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Conserved domains on  [gi|446690104|ref|WP_000767450|]
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exodeoxyribonuclease III [Streptococcus oralis]

Protein Classification

exodeoxyribonuclease III( domain architecture ID 10173395)

exodeoxyribonuclease III is a Mg-dependent 3' to 5' exonuclease acting on dsDNA, which releases 5' phosphomononucleotides as degradation products; similar to bacterial exodeoxyribonuclease III and eukaryotic DNA-(apurinic or apyrimidinic site) endonuclease

CATH:  3.60.10.10
EC:  3.1.11.2
Gene Ontology:  GO:0003677|GO:0046872|GO:0004519|GO:0004527|GO:0006281|GO:0008311
PubMed:  7885481|10838565
SCOP:  4002213

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 ...
 1-273 1.62e-116

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: 334.52  E-value: 1.62e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLNAALTSDsaraklsqeVLQTLVAENADIIAIQETKLSAKGPTKKhleiLEELFPGYENTWRSSQepaRK 80
Cdd:cd09087    1 LKIISWNVNGLRALLKKG---------LLDYVKKEDPDILCLQETKLQEGDVPKE----LKELLKGYHQYWNAAE---KK 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  81 GYAGTMFLYKKEltPTISFPEIGAPStMDLEGRIITLEFDTFFVTQVYTPNAGDGLKRLEERQVWDVKYAEYLAQLDKEK 160
Cdd:cd09087   65 GYSGTAILSKKK--PLSVTYGIGIEE-HDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKK 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 161 PVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDVPERYTWWAQRSKtSKINNTGWRID 240
Cdd:cd09087  142 PVIWCGDLNVAHEEIDLANPKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGN-ARAKNVGWRLD 220

                        250       260       270
                 ....*....|....*....|....*....|...
gi 446690104 241 YWLTSNRVAEKVTKSDMIDSGARQDHTPIVLEI 273
Cdd:cd09087  221 YFLVSERLKDRVVDSFIRSDIMGSDHCPIGLEL 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 ...
 1-273 1.62e-116

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: 334.52  E-value: 1.62e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLNAALTSDsaraklsqeVLQTLVAENADIIAIQETKLSAKGPTKKhleiLEELFPGYENTWRSSQepaRK 80
Cdd:cd09087    1 LKIISWNVNGLRALLKKG---------LLDYVKKEDPDILCLQETKLQEGDVPKE----LKELLKGYHQYWNAAE---KK 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  81 GYAGTMFLYKKEltPTISFPEIGAPStMDLEGRIITLEFDTFFVTQVYTPNAGDGLKRLEERQVWDVKYAEYLAQLDKEK 160
Cdd:cd09087   65 GYSGTAILSKKK--PLSVTYGIGIEE-HDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKK 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 161 PVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDVPERYTWWAQRSKtSKINNTGWRID 240
Cdd:cd09087  142 PVIWCGDLNVAHEEIDLANPKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGN-ARAKNVGWRLD 220

                        250       260       270
                 ....*....|....*....|....*....|...
gi 446690104 241 YWLTSNRVAEKVTKSDMIDSGARQDHTPIVLEI 273
Cdd:cd09087  221 YFLVSERLKDRVVDSFIRSDIMGSDHCPIGLEL 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-274 6.46e-111

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: 320.38  E-value: 6.46e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104    1 MKLISWNIDSLnaaltsdsaRAKLSQEVLQTLVAENADIIAIQETKLSAkGPTKKHLEileeLFPGYENTWRSSQeparK 80
Cdd:TIGR00633   1 MKIISWNVNGL---------RARLHKLFLDWLKEEQPDVLCLQETKVAD-EQFPAELF----EELGYHVFFHGAK----K 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   81 GYAGTMFLYKKEltPTISFPEIGApSTMDLEGRIITLEFDTFFVTQVYTPNAG-DGLKRLEER-QVWDVKYAEYLAQLDK 158
Cdd:TIGR00633  63 GYSGVAILSKVE--PLDVRYGFGG-EPHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKlQFWDALFQYLEKELDA 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  159 EKPVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDVPERYTWWAQRSKtSKINNTGWR 238
Cdd:TIGR00633 140 GKPVVICGDMNVAHTEIDLGNPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDAYTWWDYRSG-ARDRNRGWR 218

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 446690104  239 IDYWLTSNRVAEKVTKSdMIDSGARQ-DHTPIVLEIE 274
Cdd:TIGR00633 219 IDYFLVSEPLAERVVDS-YIDSEIRGsDHCPIVLELD 254
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-274 3.61e-89

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 265.02  E-value: 3.61e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLNAALtsdsaraklsQEVLQTLVAENADIIAIQETKLSAKGPTKKHLEileelFPGYENTWRSsqepaRK 80
Cdd:COG0708    1 MKIASWNVNGIRARL----------PKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFE-----AAGYHVYFHG-----QK 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  81 GYAGTMFLYKKELTP-TISFPEigapSTMDLEGRIITLEFDTFFVTQVYTPNAGD-GLKRLEERQVWDVKYAEYLAQLDK 158
Cdd:COG0708   61 GYNGVAILSRLPPEDvRRGLGG----DEFDAEGRYIEADFGGVRVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLA 136

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 159 -EKPVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDVPERYTWWAQRSKtSKINNTGW 237
Cdd:COG0708  137 pGRPLILCGDFNIAPTEIDVKNPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAG-AFARNRGW 215

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 446690104 238 RIDYWLTSNRVAEKVTKSDmIDSGARQ-----DHTPIVLEIE 274
Cdd:COG0708  216 RIDYILASPALADRLKDAG-IDREPRGderpsDHAPVVVELD 256
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-273 6.36e-59

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 187.98  E-value: 6.36e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLnaaltsdsaRAKLSQEVLQTLVAENADIIAIQETKLSAKGPTKKhleileelFPGYENTWRSSqepARK 80
Cdd:PRK13911   1 MKLISWNVNGL---------RACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFE--------FKGYFDFWNCA---IKK 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  81 GYAGTMFLYKKE---LTPTISFPEigapstMDLEGRIITLEFDTFFVTQVYTPNAGDGLKRLEERQVWDVKYAEYLAQLD 157
Cdd:PRK13911  61 GYSGVVTFTKKEplsVSYGINIEE------HDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALE 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 158 KEKPVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDVPERYTWWAQRSKtSKINNTGW 237
Cdd:PRK13911 135 LKKPVIVCGDLNVAHNEIDLENPKTNRKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKEKAYTWWSYMQQ-ARDKNIGW 213

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 446690104 238 RIDYWLTSNRVAEKVTKSDMIDSGARQDHTPIVLEI 273
Cdd:PRK13911 214 RIDYFLCSNPLKTRLKDALIYKDILGSDHCPVGLEL 249
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-170 9.11e-15

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: 70.72  E-value: 9.11e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104    4 ISWNIDSLNAALTSDSARAKlsqEVLQTLVAENADIIAIQETKLSakgptkkHLEILEELFPGYENTWRSSQEPARKGYA 83
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRKLD---ALAALIRAYDPDVVALQETDDD-------DASRLLLALLAYGGFLSYGGPGGGGGGG 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   84 GTMFLYKKELTPTI--SFPEIGAPSTmdleGRIITLEFDTFFVTQVYTPNAGDGLKRLEERQVWDVKYAEYLAQLDKEKP 161
Cdd:pfam03372  71 GVAILSRYPLSSVIlvDLGEFGDPAL----RGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEP 146


                  ....*....
gi 446690104  162 VLATGDYNV 170
Cdd:pfam03372 147 VILAGDFNA 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 ...
 1-273 1.62e-116

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: 334.52  E-value: 1.62e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLNAALTSDsaraklsqeVLQTLVAENADIIAIQETKLSAKGPTKKhleiLEELFPGYENTWRSSQepaRK 80
Cdd:cd09087    1 LKIISWNVNGLRALLKKG---------LLDYVKKEDPDILCLQETKLQEGDVPKE----LKELLKGYHQYWNAAE---KK 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  81 GYAGTMFLYKKEltPTISFPEIGAPStMDLEGRIITLEFDTFFVTQVYTPNAGDGLKRLEERQVWDVKYAEYLAQLDKEK 160
Cdd:cd09087   65 GYSGTAILSKKK--PLSVTYGIGIEE-HDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKK 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 161 PVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDVPERYTWWAQRSKtSKINNTGWRID 240
Cdd:cd09087  142 PVIWCGDLNVAHEEIDLANPKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGN-ARAKNVGWRLD 220

                        250       260       270
                 ....*....|....*....|....*....|...
gi 446690104 241 YWLTSNRVAEKVTKSDMIDSGARQDHTPIVLEI 273
Cdd:cd09087  221 YFLVSERLKDRVVDSFIRSDIMGSDHCPIGLEL 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-274 6.46e-111

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: 320.38  E-value: 6.46e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104    1 MKLISWNIDSLnaaltsdsaRAKLSQEVLQTLVAENADIIAIQETKLSAkGPTKKHLEileeLFPGYENTWRSSQeparK 80
Cdd:TIGR00633   1 MKIISWNVNGL---------RARLHKLFLDWLKEEQPDVLCLQETKVAD-EQFPAELF----EELGYHVFFHGAK----K 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   81 GYAGTMFLYKKEltPTISFPEIGApSTMDLEGRIITLEFDTFFVTQVYTPNAG-DGLKRLEER-QVWDVKYAEYLAQLDK 158
Cdd:TIGR00633  63 GYSGVAILSKVE--PLDVRYGFGG-EPHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKlQFWDALFQYLEKELDA 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  159 EKPVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDVPERYTWWAQRSKtSKINNTGWR 238
Cdd:TIGR00633 140 GKPVVICGDMNVAHTEIDLGNPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDAYTWWDYRSG-ARDRNRGWR 218

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 446690104  239 IDYWLTSNRVAEKVTKSdMIDSGARQ-DHTPIVLEIE 274
Cdd:TIGR00633 219 IDYFLVSEPLAERVVDS-YIDSEIRGsDHCPIVLELD 254
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-274 3.61e-89

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 265.02  E-value: 3.61e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLNAALtsdsaraklsQEVLQTLVAENADIIAIQETKLSAKGPTKKHLEileelFPGYENTWRSsqepaRK 80
Cdd:COG0708    1 MKIASWNVNGIRARL----------PKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFE-----AAGYHVYFHG-----QK 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  81 GYAGTMFLYKKELTP-TISFPEigapSTMDLEGRIITLEFDTFFVTQVYTPNAGD-GLKRLEERQVWDVKYAEYLAQLDK 158
Cdd:COG0708   61 GYNGVAILSRLPPEDvRRGLGG----DEFDAEGRYIEADFGGVRVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLA 136

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 159 -EKPVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDVPERYTWWAQRSKtSKINNTGW 237
Cdd:COG0708  137 pGRPLILCGDFNIAPTEIDVKNPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAG-AFARNRGW 215

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 446690104 238 RIDYWLTSNRVAEKVTKSDmIDSGARQ-----DHTPIVLEIE 274
Cdd:COG0708  216 RIDYILASPALADRLKDAG-IDREPRGderpsDHAPVVVELD 256
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-273 1.42e-71

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: 220.24  E-value: 1.42e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   2 KLISWNIDSLnaaltsdsaRAKLSQEVLQTLVAENADIIAIQETKLSAKgptkkhlEILEELF--PGYENTWRSSQepaR 79
Cdd:cd09073    1 KIISWNVNGL---------RARLKKGVLKWLKEEKPDILCLQETKADED-------KLPEELQhvEGYHSYWSPAR---K 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  80 KGYAGTMFLYKKE-LTPTISFPEigapSTMDLEGRIITLEFDTFFVTQVYTPNAGDGLKRLEERQVWDVKYAEYL-AQLD 157
Cdd:cd09073   62 KGYSGVATLSKEEpLDVSYGIGG----EEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLeKLRK 137

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 158 KEKPVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDVPeRYTWWAQRSKtSKINNTGW 237
Cdd:cd09073  138 RGKPVVICGDFNVAHEEIDLARPKKNEKNAGFTPEERAWFDKLLSLGYVDTFRHFHPEPG-AYTWWSYRGN-ARERNVGW 215

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 446690104 238 RIDYWLTSNRVAEKVTKSDmIDSGAR-QDHTPIVLEI 273
Cdd:cd09073  216 RIDYFLVSEELAEKVKDSG-ILSKVKgSDHAPVTLEL 251
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-273 3.27e-68

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: 211.75  E-value: 3.27e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLnaaltsdsaRAKLSQEVLQTLVAENADIIAIQETKLSAKgptkkhlEILEELF--PGYENTWRSSQepa 78
Cdd:cd09085    1 MKIISWNVNGL---------RAVHKKGFLDWFKEEKPDILCLQETKAQPE-------QLPEDLRniEGYHSYFNSAE--- 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  79 RKGYAGTMfLYKKelTPTISFPEIGAPSTMDLEGRIITLEFDTFFVTQVYTPNAGDGLKRLeerqvwDVK---YAEYLAQ 155
Cdd:cd09085   62 RKGYSGVA-LYSK--IEPDSVREGLGVEEFDNEGRILIADFDDFTLFNIYFPNGQMSEERL------DYKlefYDAFLEY 132

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 156 LDKE----KPVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDvPERYTWWAQRSKtSK 231
Cdd:cd09085  133 LNELrdsgKNVIICGDFNTAHKEIDLARPKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKE-PGQYTWWSYRTR-AR 210

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 446690104 232 INNTGWRIDYWLTSNRVAEKVTKSDMIDSGARQDHTPIVLEI 273
Cdd:cd09085  211 ERNVGWRIDYFFVNEEFKPKVKDAGILPDVMGSDHCPVSLEL 252
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-273 3.98e-64

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: 201.46  E-value: 3.98e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104    1 MKLISWNIDSLNAALtsdsaraklsQEVLQTLVAENADIIAIQETKLSakgPTKKHLEILEELfpGYENTWRSSqeparK 80
Cdd:TIGR00195   1 MKIISWNVNGLRARP----------HKGLAWLKENQPDVLCLQETKVQ---DEQFPLEPFHKE--GYHVFFSGQ-----K 60

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   81 GYAGTMFLYKKE-LTPTISFPEigapSTMDLEGRIITLEFDTFFVTQVYTPNAG-DGLKRLEERQVWDVKYAEYLAQL-D 157
Cdd:TIGR00195  61 GYSGVAIFSKEEpISVRRGFGV----EEEDAEGRIIMAEFDSFLVINGYFPNGSrDDSEKLPYKLQWLEALQNYLEKLvD 136

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  158 KEKPVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDvPERYTWWAQRSKtSKINNTGW 237
Cdd:TIGR00195 137 KDKPVLICGDMNIAPTEIDLHIPDENRNHTGFLPEEREWLDRLLEAGLVDTFRKFNPD-EGAYSWWDYRTK-ARDRNRGW 214

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 446690104  238 RIDYWLTSNRVAEKVTKS----DMIDSGARQDHTPIVLEI 273
Cdd:TIGR00195 215 RIDYFLVSEPLKERCVDCgidyDIRGSEKPSDHCPVVLEF 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-273 6.36e-59

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 187.98  E-value: 6.36e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLnaaltsdsaRAKLSQEVLQTLVAENADIIAIQETKLSAKGPTKKhleileelFPGYENTWRSSqepARK 80
Cdd:PRK13911   1 MKLISWNVNGL---------RACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFE--------FKGYFDFWNCA---IKK 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  81 GYAGTMFLYKKE---LTPTISFPEigapstMDLEGRIITLEFDTFFVTQVYTPNAGDGLKRLEERQVWDVKYAEYLAQLD 157
Cdd:PRK13911  61 GYSGVVTFTKKEplsVSYGINIEE------HDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALE 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 158 KEKPVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDVPERYTWWAQRSKtSKINNTGW 237
Cdd:PRK13911 135 LKKPVIVCGDLNVAHNEIDLENPKTNRKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKEKAYTWWSYMQQ-ARDKNIGW 213

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 446690104 238 RIDYWLTSNRVAEKVTKSDMIDSGARQDHTPIVLEI 273
Cdd:PRK13911 214 RIDYFLCSNPLKTRLKDALIYKDILGSDHCPVGLEL 249
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-273 7.69e-53

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: 172.41  E-value: 7.69e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLNAALTSDsaraklsqeVLQTLVAENADIIAIQETKLSAkgptkkhlEILEELF---PGYENTWRSSQEp 77
Cdd:cd10281    1 MRVISVNVNGIRAAAKKG---------FLEWLAAQDADVVCLQEVRAQE--------EQLDDDFfepEGYNAYFFDAEK- 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  78 arKGYAGTMFLYKKELTPTISfpEIGAPsTMDLEGRIITLEFDTFFVTQVYTPNAGDGLKRLEERQVWDVKYAEYLAQLD 157
Cdd:cd10281   63 --KGYAGVAIYSRTQPKAVIY--GLGFE-EFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELR 137

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 158 KEKP-VLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLL-ATGFTDTFRHIHGDvPERYTWWAQRSKtSKINNT 235
Cdd:cd10281  138 RKRReFIVCGDFNIAHTEIDIKNWKANQKNSGFLPEERAWLDQVFgELGYVDAFRELNPD-EGQYTWWSNRGQ-ARANNV 215

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 446690104 236 GWRIDYWLTSNRVAEKVTKSDmIDSGAR-QDHTPIVLEI 273
Cdd:cd10281  216 GWRIDYQIATPGLASKVVSAW-IYREERfSDHAPLIVDY 253
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-273 2.47e-46

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: 155.75  E-value: 2.47e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLnaaltsdsaRAKLSQeVLQTLVAENADIIAIQETKLSakgptkkhleilEELFP-------GYENTWRS 73
Cdd:cd09086    1 MKIATWNVNSI---------RARLEQ-VLDWLKEEDPDVLCLQETKVE------------DDQFPadafealGYHVAVHG 58

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  74 sqepaRKGYAGTMFLYKKELT-PTISFPEIGApstmDLEGRIITLEFDTFFVTQVYTPNAGD-GLKRLEERQVWDVKYAE 151
Cdd:cd09086   59 -----QKAYNGVAILSRLPLEdVRTGFPGDPD----DDQARLIAARVGGVRVINLYVPNGGDiGSPKFAYKLDWLDRLIR 129

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 152 YLAQ-LDKEKPVLATGDYNVAHKEIDLANPASNRRSPGFTDEERAGFTNLLATGFTDTFRHIHGDvPERYTWWAQRSKtS 230
Cdd:cd09086  130 YLQKlLKPDDPLVLVGDFNIAPEDIDVWDPKQLLGKVLFTPEEREALRALLDLGFVDAFRALHPD-EKLFTWWDYRAG-A 207

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 446690104 231 KINNTGWRIDYWLTSNRVAEKVTKSDmIDSGARQ-----DHTPIVLEI 273
Cdd:cd09086  208 FERNRGLRIDHILASPALADRLKDVG-IDREPRGwekpsDHAPVVAEL 254
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-273 1.93e-29

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: 113.18  E-value: 1.93e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   2 KLISWNIDSLNAALTSDSARAKLS-QEVLQTLvaeNADIIAIQETKLsakgpTKKHLEILEELFPGYENTWRSSQepARK 80
Cdd:cd09088    1 RIVTWNVNGIRTRLQYQPWNKENSlKSFLDSL---DADIICLQETKL-----TRDELDEPSAIVEGYDSFFSFSR--GRK 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  81 GYAGTMFLYKKE--------------LTPTISFPE------IGA------------PSTMDLEGRIITLEFDTFFVTQVY 128
Cdd:cd09088   71 GYSGVATYCRDSaatpvaaeegltgvLSSPNQKNElsenddIGCygemleftdskeLLELDSEGRCVLTDHGTFVLINVY 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 129 TPNAGDGlkrLEERQVWDVKYAEYL-----AQLDKEKPVLATGDYNVAHKEIDLANPASNRRSPGFTDEE---RAGFTNL 200
Cdd:cd09088  151 CPRADPE---KEERLEFKLDFYRLLeerveALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQL 227

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 201 LATG----------FTDTFRHIHGDVPERYTWWAQRSkTSKINNTGWRIDYWLTSNRVAEKVTKSDMIDSGARQDHTPIV 270
Cdd:cd09088  228 LGDSgegggspgglLIDSFRYFHPTRKGAYTCWNTLT-GARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVY 306


                 ...
gi 446690104 271 LEI 273
Cdd:cd09088  307 ADL 309
PRK11756 PRK11756
exonuclease III; Provisional
 1-275 5.16e-24

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 97.66  E-value: 5.16e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLnaaltsdsaRAKLSQevLQTLVAE-NADIIAIQETKLSakgptkkhleilEELFP-------GYeNTWR 72
Cdd:PRK11756   1 MKFVSFNINGL---------RARPHQ--LEAIIEKhQPDVIGLQETKVH------------DEMFPleevealGY-HVFY 56

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  73 SSQeparKGYAGTMFLYKKE-LTPTISFPEIGApstmDLEGRIITLEFDTFF----VTQVYTPNaGDG----LKRLEERQ 143
Cdd:PRK11756  57 HGQ----KGHYGVALLSKQTpIAVRKGFPTDDE----EAQRRIIMATIPTPNgnltVINGYFPQ-GESrdhpTKFPAKRQ 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 144 VwdvkYAE---YL-AQLDKEKPVLATGDYNVAHKEIDLANPASNRR---SPG---FTDEERAGFTNLLATGFTDTFRHIH 213
Cdd:PRK11756 128 F----YQDlqnYLeTELSPDNPLLIMGDMNISPTDLDIGIGEENRKrwlRTGkcsFLPEEREWLDRLMDWGLVDTFRQLN 203

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446690104 214 GDVPERYTWWAQRSKtSKINNTGWRIDYWLTSNRVAEKVTKSDmIDSGAR-----QDHTPIVLEIEL 275
Cdd:PRK11756 204 PDVNDRFSWFDYRSK-GFDDNRGLRIDLILATQPLAERCVETG-IDYDIRgmekpSDHAPIWATFKL 268
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-273 1.33e-19

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: 85.23  E-value: 1.33e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   3 LISWNIDSLNAAlTSDSARAKLSQEvlqtlvaENADIIAIQETKLSakgpTKKHLEILEELFPGYENTWrsSQEPARKGY 82
Cdd:cd08372    1 VASYNVNGLNAA-TRASGIARWVRE-------LDPDIVCLQEVKDS----QYSAVALNQLLPEGYHQYQ--SGPSRKEGY 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  83 AGTMFLYKKELTPTISFPEIGAPSTMDLEGRIITLEF---DTFFVtqVYTPNAGDGLKRLEERQVWDVKYAEYL--AQLD 157
Cdd:cd08372   67 EGVAILSKTPKFKIVEKHQYKFGEGDSGERRAVVVKFdvhDKELC--VVNAHLQAGGTRADVRDAQLKEVLEFLkrLRQP 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 158 KEKPVLATGDYNVAHKEIDLANPASNRRSPGFTDeeragftnllatgFTDTFRHIHGDvperYTWWAQRSktskinNTGW 237
Cdd:cd08372  145 NSAPVVICGDFNVRPSEVDSENPSSMLRLFVALN-------------LVDSFETLPHA----YTFDTYMH------NVKS 201

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 446690104 238 RIDYWLTSNRVAEKVTKSDMIDSGARQ----DHTPIVLEI 273
Cdd:cd08372  202 RLDYIFVSKSLLPSVKSSKILSDAARAripsDHYPIEVTL 241
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-273 1.07e-17

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: 79.70  E-value: 1.07e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   3 LISWNIDSLNAaltsdsaRAKLsQEVLQTLVAENADIIAIQETKLSAKGPTKKHLEileelfpGYENTWRSSQEPARKGY 82
Cdd:cd09076    1 IGTLNVRGLRS-------PGKR-AQLLEELKRKKLDILGLQETHWTGEGELKKKRE-------GGTILYSGSDSGKSRGV 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  83 AgtmFLYKKELTP-TISFpeigapsTMDLEGRIITLEFD----TFFVTQVYTPNAGDGLKRleeRQVWDvKYAEYLAQLD 157
Cdd:cd09076   66 A---ILLSKTAANkLLEY-------TKVVSGRIIMVRFKikgkRLTIINVYAPTARDEEEK---EEFYD-QLQDVLDKVP 131

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 158 KEKPVLATGDYNVAHKEIDLANPASNRRSpgfTDEERAGFTNLLATGFTDTFRHIHGDVPeRYTWwaqRSKTSKINNtgw 237
Cdd:cd09076  132 RHDTLIIGGDFNAVLGPKDDGRKGLDKRN---ENGERALSALIEEHDLVDVWRENNPKTR-EYTW---RSPDHGSRS--- 201

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 446690104 238 RIDYWLTSNRVAEKVTKSdMIDSGARQDHTPIVLEI 273
Cdd:cd09076  202 RIDRILVSKRLRVKVKKT-KITPGAGSDHRLVTLKL 236
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-170 9.11e-15

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: 70.72  E-value: 9.11e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104    4 ISWNIDSLNAALTSDSARAKlsqEVLQTLVAENADIIAIQETKLSakgptkkHLEILEELFPGYENTWRSSQEPARKGYA 83
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRKLD---ALAALIRAYDPDVVALQETDDD-------DASRLLLALLAYGGFLSYGGPGGGGGGG 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   84 GTMFLYKKELTPTI--SFPEIGAPSTmdleGRIITLEFDTFFVTQVYTPNAGDGLKRLEERQVWDVKYAEYLAQLDKEKP 161
Cdd:pfam03372  71 GVAILSRYPLSSVIlvDLGEFGDPAL----RGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEP 146


                  ....*....
gi 446690104  162 VLATGDYNV 170
Cdd:pfam03372 147 VILAGDFNA 155
MnuA_DNase1-like cd10283
Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a ...
 2-273 3.90e-08

Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a membrane-associated nuclease related to Deoxyribonuclease 1 (DNase1 or DNase I, EC 3.1.21.1). The in vivo role of MnuA is as yet undetermined. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197338 [Multi-domain]  Cd Length: 266  Bit Score: 53.17  E-value: 3.90e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   2 KLISWNIdsLNAALTSDSARAKLSQEVLQTLvaeNADIIAIQEtkLSAKGPTKKHLEILEELFPGYENTWRSSQEPARKG 81
Cdd:cd10283    2 RIASWNI--LNFGNSKGKEKNPAIAEIISAF---DLDLIALQE--VMDNGGGLDALAKLVNELNKPGGTWKYIVSDKTGG 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  82 YAGTM----FLYKKELTPTISfPEIGAPSTMDLEG---------RIITLEFDTFFVT-QVYTP---NAGDGLKRLEE-RQ 143
Cdd:cd10283   75 SSGDKeryaFLYKSSKVRKVG-KAVLEKDSNTDGFarppyaakfKSGGTGFDFTLVNvHLKSGgssKSGQGAKRVAEaQA 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 144 VwdVKYAEYLAQLDKEKPVLATGDYNvahkeIDLANPA-SNRRSPGFTD-EERAGFTNLLATGFTDTFRHIhgdvperyt 221
Cdd:cd10283  154 L--AEYLKELADEDPDDDVILLGDFN-----IPADEDAfKALTKAGFKSlLPDSTNLSTSFKGYANSYDNI--------- 217

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446690104 222 wWAQRSKTSKINNTGwRIDYWltsNRVAEKVTKSDMIDSGARQ--DHTPIVLEI 273
Cdd:cd10283  218 -FVSGNLKEKFSNSG-VFDFN---ILVDEAGEEDLDYSKWRKQisDHDPVWVEF 266
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-275 2.19e-07

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 51.15  E-value: 2.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLNAAltsdsaraklSQEVLQTLVAENADIIAIQETklsakgpTKKHLEILEELFPGYENtwrsSQEPARK 80
Cdd:COG3021   95 LRVLTANVLFGNAD----------AEALAALVREEDPDVLVLQET-------TPAWEEALAALEADYPY----RVLCPLD 153

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104  81 GYAGTMFLYKKELTP--TISFPEIGAPS---TMDLEGRIITLefdtfFVTQVYTPNAGDGLKRLEERQVwdvkyAEYLAQ 155
Cdd:COG3021  154 NAYGMALLSRLPLTEaeVVYLVGDDIPSiraTVELPGGPVRL-----VAVHPAPPVGGSAERDAELAAL-----AKAVAA 223

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104 156 LDkeKPVLATGDYNVAhkeidlanpasnRRSPGFtdeerAGFTNllATGFTDTfRHIHGDVPeryTWWAQRSktskinNT 235
Cdd:COG3021  224 LD--GPVIVAGDFNAT------------PWSPTL-----RRLLR--ASGLRDA-RAGRGLGP---TWPANLP------FL 272

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 446690104 236 GWRIDYWLTSNRVA-EKVTKSDMIDSgarqDHTPIVLEIEL 275
Cdd:COG3021  273 RLPIDHVLVSRGLTvVDVRVLPVIGS----DHRPLLAELAL 309
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 1-102 1.43e-03

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: 39.25  E-value: 1.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446690104   1 MKLISWNIDSLNaaltsDSARAKLSQEVLQTLVAENADIIAIQETklsakgpTKKHLEILEELFPgyentWRS------- 73
Cdd:cd09080    1 LKVLTWNVDFLD-----DVNLAERMRAILKLLEELDPDVIFLQEV-------TPPFLAYLLSQPW-----VRKnyyfseg 63

                         90       100       110
                 ....*....|....*....|....*....|
gi 446690104  74 SQEPARKGYaGTMFLYKKELTPTIS-FPEI 102
Cdd:cd09080   64 PPSPAVDPY-GVLILSKKSLVVRRVpFTST 92
 
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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