGNVRASDHQPVLLDL 283
Cdd:COG3568  128 -------DIDYILVSPGL--RVLSAEVldsPLGRAASDHLPVVADL 164
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 1-226 2.72e-17

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: 78.92  E-value: 2.72e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   1 MRLIDWNIQWGRDadgVVDLPRTVAAIR--ELGDFDVLCLQEVTRGF-DALPGRPgpdqfgelaALLPGYTVVDaigadl 77
Cdd:cd09080    1 LKVLTWNVDFLDD---VNLAERMRAILKllEELDPDVIFLQEVTPPFlAYLLSQP---------WVRKNYYFSE------ 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  78 paIRPGAPRRQFGNAIATRLPvgrVLRQSLPWPADagapSMPR--VALDIELQAPfGPLRVVTTHLE--YYSARQRLAQV 153
Cdd:cd09080   63 --GPPSPAVDPYGVLILSKKS---LVVRRVPFTST----RMGRnlLAAEINLGSG-EPLRLATTHLEslKSHSSERTAQL 132

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493530444 154 DALRDRhreacahathparaetaegpFSATGQPRDAIVCGDFNsaFGSDAYRRFLAPladaPDFIDAWVARHP 226
Cdd:cd09080  133 EEIAKK--------------------LKKPPGAANVILGGDFN--LRDKEDDTGGLP----NGFVDAWEELGP 179
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 2-283 3.69e-15

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: 73.41  E-value: 3.69e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   2 RLIDWNIQWGRDADGVVD----LPRTVAAIRELgDFDVLCLQEVTrgfdalpgrpgPDQFGELAALLPGYtvvDAIGADl 77
Cdd:cd09083    1 RVMTFNIRYDNPSDGENSwenrKDLVAELIKFY-DPDIIGTQEAL-----------PHQLADLEELLPEY---DWIGVG- 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  78 paiRPGapRRQFG--NAI---ATRLpvgRVLRQSLPW--PADAGAPSM------PRVA-----LDIELQAPFgplRVVTT 139
Cdd:cd09083   65 ---RDD--GKEKGefSAIfyrKDRF---ELLDSGTFWlsETPDVVGSKgwdaalPRICtwarfKDKKTGKEF---YVFNT 133

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 140 HLEYYSARQRLAQVDALRDRHREACAhaTHPAraetaegpfsatgqprdaIVCGDFNSAFGSDAYRRFLAPLadapdFID 219
Cdd:cd09083  134 HLDHVGEEAREESAKLILERIKEIAG--DLPV------------------ILTGDFNAEPDSEPYKTLTSGG-----LKD 188

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 493530444 220 AW-VARHPGRTPPPTAGVYDTVqwsDGPLACDFVFVTDTLlpRVTRCEID----GNVRASDHQPVLLDL 283
Cdd:cd09083  189 ARdTAATTDGGPEGTFHGFKGP---PGGSRIDYIFVSPGV--KVLSYEILtdryDGRYPSDHFPVVADL 252
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 6-283 1.12e-12

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: 66.17  E-value: 1.12e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   6 WNIQWGRDADGVVDLPRTVAAIRELgDFDVLCLQEvtrgfdaLPGRpGPDQFGELAALLPGYTVVdaigadlpAIRPGAP 85
Cdd:cd09084    4 YNVRSFNRYKWKDDPDKILDFIKKQ-DPDILCLQE-------YYGS-EGDKDDDLRLLLKGYPYY--------YVVYKSD 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  86 RRQFGNAIATRLPVgrVLRQSLPWPAdaGAPSMPRVALDIELQApfgpLRVVTTHLE-----------YYSARQRLAQVD 154
Cdd:cd09084   67 SGGTGLAIFSKYPI--LNSGSIDFPN--TNNNAIFADIRVGGDT----IRVYNVHLEsfritpsdkelYKEEKKAKELSR 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 155 ALRDRHREACAhathpARAETAEGpFSAT--GQPRDAIVCGDFNSAFGSDAYRRFLAPLADApdFIDAWvaRHPGRTppp 232
Cdd:cd09084  139 NLLRKLAEAFK-----RRAAQADL-LAADiaASPYPVIVCGDFNDTPASYVYRTLKKGLTDA--FVEAG--SGFGYT--- 205

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 493530444 233 tagvydtvqWSDG--PLACDFVFVTDTLlpRVTRCEIDgNVRASDHQPVLLDL 283
Cdd:cd09084  206 ---------FNGLffPLRIDYILTSKGF--KVLRYRVD-PGKYSDHYPIVATL 246
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-283 1.04e-11

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 63.56  E-value: 1.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   1 MRLIDWNIqwgrdaDGVvdlpRtvAAIRELGDF------DVLCLQEvTRGFDalpgrpgpDQFGELAALLPGYTVVdaig 74
Cdd:COG0708    1 MKIASWNV------NGI----R--ARLPKLLDWlaeedpDVLCLQE-TKAQD--------EQFPLEAFEAAGYHVY---- 55

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  75 adlpairpGAPRRQF-GNAIATRLPVGRVLRqSLPW-PADAGApsmpRValdieLQAPFGPLRVVTTHL----EYYSARQ 148
Cdd:COG0708   56 --------FHGQKGYnGVAILSRLPPEDVRR-GLGGdEFDAEG----RY-----IEADFGGVRVVSLYVpnggSVGSEKF 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 149 --RLAQVDALRDRhreacahathpARAETAEGpfsatgqpRDAIVCGDFNSAF------------GS--------DAYRR 206
Cdd:COG0708  118 dyKLRFLDALRAY-----------LAELLAPG--------RPLILCGDFNIAPteidvknpkanlKNagflpeerAWFDR 178

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 207 FLapladAPDFIDAWVARHPGRTppptaGVYdTVqWSDGPLA--------CDFVFVTDTLLPRVTRCEID----GNVRAS 274
Cdd:COG0708  179 LL-----ELGLVDAFRALHPDVE-----GQY-TW-WSYRAGAfarnrgwrIDYILASPALADRLKDAGIDreprGDERPS 246


                 ....*....
gi 493530444 275 DHQPVLLDL 283
Cdd:COG0708  247 DHAPVVVEL 255
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-283 1.38e-10

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 60.78  E-value: 1.38e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   1 MRLIDWNIQWGRDadgvvDLPRTVAAIRELgDFDVLCLQEVTRGFDAlpgrpgpdqfgelaallpgytVVDAIGADLPAI 80
Cdd:COG3021   95 LRVLTANVLFGNA-----DAEALAALVREE-DPDVLVLQETTPAWEE---------------------ALAALEADYPYR 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  81 RPGAPRRQFGNAIATRLPVGRVlrqslpWPADAGAPSMPRVALDIELQApfGPLRVVTTHLE--YYSARQRLAQVDALRD 158
Cdd:COG3021  148 VLCPLDNAYGMALLSRLPLTEA------EVVYLVGDDIPSIRATVELPG--GPVRLVAVHPAppVGGSAERDAELAALAK 219

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 159 RHReacahathparaetaegpfsatGQPRDAIVCGDFNSAFGSDAYRRFLApladAPDFIDAWVARHPGRTPP---PTAG 235
Cdd:COG3021  220 AVA----------------------ALDGPVIVAGDFNATPWSPTLRRLLR----ASGLRDARAGRGLGPTWPanlPFLR 273

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 493530444 236 VydtvqwsdgPLacDFVFVTDTLlpRVTRCEIdGNVRASDHQPVLLDL 283
Cdd:COG3021  274 L---------PI--DHVLVSRGL--TVVDVRV-LPVIGSDHRPLLAEL 307
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-283 1.49e-10

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 59.99  E-value: 1.49e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444    1 MRLIDWNIqwgrdaDGVVDLPRTVA-AIRELGDFDVLCLQEVtrgfdalpgRPGPDQFGELAALLPGYTVVDAigadlpa 79
Cdd:TIGR00633   1 MKIISWNV------NGLRARLHKLFlDWLKEEQPDVLCLQET---------KVADEQFPAELFEELGYHVFFH------- 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   80 irpGAPRRQFGNAIATRLPVGRVlRQSLPW-PADAGAPsmprvaldiELQAPFGPLRVVTT-----------HLEYysar 147
Cdd:TIGR00633  59 ---GAKKGYSGVAILSKVEPLDV-RYGFGGePHDEEGR---------VITAEFDGFTVVNVyvpnggsrdleRLEY---- 121

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  148 qRLAQVDALRDRH-REACAhathparaetaegpfsatGQPrdAIVCGDFNSA-----------------FgSDAYRRFLA 209
Cdd:TIGR00633 122 -KLQFWDALFQYLeKELDA------------------GKP--VVICGDMNVAhteidlgnpkenkgnagF-TPEEREWFD 179

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 493530444  210 PLADApDFIDAWVARHPGRTPPPTAGVYDTVQWSDGP-LACDFVFVTDTLLPRVTRCEIDGNVRASDHQPVLLDL 283
Cdd:TIGR00633 180 ELLEA-GFVDTFRHFNPDTGDAYTWWDYRSGARDRNRgWRIDYFLVSEPLAERVVDSYIDSEIRGSDHCPIVLEL 253
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 6-283 8.95e-10

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: 57.88  E-value: 8.95e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   6 WNIqwgRDADGVVDLPRTVAAIRELgDFDVLCLQEV-----TRGFDALPGRPGPDQFGELAALLPGYtvvdaigadlpai 80
Cdd:cd08372    4 YNV---NGLNAATRASGIARWVREL-DPDIVCLQEVkdsqySAVALNQLLPEGYHQYQSGPSRKEGY------------- 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  81 rpgaprrqFGNAIATRLPVGRVLRQSLPWPADAGAPSMPRVALDIELQAPFgpLRVVTTHLEYYSARQ--RLAQVDALRD 158
Cdd:cd08372   67 --------EGVAILSKTPKFKIVEKHQYKFGEGDSGERRAVVVKFDVHDKE--LCVVNAHLQAGGTRAdvRDAQLKEVLE 136

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 159 ---RHREACAhathparaetaegpfsatgqpRDAIVCGDFNSAfGSDAYRRFLAPLAD---APDFIDAWVARHpgrtppp 232
Cdd:cd08372  137 flkRLRQPNS---------------------APVVICGDFNVR-PSEVDSENPSSMLRlfvALNLVDSFETLP------- 187

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 493530444 233 TAGVYDTvQWSDGPLACDFVFVTDTLLPRVTRCEIDGNVRA----SDHQPVLLDL 283
Cdd:cd08372  188 HAYTFDT-YMHNVKSRLDYIFVSKSLLPSVKSSKILSDAARaripSDHYPIEVTL 241
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 32-282 6.23e-09

Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and 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 example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.


Pssm-ID: 197336 [Multi-domain]  Cd Length: 253  Bit Score: 55.31  E-value: 6.23e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  32 DFDVLCLQEVtrgfdalpgRPGPDQFGELAALLPGYtvvdaIGADLPAIRPGaprrQFGNAIATRLPVGRVlRQSLPWPA 111
Cdd:cd10281   27 DADVVCLQEV---------RAQEEQLDDDFFEPEGY-----NAYFFDAEKKG----YAGVAIYSRTQPKAV-IYGLGFEE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 112 DagapsmprvalDIE---LQAPFGPLRVVTTHL---EYYSARQ--RLAQVDALRDRHREacahathparaETAEGpfsat 183
Cdd:cd10281   88 F-----------DDEgryIEADFDNVSVASLYVpsgSSGDERQeaKMAFLDAFLEHLKE-----------LRRKR----- 140

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 184 gqpRDAIVCGDFNSAFG----SDAYRR-----FLAP-------LADAPDFIDAWVARHPGRTPpptagvyDTvQWSDGPL 247
Cdd:cd10281  141 ---REFIVCGDFNIAHTeidiKNWKANqknsgFLPEerawldqVFGELGYVDAFRELNPDEGQ-------YT-WWSNRGQ 209

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 493530444 248 A--------CDFVFVTDTLLPRVTRCEIDGNVRASDHQPVLLD 282
Cdd:cd10281  210 ArannvgwrIDYQIATPGLASKVVSAWIYREERFSDHAPLIVD 252
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 6-197 4.79e-08

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: 51.84  E-value: 4.79e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444    6 WNIQWGR-DADGVVDLPRTVAAIRELGDFDVLCLQEVTrgfdalpgrpgPDQFGELAALLPGYtvvdaiGADLPAIRPGA 84
Cdd:pfam03372   3 WNVNGGNaDAAGDDRKLDALAALIRAYDPDVVALQETD-----------DDDASRLLLALLAY------GGFLSYGGPGG 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444   85 PRRQFGNAIATRLPVGRVLRQSLPwpaDAGAPSMPRVALDIELQAPFGPLRVVTTHLEYYSARQRlaQVDALRDRHREAC 164
Cdd:pfam03372  66 GGGGGGVAILSRYPLSSVILVDLG---EFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDE--QRADLLLLLLALL 140

                         170       180       190
                  ....*....|....*....|....*....|...
gi 493530444  165 AHATHParaetaegpfsatgqprdAIVCGDFNS 197
Cdd:pfam03372 141 APRSEP------------------VILAGDFNA 155
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
22-283 4.00e-06

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 47.32  E-value: 4.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  22 RTVAAIRELgDFDVLCLQEVTRGFDALpgrpgpDQF-GELAALLPGYTVVDAI-GADLPAIRpgaprrqfgNAIATRL-- 97
Cdd:COG2374  105 KIAAAIAAL-DADIVGLQEVENNGSAL------QDLvAALNLAGGTYAFVHPPdGPDGDGIR---------VALLYRPdr 168

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444  98 --PVGRVLRQSLPWPADaGAPSMPRVALDIELQAPFG-PLRVVTTHL-----------EYYSARQRLAQVDALRDRHrea 163
Cdd:COG2374  169 vtLVGSATIADLPDSPG-NPDRFSRPPLAVTFELANGePFTVIVNHFkskgsddpgdgQGASEAKRTAQAEALRAFV--- 244

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 164 cahATHPARAETAegpfsatgqprDAIVCGDFNSAFGSDAYRrflaPLADAPDFIDAWvarhpGRTPPPTAG--VYDTvQ 241
Cdd:COG2374  245 ---DSLLAADPDA-----------PVIVLGDFNDYPFEDPLR----ALLGAGGLTNLA-----EKLPAAERYsyVYDG-N 300

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 493530444 242 WsdGPLacDFVFVTDTLLPRVTRCEI--------------------DGNVRASDHQPVLLDL 283
Cdd:COG2374  301 S--GLL--DHILVSPALAARVTGADIwhinadiynddfkpdfrtyaDDPGRASDHDPVVVGL 358
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 190-283 1.33e-04

Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) 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 example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase 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: 197321 [Multi-domain]  Cd Length: 253  Bit Score: 42.54  E-value: 1.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 190 IVCGDFNSAF------------GS--------DAYRRFLAPladapDFIDAWVARHPGRTP------PPTAGVYDTVQWS 243
Cdd:cd09087  144 IWCGDLNVAHeeidlanpktnkKSagftpeerESFTELLEA-----GFVDTFRHLHPDKEGaytfwsYRGNARAKNVGWR 218

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 493530444 244 dgplaCDFVFVTDTLLPRVTRCEIDGNVRASDHQPVLLDL 283
Cdd:cd09087  219 -----LDYFLVSERLKDRVVDSFIRSDIMGSDHCPIGLEL 253
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 187-283 1.97e-04

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: 42.30  E-value: 1.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 187 RDAIVCGDFN-------SAFGSDA----------------YRRFLAPL-----ADAPDFIDAWVARHPGRTppptaGVYd 238
Cdd:cd09088  184 RRVILVGDVNvshrpidHCDPDDSedfggesfednpsrqwLDQLLGDSgegggSPGGLLIDSFRYFHPTRK-----GAY- 257

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 493530444 239 TVqWSDgpLAC----------DFVFVTDTLLPRVTRCEIDGNVRASDHQPVLLDL 283
Cdd:cd09088  258 TC-WNT--LTGarptnygtriDYILADRGLLPWVKAADILPEVEGSDHCPVYADL 309
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 250-283 9.43e-04

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: 39.81  E-value: 9.43e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 493530444 250 DFVFVTDTLLPRVTRCEIDGNVRA----SDHQPVLLDL 283
Cdd:cd09086  217 DHILASPALADRLKDVGIDREPRGwekpSDHAPVVAEL 254
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 190-283 1.16e-03

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: 39.64  E-value: 1.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493530444 190 IVCGDFNSAFGSDAY------------RRFLAPLADAPDFIDAWVARHPgrtppptagvyDTVQW----SDGPLAC--DF 251
Cdd:cd09076  137 IIGGDFNAVLGPKDDgrkgldkrnengERALSALIEEHDLVDVWRENNP-----------KTREYtwrsPDHGSRSriDR 205

                         90       100       110
                 ....*....|....*....|....*....|..
gi 493530444 252 VFVTDTLLPRVTRCEIdGNVRASDHQPVLLDL 283
Cdd:cd09076  206 ILVSKRLRVKVKKTKI-TPGAGSDHRLVTLKL 236
 
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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