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Conserved domains on  [gi|113984|sp|P27695|]
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RecName: Full=DNA repair nuclease/redox regulator APEX1; AltName: Full=APEX nuclease; Short=APEN; AltName: Full=Apurinic-apyrimidinic endonuclease 1; Short=AP endonuclease 1; Short=APE-1; AltName: Full=DNA-(apurinic or apyrimidinic site) endonuclease; AltName: Full=Redox factor-1; Short=REF-1; Contains: RecName: Full=DNA repair nuclease/redox regulator APEX1, mitochondrial

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 62-316 1.34e-163

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: 455.47  E-value: 1.34e-163
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    62 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSApSDKEGYSGVGLLSRQCPLK 141
Cdd:cd09087   1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGYHQYWNA-AEKKGYSGTAILSKKKPLS 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLR 221
Cdd:cd09087  80 VTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLA 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   222 NPKGNKKNAGFTPQERQGFGELLQAvPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 301
Cdd:cd09087 160 NPKTNKKSAGFTPEERESFTELLEA-GFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIR 238

                       250
                ....*....|....*
gi 113984   302 SKALGSDHCPITLYL 316
Cdd:cd09087 239 SDIMGSDHCPIGLEL 253
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 62-316 1.34e-163

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: 455.47  E-value: 1.34e-163
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    62 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSApSDKEGYSGVGLLSRQCPLK 141
Cdd:cd09087   1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGYHQYWNA-AEKKGYSGTAILSKKKPLS 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLR 221
Cdd:cd09087  80 VTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLA 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   222 NPKGNKKNAGFTPQERQGFGELLQAvPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 301
Cdd:cd09087 160 NPKTNKKSAGFTPEERESFTELLEA-GFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIR 238

                       250
                ....*....|....*
gi 113984   302 SKALGSDHCPITLYL 316
Cdd:cd09087 239 SDIMGSDHCPIGLEL 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 62-317 2.22e-143

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: 404.35  E-value: 2.22e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984      62 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSApsdKEGYSGVGLLSRQCPLK 141
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGA---KKGYSGVAILSKVEPLD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984     142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAG-RGLVRLEYR-QRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEID 219
Cdd:TIGR00633  78 VRYGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKlQFWDALFQYLEKELDAGKPVVICGDMNVAHTEID 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984     220 LRNPKGNKKNAGFTPQERQGFGELLQAVpLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSK 299
Cdd:TIGR00633 158 LGNPKENKGNAGFTPEEREWFDELLEAG-FVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSY 236

                         250
                  ....*....|....*...
gi 113984     300 IRSKALGSDHCPITLYLA 317
Cdd:TIGR00633 237 IDSEIRGSDHCPIVLELD 254
XthA COG0708
Exonuclease III [Replication, recombination and repair];
62-317 2.56e-115

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 333.20  E-value: 2.56e-115
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    62 LKICSWNVDGLRAwIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLsHQYWSapsDKEGYSGVGLLSRQCPLK 141
Cdd:COG0708   1 MKIASWNVNGIRA-RLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGY-HVYFH---GQKGYNGVAILSRLPPED 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAG-RGLVRLEYRQRWDEAFRKFLKGL-ASRKPLVLCGDLNVAHEEID 219
Cdd:COG0708  76 VRRGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELlAPGRPLILCGDFNIAPTEID 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   220 LRNPKGNKKNAGFTPQERQGFGELLQAvPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSK 299
Cdd:COG0708 156 VKNPKANLKNAGFLPEERAWFDRLLEL-GLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAG 234

                       250       260
                ....*....|....*....|..
gi 113984   300 I----RSKALGSDHCPITLYLA 317
Cdd:COG0708 235 IdrepRGDERPSDHAPVVVELD 256
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 62-316 1.22e-88

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 265.40  E-value: 1.22e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984     62 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELpglsHQYWSApSDKEGYSGVGLLSRQCPLK 141
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGY----FDFWNC-AIKKGYSGVVTFTKKEPLS 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLR 221
Cdd:PRK13911  76 VSYGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKKPVIVCGDLNVAHNEIDLE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    222 NPKGNKKNAGFTPQERQGFGELLQAvPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 301
Cdd:PRK13911 156 NPKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIY 234

                        250
                 ....*....|....*
gi 113984    302 SKALGSDHCPITLYL 316
Cdd:PRK13911 235 KDILGSDHCPVGLEL 249
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 65-213 1.59e-21

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: 89.98  E-value: 1.59e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984      65 CSWNVDGLRAWIKKKG------LDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSaPSDKEGYSGVGLLSRQC 138
Cdd:pfam03372   1 LTWNVNGGNADAAGDDrkldalAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGG-PGGGGGGGGVAILSRYP 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 113984     139 PLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYR-QRWDEAFRKFLKGLASRKPLVLCGDLNV 213
Cdd:pfam03372  80 LSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDeQRADLLLLLLALLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 62-316 1.34e-163

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: 455.47  E-value: 1.34e-163
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    62 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSApSDKEGYSGVGLLSRQCPLK 141
Cdd:cd09087   1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGYHQYWNA-AEKKGYSGTAILSKKKPLS 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLR 221
Cdd:cd09087  80 VTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLA 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   222 NPKGNKKNAGFTPQERQGFGELLQAvPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 301
Cdd:cd09087 160 NPKTNKKSAGFTPEERESFTELLEA-GFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIR 238

                       250
                ....*....|....*
gi 113984   302 SKALGSDHCPITLYL 316
Cdd:cd09087 239 SDIMGSDHCPIGLEL 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 62-317 2.22e-143

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: 404.35  E-value: 2.22e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984      62 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSApsdKEGYSGVGLLSRQCPLK 141
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGA---KKGYSGVAILSKVEPLD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984     142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAG-RGLVRLEYR-QRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEID 219
Cdd:TIGR00633  78 VRYGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKlQFWDALFQYLEKELDAGKPVVICGDMNVAHTEID 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984     220 LRNPKGNKKNAGFTPQERQGFGELLQAVpLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSK 299
Cdd:TIGR00633 158 LGNPKENKGNAGFTPEEREWFDELLEAG-FVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSY 236

                         250
                  ....*....|....*...
gi 113984     300 IRSKALGSDHCPITLYLA 317
Cdd:TIGR00633 237 IDSEIRGSDHCPIVLELD 254
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 63-316 2.28e-140

Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases 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, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range 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 functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197307 [Multi-domain]  Cd Length: 251  Bit Score: 396.66  E-value: 2.28e-140
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    63 KICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGlSHQYWSaPSDKEGYSGVGLLSRQCPLKV 142
Cdd:cd09073   1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEG-YHSYWS-PARKKGYSGVATLSKEEPLDV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   143 SYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASR-KPLVLCGDLNVAHEEIDLR 221
Cdd:cd09073  79 SYGIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRgKPVVICGDFNVAHEEIDLA 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   222 NPKGNKKNAGFTPQERQGFGELLQAvPLADSFRHLYPNtPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 301
Cdd:cd09073 159 RPKKNEKNAGFTPEERAWFDKLLSL-GYVDTFRHFHPE-PGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGIL 236

                       250
                ....*....|....*
gi 113984   302 SKALGSDHCPITLYL 316
Cdd:cd09073 237 SKVKGSDHAPVTLEL 251
XthA COG0708
Exonuclease III [Replication, recombination and repair];
62-317 2.56e-115

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 333.20  E-value: 2.56e-115
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    62 LKICSWNVDGLRAwIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLsHQYWSapsDKEGYSGVGLLSRQCPLK 141
Cdd:COG0708   1 MKIASWNVNGIRA-RLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGY-HVYFH---GQKGYNGVAILSRLPPED 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAG-RGLVRLEYRQRWDEAFRKFLKGL-ASRKPLVLCGDLNVAHEEID 219
Cdd:COG0708  76 VRRGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELlAPGRPLILCGDFNIAPTEID 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   220 LRNPKGNKKNAGFTPQERQGFGELLQAvPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSK 299
Cdd:COG0708 156 VKNPKANLKNAGFLPEERAWFDRLLEL-GLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAG 234

                       250       260
                ....*....|....*....|..
gi 113984   300 I----RSKALGSDHCPITLYLA 317
Cdd:COG0708 235 IdrepRGDERPSDHAPVVVELD 256
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 62-316 5.65e-102

Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and 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. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.


Pssm-ID: 197319 [Multi-domain]  Cd Length: 252  Bit Score: 299.19  E-value: 5.65e-102
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    62 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLsHQYWSaPSDKEGYSGVGLLSRQCPLK 141
Cdd:cd09085   1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGY-HSYFN-SAERKGYSGVALYSKIEPDS 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGL-ASRKPLVLCGDLNVAHEEIDL 220
Cdd:cd09085  79 VREGLGVEEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELrDSGKNVIICGDFNTAHKEIDL 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   221 RNPKGNKKNAGFTPQERQGFGELLQAvPLADSFRHLYPNtPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKI 300
Cdd:cd09085 159 ARPKENEKVSGFLPEERAWMDKFIEN-GYVDTFRMFNKE-PGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGI 236

                       250
                ....*....|....*.
gi 113984   301 RSKALGSDHCPITLYL 316
Cdd:cd09085 237 LPDVMGSDHCPVSLEL 252
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 62-314 3.28e-98

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


Pssm-ID: 272954 [Multi-domain]  Cd Length: 254  Bit Score: 290.05  E-value: 3.28e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984      62 LKICSWNVDGLRAwIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLsHQYWSApsdKEGYSGVGLLSRQCPLK 141
Cdd:TIGR00195   1 MKIISWNVNGLRA-RPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGY-HVFFSG---QKGYSGVAIFSKEEPIS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984     142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGR-GLVRLEYRQRWDEAFRKFLKGLA-SRKPLVLCGDLNVAHEEID 219
Cdd:TIGR00195  76 VRRGFGVEEEDAEGRIIMAEFDSFLVINGYFPNGSRdDSEKLPYKLQWLEALQNYLEKLVdKDKPVLICGDMNIAPTEID 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984     220 LRNPKGNKKNAGFTPQERQGFGELLQAvPLADSFRHLYPNTPYaYTFWTYMMNARSKNVGWRLDYFLLSHSL----LPAL 295
Cdd:TIGR00195 156 LHIPDENRNHTGFLPEEREWLDRLLEA-GLVDTFRKFNPDEGA-YSWWDYRTKARDRNRGWRIDYFLVSEPLkercVDCG 233

                         250
                  ....*....|....*....
gi 113984     296 CDSKIRSKALGSDHCPITL 314
Cdd:TIGR00195 234 IDYDIRGSEKPSDHCPVVL 252
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 62-316 1.22e-88

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 265.40  E-value: 1.22e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984     62 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELpglsHQYWSApSDKEGYSGVGLLSRQCPLK 141
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGY----FDFWNC-AIKKGYSGVVTFTKKEPLS 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLR 221
Cdd:PRK13911  76 VSYGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKKPVIVCGDLNVAHNEIDLE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    222 NPKGNKKNAGFTPQERQGFGELLQAvPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIR 301
Cdd:PRK13911 156 NPKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIY 234

                        250
                 ....*....|....*
gi 113984    302 SKALGSDHCPITLYL 316
Cdd:PRK13911 235 KDILGSDHCPVGLEL 249
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 62-314 5.35e-83

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: 250.99  E-value: 5.35e-83
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    62 LKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLsHQYWsAPSDKEGYSGVGLLSRQCPLK 141
Cdd:cd10281   1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGY-NAYF-FDAEKKGYAGVAIYSRTQPKA 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   142 VSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGL-ASRKPLVLCGDLNVAHEEIDL 220
Cdd:cd10281  79 VIYGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELrRKRREFIVCGDFNIAHTEIDI 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   221 RNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNtPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKI 300
Cdd:cd10281 159 KNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPD-EGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWI 237

                       250
                ....*....|....
gi 113984   301 RSKALGSDHCPITL 314
Cdd:cd10281 238 YREERFSDHAPLIV 251
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 62-312 6.94e-75

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: 230.48  E-value: 6.94e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    62 LKICSWNVDGLRAwikKKG--LDWVKEEAPDILCLQETKCSENKLPAELQELPGLsHQYWSApsdKEGYSGVGLLSRQCP 139
Cdd:cd09086   1 MKIATWNVNSIRA---RLEqvLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGY-HVAVHG---QKAYNGVAILSRLPL 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   140 LKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAG-RGLVRLEYRQRWDEAFRKFLKGLASR-KPLVLCGDLNVAHEE 217
Cdd:cd09086  74 EDVRTGFPGDPDDDQARLIAARVGGVRVINLYVPNGGdIGSPKFAYKLDWLDRLIRYLQKLLKPdDPLVLVGDFNIAPED 153

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   218 IDLRNPKGNKKNAGFTPQERQGFGELLQAvPLADSFRHLYPNTPYaYTFWTYMMNARSKNVGWRLDYFLLSHSLLPAL-- 295
Cdd:cd09086 154 IDVWDPKQLLGKVLFTPEEREALRALLDL-GFVDAFRALHPDEKL-FTWWDYRAGAFERNRGLRIDHILASPALADRLkd 231

                       250
                ....*....|....*....
gi 113984   296 C--DSKIRSKALGSDHCPI 312
Cdd:cd09086 232 VgiDREPRGWEKPSDHAPV 250
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 64-316 1.07e-71

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: 221.97  E-value: 1.07e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    64 ICSWNVDGLRA-WIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQC---P 139
Cdd:cd08372   1 VASYNVNGLNAaTRASGIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGYHQYQSGPSRKEGYEGVAILSKTPkfkI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   140 LKVSYGIGDEEHDQEGRVIVAEFDS----FVLVTAYVPNAGRglvRLEYRQRWDEAFRKFLKGLA--SRKPLVLCGDLNV 213
Cdd:cd08372  81 VEKHQYKFGEGDSGERRAVVVKFDVhdkeLCVVNAHLQAGGT---RADVRDAQLKEVLEFLKRLRqpNSAPVVICGDFNV 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   214 AHEEIDLRNPkgnkknagftpqerQGFGELLQAVPLADSFRHLypntPYAYTFWTYMmnarsKNVGWRLDYFLLSHSLLP 293
Cdd:cd08372 158 RPSEVDSENP--------------SSMLRLFVALNLVDSFETL----PHAYTFDTYM-----HNVKSRLDYIFVSKSLLP 214

                       250       260
                ....*....|....*....|....*..
gi 113984   294 ALCDSKIRSKA----LGSDHCPITLYL 316
Cdd:cd08372 215 SVKSSKILSDAararIPSDHYPIEVTL 241
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 63-312 4.73e-51

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: 170.96  E-value: 4.73e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    63 KICSWNVDGLRA------WIKKKGLDWVKEE-APDILCLQETKCSENKLPAELQELPGLsHQYWSAPSDKEGYSGV---- 131
Cdd:cd09088   1 RIVTWNVNGIRTrlqyqpWNKENSLKSFLDSlDADIICLQETKLTRDELDEPSAIVEGY-DSFFSFSRGRKGYSGVatyc 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   132 ------------GLLSRQCPLKVSYGIGDE-------------------EHDQEGRVIVAEFDSFVLVTAYVPNAGRG-L 179
Cdd:cd09088  80 rdsaatpvaaeeGLTGVLSSPNQKNELSENddigcygemleftdskellELDSEGRCVLTDHGTFVLINVYCPRADPEkE 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   180 VRLEYRQRWDEAFRKFLKGL-ASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQE---RQGFGELLQ---------A 246
Cdd:cd09088 160 ERLEFKLDFYRLLEERVEALlKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLGdsgegggspG 239

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 113984   247 VPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPI 312
Cdd:cd09088 240 GLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPV 305
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 64-314 1.78e-28

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: 109.75  E-value: 1.78e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    64 ICSWNVDGLRAWIKKKGL-DWVKEEAPDILCLQETKCSENKlpaELQELPGLSHQYWSApSDKEGYSGVG-LLSRQCPLK 141
Cdd:cd09076   1 IGTLNVRGLRSPGKRAQLlEELKRKKLDILGLQETHWTGEG---ELKKKREGGTILYSG-SDSGKSRGVAiLLSKTAANK 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   142 -VSYgigdeEHDQEGRVIVAEFD----SFVLVTAYVPNAGRGLVRLEYRQRwdeaFRKFLKGLASRKPLVLCGDLN---- 212
Cdd:cd09076  77 lLEY-----TKVVSGRIIMVRFKikgkRLTIINVYAPTARDEEEKEEFYDQ----LQDVLDKVPRHDTLIIGGDFNavlg 147

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   213 ---VAHEEIDLRNPKGNKKNAGFTPQERqgfgellqavpLADSFRHLYPNTpYAYTFwtymmNARSKNVGWRLDYFLLSH 289
Cdd:cd09076 148 pkdDGRKGLDKRNENGERALSALIEEHD-----------LVDVWRENNPKT-REYTW-----RSPDHGSRSRIDRILVSK 210

                       250       260
                ....*....|....*....|....*
gi 113984   290 SLLPALCDSKIrSKALGSDHCPITL 314
Cdd:cd09076 211 RLRVKVKKTKI-TPGAGSDHRLVTL 234
PRK11756 PRK11756
exonuclease III; Provisional
 62-312 5.48e-27

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 106.52  E-value: 5.48e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984     62 LKICSWNVDGLRAwiKKKGLDWVKEE-APDILCLQETKCSENKLPAELQElpglSHQYWSAPSDKEGYSGVGLLSRQCPL 140
Cdd:PRK11756   1 MKFVSFNINGLRA--RPHQLEAIIEKhQPDVIGLQETKVHDEMFPLEEVE----ALGYHVFYHGQKGHYGVALLSKQTPI 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    141 KVSYGIGDEEHDQEGRVIVAEF-DSFVLVT---AYVPNagrG-----LVRLEYRQRWDEAFRKFLKGLASR-KPLVLCGD 210
Cdd:PRK11756  75 AVRKGFPTDDEEAQRRIIMATIpTPNGNLTvinGYFPQ---GesrdhPTKFPAKRQFYQDLQNYLETELSPdNPLLIMGD 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    211 LNVAHEEIDLRNPKGNKK------NAGFTPQERQGFGELLQAvPLADSFRHLYPNTPYAYTFWTYmmnaRSK----NVGW 280
Cdd:PRK11756 152 MNISPTDLDIGIGEENRKrwlrtgKCSFLPEEREWLDRLMDW-GLVDTFRQLNPDVNDRFSWFDY----RSKgfddNRGL 226

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 113984    281 RLDYFLLSHSLLPALCDS----KIRSKALGSDHCPI 312
Cdd:PRK11756 227 RIDLILATQPLAERCVETgidyDIRGMEKPSDHAPI 262
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 65-213 1.59e-21

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: 89.98  E-value: 1.59e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984      65 CSWNVDGLRAWIKKKG------LDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSaPSDKEGYSGVGLLSRQC 138
Cdd:pfam03372   1 LTWNVNGGNADAAGDDrkldalAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGG-PGGGGGGGGVAILSRYP 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 113984     139 PLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYR-QRWDEAFRKFLKGLASRKPLVLCGDLNV 213
Cdd:pfam03372  80 LSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDeQRADLLLLLLALLAPRSEPVILAGDFNA 155
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 48-312 6.16e-11

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 62.32  E-value: 6.16e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    48 PPDQKTSPSGKPaTLKICSWNVdglraWIKKKG----LDWVKEEAPDILCLQETKcsenklPAELQELPGLSHQY-WSAP 122
Cdd:COG3021  82 LPAPKSAPAGGP-DLRVLTANV-----LFGNADaealAALVREEDPDVLVLQETT------PAWEEALAALEADYpYRVL 149

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   123 SDKEGYSGVGLLSRQcPL---KVSYGIGDeehdqEGRVIVAEFD------SFVLVTAYVPnagrglvrLEYRQRWDEAFR 193
Cdd:COG3021 150 CPLDNAYGMALLSRL-PLteaEVVYLVGD-----DIPSIRATVElpggpvRLVAVHPAPP--------VGGSAERDAELA 215

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   194 KFLKGLASRK-PLVLCGDLNVaheeidlrnpkgnkknagfTPQERqGFGELLQAVPLADSF--RHLYPntpyayTFwtym 270
Cdd:COG3021 216 ALAKAVAALDgPVIVAGDFNA-------------------TPWSP-TLRRLLRASGLRDARagRGLGP------TW---- 265

                       250       260       270       280
                ....*....|....*....|....*....|....*....|..
gi 113984   271 mNARSKNVGWRLDYFLLSHSLLPALCDskiRSKALGSDHCPI 312
Cdd:COG3021 266 -PANLPFLRLPIDHVLVSRGLTVVDVR---VLPVIGSDHRPL 303
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 66-316 3.56e-10

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: 59.23  E-value: 3.56e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    66 SWNVDGLR----AWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQEL-PGLSHqYWSAPSDKEGYSGVGLLSR---- 136
Cdd:cd09084   3 SYNVRSFNrykwKDDPDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLLlKGYPY-YYVVYKSDSGGTGLAIFSKypil 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   137 ---------------QCPLKV-------------SYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRglvrleyRQRW 188
Cdd:cd09084  82 nsgsidfpntnnnaiFADIRVggdtirvynvhleSFRITPSDKELYKEEKKAKELSRNLLRKLAEAFKR-------RAAQ 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   189 DEAFRKFLKglASRKPLVLCGDLN-----VAHEEIdlrnpKGNKKNAgFtpqERQGFGellqavpladsfrhlypntpYA 263
Cdd:cd09084 155 ADLLAADIA--ASPYPVIVCGDFNdtpasYVYRTL-----KKGLTDA-F---VEAGSG--------------------FG 203

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
gi 113984   264 YTFWTYMMnarsknvGWRLDYFLLSHSL--LPALCDSKIrskalGSDHCPITLYL 316
Cdd:cd09084 204 YTFNGLFF-------PLRIDYILTSKGFkvLRYRVDPGK-----YSDHYPIVATL 246
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 55-219 3.70e-08

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 52.22  E-value: 3.70e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    55 PSGKPATLKICSWNVDGLRAWIKKKGLD----WVKEEAPDILCLQEtkcsenklpaelqelpglshqywsapsdkegysg 130
Cdd:COG3568   1 AAAAAATLRVMTYNIRYGLGTDGRADLEriarVIRALDPDVVALQE---------------------------------- 46

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   131 VGLLSRqcplkvsYGIGDEEH------DQEGR-VIVAEFD----SFVLVTAYVpnagrGLVRLEYRQRWDEAFRKFLKGL 199
Cdd:COG3568  47 NAILSR-------YPIVSSGTfdlpdpGGEPRgALWADVDvpgkPLRVVNTHL-----DLRSAAARRRQARALAELLAEL 114

                       170       180
                ....*....|....*....|
gi 113984   200 ASRKPLVLCGDLNvaheEID 219
Cdd:COG3568 115 PAGAPVILAGDFN----DID 130
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 62-233 2.10e-05

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: 45.03  E-value: 2.10e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984    62 LKICSWNVDGLRAW--------IKKKgldwVKEEAPDILCLQETkcsenkLPAELQELpgLSHQYWSA--------PSDK 125
Cdd:cd09080   1 LKVLTWNVDFLDDVnlaermraILKL----LEELDPDVIFLQEV------TPPFLAYL--LSQPWVRKnyyfsegpPSPA 68

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113984   126 EGYSGVGLLSRQCPLKVSYGIgdeEHDQEGRvivaefdSFVLVTAYVPNAGRglVRL------------EYRQRWDEAFR 193
Cdd:cd09080  69 VDPYGVLILSKKSLVVRRVPF---TSTRMGR-------NLLAAEINLGSGEP--LRLatthleslkshsSERTAQLEEIA 136

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 113984   194 KFLKGLASRKPLVLCGDLNVAHEEIDLRNPK----------GNKKNAGFT 233
Cdd:cd09080 137 KKLKKPPGAANVILGGDFNLRDKEDDTGGLPngfvdaweelGPPGEPGYT 186
 
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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