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Conserved domains on  [gi|643730857|ref|WP_025253643|]
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exodeoxyribonuclease III [Corynebacterium vitaeruminis]

Protein Classification

XthA family protein( domain architecture ID 10002229)

XthA family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-254 1.62e-106

Exonuclease III [Replication, recombination and repair];


:

Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 308.54  E-value: 1.62e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTRVERVQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGLNQWNGVAIISRVGIEDVATSF 80
Cdd:COG0708    1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLPPEDVRRGL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  81 PGQPGfnkDPgkkqaiEARALGATCGGVRVWSLYVPNGREIADPHYDYKLRWLYALSCYVGA--APDERMVLLGDYNIAP 158
Cdd:COG0708   81 GGDEF---DA------EGRYIEADFGGVRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAEllAPGRPLILCGDFNIAP 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 159 RDQDVWDIRAFEGKTHVTEPERQAFESLLDAGL-DITSPLEG-----YSYWDYKGGRFQRGQGMLIDFQL-SRGLRP--T 229
Cdd:COG0708  152 TEIDVKNPKANLKNAGFLPEERAWFDRLLELGLvDAFRALHPdvegqYTWWSYRAGAFARNRGWRIDYILaSPALADrlK 231

                        250       260
                 ....*....|....*....|....*
gi 643730857 230 NSFIDVDERRGTGASDHAPVVVDYE 254
Cdd:COG0708  232 DAGIDREPRGDERPSDHAPVVVELD 256
 
Name Accession Description Interval E-value
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-254 1.62e-106

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 308.54  E-value: 1.62e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTRVERVQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGLNQWNGVAIISRVGIEDVATSF 80
Cdd:COG0708    1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLPPEDVRRGL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  81 PGQPGfnkDPgkkqaiEARALGATCGGVRVWSLYVPNGREIADPHYDYKLRWLYALSCYVGA--APDERMVLLGDYNIAP 158
Cdd:COG0708   81 GGDEF---DA------EGRYIEADFGGVRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAEllAPGRPLILCGDFNIAP 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 159 RDQDVWDIRAFEGKTHVTEPERQAFESLLDAGL-DITSPLEG-----YSYWDYKGGRFQRGQGMLIDFQL-SRGLRP--T 229
Cdd:COG0708  152 TEIDVKNPKANLKNAGFLPEERAWFDRLLELGLvDAFRALHPdvegqYTWWSYRAGAFARNRGWRIDYILaSPALADrlK 231

                        250       260
                 ....*....|....*....|....*
gi 643730857 230 NSFIDVDERRGTGASDHAPVVVDYE 254
Cdd:COG0708  232 DAGIDREPRGDERPSDHAPVVVELD 256
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-252 2.74e-106

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: 307.90  E-value: 2.74e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTRVERVQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGLNQWNGVAIISRVGIEDVATSF 80
Cdd:cd09086    1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHGQKAYNGVAILSRLPLEDVRTGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  81 PGQPgfnKDPgkkqaiEARALGATCGGVRVWSLYVPNGREIADPHYDYKLRWLYALSCYVGA--APDERMVLLGDYNIAP 158
Cdd:cd09086   81 PGDP---DDD------QARLIAARVGGVRVINLYVPNGGDIGSPKFAYKLDWLDRLIRYLQKllKPDDPLVLVGDFNIAP 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 159 RDQDVWDIRAFEGKTHVTEPERQAFESLLDAGL-DI---TSPLEG-YSYWDYKGGRFQRGQGMLIDFQL-SRGLRP--TN 230
Cdd:cd09086  152 EDIDVWDPKQLLGKVLFTPEEREALRALLDLGFvDAfraLHPDEKlFTWWDYRAGAFERNRGLRIDHILaSPALADrlKD 231

                        250       260
                 ....*....|....*....|..
gi 643730857 231 SFIDVDERRGTGASDHAPVVVD 252
Cdd:cd09086  232 VGIDREPRGWEKPSDHAPVVAE 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-254 2.18e-76

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: 231.78  E-value: 2.18e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857    1 MRIVNWNVNSMRTRVERVQ-AFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGL-NQWNGVAIISRVGIEDVAT 78
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFlDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAkKGYSGVAILSKVEPLDVRY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   79 SFPGQPGFNkdpgkkqaiEARALGATCGGVRVWSLYVPNGREIADPHYDYKL-RWLYALSCYVGAAPDERMVLL-GDYNI 156
Cdd:TIGR00633  81 GFGGEPHDE---------EGRVITAEFDGFTVVNVYVPNGGSRDLERLEYKLqFWDALFQYLEKELDAGKPVVIcGDMNV 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  157 APRDQDVWDIRAFEGKTHVTEPERQAFESLLDAGLDIT------SPLEGYSYWDYKGGRFQRGQGMLIDFQL-SRGL--R 227
Cdd:TIGR00633 152 AHTEIDLGNPKENKGNAGFTPEEREWFDELLEAGFVDTfrhfnpDTGDAYTWWDYRSGARDRNRGWRIDYFLvSEPLaeR 231

                         250       260
                  ....*....|....*....|....*..
gi 643730857  228 PTNSFIDVDERrgtgASDHAPVVVDYE 254
Cdd:TIGR00633 232 VVDSYIDSEIR----GSDHCPIVLELD 254
PRK11756 PRK11756
exonuclease III; Provisional
 1-255 6.97e-35

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 125.78  E-value: 6.97e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTRVERVQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGLNQWNGVAIISRVGIEDVATSF 80
Cdd:PRK11756   1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVALLSKQTPIAVRKGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  81 PGqpgfNKDPGKKQAIEARALGATcGGVRVWSLYVPNGREIADP-HYDYKLRWLYALSCYVGA--APDERMVLLGDYNIA 157
Cdd:PRK11756  81 PT----DDEEAQRRIIMATIPTPN-GNLTVINGYFPQGESRDHPtKFPAKRQFYQDLQNYLETelSPDNPLLIMGDMNIS 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 158 PRDQDV---------WdIRafEGKTHVTEPERQAFESLLDAGL-DITSPL-----EGYSYWDYKGGRFQRGQGMLIDFQL 222
Cdd:PRK11756 156 PTDLDIgigeenrkrW-LR--TGKCSFLPEEREWLDRLMDWGLvDTFRQLnpdvnDRFSWFDYRSKGFDDNRGLRIDLIL 232

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 643730857 223 -SRGL--RPTNSFIDVDERRGTGASDHAPVVVDYEL 255
Cdd:PRK11756 233 aTQPLaeRCVETGIDYDIRGMEKPSDHAPIWATFKL 268
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-156 3.82e-13

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


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 66.09  E-value: 3.82e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857    4 VNWNVNS-------MRTRVERVQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGLNQ---WNGVAIISRVGI 73
Cdd:pfam03372   1 LTWNVNGgnadaagDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGgggGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   74 EDVATSFPGQPGFNKDPGKKQAIEARALGATCGGVRVWSLYVPNGREIADPHYDYKLRWLyalscyvgAAPDERMVLLGD 153
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALL--------APRSEPVILAGD 152


                  ...
gi 643730857  154 YNI 156
Cdd:pfam03372 153 FNA 155
 
Name Accession Description Interval E-value
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-254 1.62e-106

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 308.54  E-value: 1.62e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTRVERVQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGLNQWNGVAIISRVGIEDVATSF 80
Cdd:COG0708    1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLPPEDVRRGL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  81 PGQPGfnkDPgkkqaiEARALGATCGGVRVWSLYVPNGREIADPHYDYKLRWLYALSCYVGA--APDERMVLLGDYNIAP 158
Cdd:COG0708   81 GGDEF---DA------EGRYIEADFGGVRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAEllAPGRPLILCGDFNIAP 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 159 RDQDVWDIRAFEGKTHVTEPERQAFESLLDAGL-DITSPLEG-----YSYWDYKGGRFQRGQGMLIDFQL-SRGLRP--T 229
Cdd:COG0708  152 TEIDVKNPKANLKNAGFLPEERAWFDRLLELGLvDAFRALHPdvegqYTWWSYRAGAFARNRGWRIDYILaSPALADrlK 231

                        250       260
                 ....*....|....*....|....*
gi 643730857 230 NSFIDVDERRGTGASDHAPVVVDYE 254
Cdd:COG0708  232 DAGIDREPRGDERPSDHAPVVVELD 256
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-252 2.74e-106

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: 307.90  E-value: 2.74e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTRVERVQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGLNQWNGVAIISRVGIEDVATSF 80
Cdd:cd09086    1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHGQKAYNGVAILSRLPLEDVRTGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  81 PGQPgfnKDPgkkqaiEARALGATCGGVRVWSLYVPNGREIADPHYDYKLRWLYALSCYVGA--APDERMVLLGDYNIAP 158
Cdd:cd09086   81 PGDP---DDD------QARLIAARVGGVRVINLYVPNGGDIGSPKFAYKLDWLDRLIRYLQKllKPDDPLVLVGDFNIAP 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 159 RDQDVWDIRAFEGKTHVTEPERQAFESLLDAGL-DI---TSPLEG-YSYWDYKGGRFQRGQGMLIDFQL-SRGLRP--TN 230
Cdd:cd09086  152 EDIDVWDPKQLLGKVLFTPEEREALRALLDLGFvDAfraLHPDEKlFTWWDYRAGAFERNRGLRIDHILaSPALADrlKD 231

                        250       260
                 ....*....|....*....|..
gi 643730857 231 SFIDVDERRGTGASDHAPVVVD 252
Cdd:cd09086  232 VGIDREPRGWEKPSDHAPVVAE 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-254 2.18e-76

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: 231.78  E-value: 2.18e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857    1 MRIVNWNVNSMRTRVERVQ-AFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGL-NQWNGVAIISRVGIEDVAT 78
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFlDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAkKGYSGVAILSKVEPLDVRY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   79 SFPGQPGFNkdpgkkqaiEARALGATCGGVRVWSLYVPNGREIADPHYDYKL-RWLYALSCYVGAAPDERMVLL-GDYNI 156
Cdd:TIGR00633  81 GFGGEPHDE---------EGRVITAEFDGFTVVNVYVPNGGSRDLERLEYKLqFWDALFQYLEKELDAGKPVVIcGDMNV 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  157 APRDQDVWDIRAFEGKTHVTEPERQAFESLLDAGLDIT------SPLEGYSYWDYKGGRFQRGQGMLIDFQL-SRGL--R 227
Cdd:TIGR00633 152 AHTEIDLGNPKENKGNAGFTPEEREWFDELLEAGFVDTfrhfnpDTGDAYTWWDYRSGARDRNRGWRIDYFLvSEPLaeR 231

                         250       260
                  ....*....|....*....|....*..
gi 643730857  228 PTNSFIDVDERrgtgASDHAPVVVDYE 254
Cdd:TIGR00633 232 VVDSYIDSEIR----GSDHCPIVLELD 254
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-251 1.43e-50

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: 166.02  E-value: 1.43e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857    1 MRIVNWNVNSMRTRVERVQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGLNQWNGVAIISRVGIEDVATSF 80
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQKGYSGVAIFSKEEPISVRRGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   81 PGQPgfnKDPgkkqaiEARALGATCGGVRVWSLYVPNGREIADPHYDYKLRWLYALSCYVGAAPDER--MVLLGDYNIAP 158
Cdd:TIGR00195  81 GVEE---EDA------EGRIIMAEFDSFLVINGYFPNGSRDDSEKLPYKLQWLEALQNYLEKLVDKDkpVLICGDMNIAP 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  159 RDQDVWDIRAFEGKTHVTEPERQAFESLLDAGLDIT----SPLEG-YSYWDYKGGRFQRGQGMLID-FQLSRGL--RPTN 230
Cdd:TIGR00195 152 TEIDLHIPDENRNHTGFLPEEREWLDRLLEAGLVDTfrkfNPDEGaYSWWDYRTKARDRNRGWRIDyFLVSEPLkeRCVD 231

                         250       260
                  ....*....|....*....|.
gi 643730857  231 SFIDVDERRGTGASDHAPVVV 251
Cdd:TIGR00195 232 CGIDYDIRGSEKPSDHCPVVL 252
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-253 3.33e-46

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: 154.75  E-value: 3.33e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   2 RIVNWNVNSMRTRVER-VQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGLNQ--WNGVAIISRVGIEDVAT 78
Cdd:cd09073    1 KIISWNVNGLRARLKKgVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPARKkgYSGVATLSKEEPLDVSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  79 SFPGQpgfNKDPgkkqaiEARALGATCGGVRVWSLYVPNGREIAdPHYDYKLRWLYALSCYVGAAPDER--MVLLGDYNI 156
Cdd:cd09073   81 GIGGE---EFDS------EGRVITAEFDDFYLINVYFPNGGRGL-ERLDYKLRFYEAFLEFLEKLRKRGkpVVICGDFNV 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 157 APRDQDVWDIRAFEGKTHVTEPERQAFESLLDAGL-D---ITSPLEG-YSYWDYKGGRFQRGQGMLIDFQL-SRGLRPT- 229
Cdd:cd09073  151 AHEEIDLARPKKNEKNAGFTPEERAWFDKLLSLGYvDtfrHFHPEPGaYTWWSYRGNARERNVGWRIDYFLvSEELAEKv 230

                        250       260
                 ....*....|....*....|....*
gi 643730857 230 -NSFIDVDERrgtgASDHAPVVVDY 253
Cdd:cd09073  231 kDSGILSKVK----GSDHAPVTLEL 251
PRK11756 PRK11756
exonuclease III; Provisional
 1-255 6.97e-35

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 125.78  E-value: 6.97e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTRVERVQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGLNQWNGVAIISRVGIEDVATSF 80
Cdd:PRK11756   1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVALLSKQTPIAVRKGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  81 PGqpgfNKDPGKKQAIEARALGATcGGVRVWSLYVPNGREIADP-HYDYKLRWLYALSCYVGA--APDERMVLLGDYNIA 157
Cdd:PRK11756  81 PT----DDEEAQRRIIMATIPTPN-GNLTVINGYFPQGESRDHPtKFPAKRQFYQDLQNYLETelSPDNPLLIMGDMNIS 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 158 PRDQDV---------WdIRafEGKTHVTEPERQAFESLLDAGL-DITSPL-----EGYSYWDYKGGRFQRGQGMLIDFQL 222
Cdd:PRK11756 156 PTDLDIgigeenrkrW-LR--TGKCSFLPEEREWLDRLMDWGLvDTFRQLnpdvnDRFSWFDYRSKGFDDNRGLRIDLIL 232

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 643730857 223 -SRGL--RPTNSFIDVDERRGTGASDHAPVVVDYEL 255
Cdd:PRK11756 233 aTQPLaeRCVETGIDYDIRGMEKPSDHAPIWATFKL 268
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-253 6.88e-33

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: 120.02  E-value: 6.88e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTRVER-VQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHF--GLNQWNGVAIISRVGIEDVA 77
Cdd:cd10281    1 MRVISVNVNGIRAAAKKgFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFdaEKKGYAGVAIYSRTQPKAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  78 TSFPGQPgFNKdpgkkqaiEARALGATCGGVRVWSLYVPNGrEIADPHYDYKLRWLYALSCYVGAAPDER--MVLLGDYN 155
Cdd:cd10281   81 YGLGFEE-FDD--------EGRYIEADFDNVSVASLYVPSG-SSGDERQEAKMAFLDAFLEHLKELRRKRreFIVCGDFN 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 156 IAPRDQDVWDIRAFEGKTHVTEPERQAFESLL------DAGLDITSPLEGYSYWDYKGGRFQRGQGMLIDFQL-SRGLRP 228
Cdd:cd10281  151 IAHTEIDIKNWKANQKNSGFLPEERAWLDQVFgelgyvDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIaTPGLAS 230

                        250       260
                 ....*....|....*....|....*..
gi 643730857 229 --TNSFIDVDERrgtgASDHAPVVVDY 253
Cdd:cd10281  231 kvVSAWIYREER----FSDHAPLIVDY 253
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-252 8.77e-28

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: 106.87  E-value: 8.77e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTRVER-VQAFLTRHDVDVLAVQETKCKDEQFP-YLAFEELGYEVAHFGLNQ--WNGVAIISRVGIEDV 76
Cdd:cd09087    1 LKIISWNVNGLRALLKKgLLDYVKKEDPDILCLQETKLQEGDVPkELKELLKGYHQYWNAAEKkgYSGTAILSKKKPLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  77 ATSFPGqPGFNKdpgkkqaiEARALGATCGGVRVWSLYVPN-GREIAdpHYDYKLRWLYALSCYVGAAPDERMVLL-GDY 154
Cdd:cd09087   81 TYGIGI-EEHDQ--------EGRVITAEFENFYLVNTYVPNsGRGLE--RLDRRKEWDVDFRAYLKKLDSKKPVIWcGDL 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 155 NIAPRDQDVWDIRAFEGKTHVTEPERQAFESLLDAGL-DI----TSPLEG-YSYWDYKGGRFQRGQGMLID-FQLSRGLR 227
Cdd:cd09087  150 NVAHEEIDLANPKTNKKSAGFTPEERESFTELLEAGFvDTfrhlHPDKEGaYTFWSYRGNARAKNVGWRLDyFLVSERLK 229

                        250       260
                 ....*....|....*....|....*..
gi 643730857 228 P--TNSFIdvdeRRGTGASDHAPVVVD 252
Cdd:cd09087  230 DrvVDSFI----RSDIMGSDHCPIGLE 252
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-253 1.95e-20

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: 86.95  E-value: 1.95e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTrVER--VQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYevahfgLNQWN--------GVAIISR 70
Cdd:cd09085    1 MKIISWNVNGLRA-VHKkgFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGY------HSYFNsaerkgysGVALYSK 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  71 VGIEDVATSFpGQPGFNkdpgkkqaIEARALGATCGGVRVWSLYVPNGREiADPHYDYKLRWLYALSCYVGA--APDERM 148
Cdd:cd09085   74 IEPDSVREGL-GVEEFD--------NEGRILIADFDDFTLFNIYFPNGQM-SEERLDYKLEFYDAFLEYLNElrDSGKNV 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 149 VLLGDYNIAPRDQDVWDIRAFEGKTHVTEPERQAFESLLDAGLDIT----SPLEG-YSYWDYKGGRFQRGQGMLID-FQL 222
Cdd:cd09085  144 IICGDFNTAHKEIDLARPKENEKVSGFLPEERAWMDKFIENGYVDTfrmfNKEPGqYTWWSYRTRARERNVGWRIDyFFV 223

                        250       260       270
                 ....*....|....*....|....*....|...
gi 643730857 223 SRGLRP--TNSFIdVDERRGtgaSDHAPVVVDY 253
Cdd:cd09085  224 NEEFKPkvKDAGI-LPDVMG---SDHCPVSLEL 252
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-156 3.82e-13

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


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 66.09  E-value: 3.82e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857    4 VNWNVNS-------MRTRVERVQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELGYEVAHFGLNQ---WNGVAIISRVGI 73
Cdd:pfam03372   1 LTWNVNGgnadaagDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGgggGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   74 EDVATSFPGQPGFNKDPGKKQAIEARALGATCGGVRVWSLYVPNGREIADPHYDYKLRWLyalscyvgAAPDERMVLLGD 153
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALL--------APRSEPVILAGD 152


                  ...
gi 643730857  154 YNI 156
Cdd:pfam03372 153 FNA 155
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-249 5.01e-12

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 63.94  E-value: 5.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTRVER-VQAFLTRHDVDVLAVQETKCKDEQFpylAFEELGYevahfgLNQWNgVAIisRVGIEDVATS 79
Cdd:PRK13911   1 MKLISWNVNGLRACMTKgFMDFFNSVDADVFCIQESKMQQEQN---TFEFKGY------FDFWN-CAI--KKGYSGVVTF 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  80 FPGQP-----GFNKDPGKKqaiEARALGATCGGVRVWSLYVPNGREiADPHYDYKLRWLYALSCYVGAAPDERMVLL-GD 153
Cdd:PRK13911  69 TKKEPlsvsyGINIEEHDK---EGRVITCEFESFYLVNVYTPNSQQ-ALSRLSYRMSWEVEFKKFLKALELKKPVIVcGD 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 154 YNIAPRDQDVWDIRAFEGKTHVTEPERQAFESLLDAGLDIT------SPLEGYSYWDYKGGRFQRGQGMLIDFQLSRGLR 227
Cdd:PRK13911 145 LNVAHNEIDLENPKTNRKNAGFSDEERGKFSELLNAGFIDTfryfypNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPL 224

                        250       260
                 ....*....|....*....|..
gi 643730857 228 PTNsFIDVDERRGTGASDHAPV 249
Cdd:PRK13911 225 KTR-LKDALIYKDILGSDHCPV 245
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-252 2.57e-10

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: 59.64  E-value: 2.57e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   2 RIVNWNVNSMRTRVER--------VQAFLTRHDVDVLAVQETKCKDEQFP-YLAFEElGYEvAHFGLNQ----WNGVAII 68
Cdd:cd09088    1 RIVTWNVNGIRTRLQYqpwnkensLKSFLDSLDADIICLQETKLTRDELDePSAIVE-GYD-SFFSFSRgrkgYSGVATY 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  69 SR----------VGIEDVATSfPGQPGFNKDPGK-------------KQA----IEARALGATCGGVRVWSLYVPNGREI 121
Cdd:cd09088   79 CRdsaatpvaaeEGLTGVLSS-PNQKNELSENDDigcygemleftdsKELleldSEGRCVLTDHGTFVLINVYCPRADPE 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 122 ADPHYDYKLRWLYALSCYVGAAPDE--RMVLLGDYNIAPRDQDVWD---IRAFEGKTHVTEPERQAFESLLDAGLDITSP 196
Cdd:cd09088  158 KEERLEFKLDFYRLLEERVEALLKAgrRVILVGDVNVSHRPIDHCDpddSEDFGGESFEDNPSRQWLDQLLGDSGEGGGS 237

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 643730857 197 LEG----------------YSYWDYKGGRFQRGQGMLIDFQL-SRGLRPtnSFIDVDERRGTGASDHAPVVVD 252
Cdd:cd09088  238 PGGllidsfryfhptrkgaYTCWNTLTGARPTNYGTRIDYILaDRGLLP--WVKAADILPEVEGSDHCPVYAD 308
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-256 2.92e-08

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 53.46  E-value: 2.92e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSMRTRVERVQAFLTRHDVDVLAVQE-TKCKDEQFPYLAfEELGYEVAHfGLNQWNGVAIISRVGIEDVATS 79
Cdd:COG3021   95 LRVLTANVLFGNADAEALAALVREEDPDVLVLQEtTPAWEEALAALE-ADYPYRVLC-PLDNAYGMALLSRLPLTEAEVV 172

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  80 FPGQPGFNkdpgkkqAIEARaLGATCGGVRVWS--LYVPNGREiadPHYDYKLRWLYALScyvgAAPDERMVLLGDYNIA 157
Cdd:COG3021  173 YLVGDDIP-------SIRAT-VELPGGPVRLVAvhPAPPVGGS---AERDAELAALAKAV----AALDGPVIVAGDFNAT 237

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 158 PRDqdvWDIRAFEGKTHVTEPERqafesllDAGLDITSPLegysywDYKGGRFQrgqgmlIDFQL-SRGLRPTNSfidvd 236
Cdd:COG3021  238 PWS---PTLRRLLRASGLRDARA-------GRGLGPTWPA------NLPFLRLP------IDHVLvSRGLTVVDV----- 290

                        250       260
                 ....*....|....*....|
gi 643730857 237 ERRGTGASDHAPVVVDYELA 256
Cdd:COG3021  291 RVLPVIGSDHRPLLAELALP 310
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-251 5.15e-07

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: 49.40  E-value: 5.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   3 IVNWNVNSMR--TRVERVQAFLTRHDVDVLAVQETKCKDEQFPYLAFEELG----YEVAHFGLNQWNGVAIISRVGIEDV 76
Cdd:cd08372    1 VASYNVNGLNaaTRASGIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEgyhqYQSGPSRKEGYEGVAILSKTPKFKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  77 AtsfpgqPGFNKDPGKKQAIEARALGA--TCGG--VRVWSLYVPNGREiadpHYDYKLRWLYALSCYVGAAPD---ERMV 149
Cdd:cd08372   81 V------EKHQYKFGEGDSGERRAVVVkfDVHDkeLCVVNAHLQAGGT----RADVRDAQLKEVLEFLKRLRQpnsAPVV 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 150 LLGDYNIAPRDQDVWDIRAFEGKTHvTEPERQAFESLLDAGLDITSPLEGYSYWDYkggrfqrgqgmlidFQLSRGL--R 227
Cdd:cd08372  151 ICGDFNVRPSEVDSENPSSMLRLFV-ALNLVDSFETLPHAYTFDTYMHNVKSRLDY--------------IFVSKSLlpS 215

                        250       260
                 ....*....|....*....|....
gi 643730857 228 PTNSFIDVDERRGTGASDHAPVVV 251
Cdd:cd08372  216 VKSSKILSDAARARIPSDHYPIEV 239
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-253 9.72e-06

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: 45.42  E-value: 9.72e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   3 IVNWNVNSMRTRVER--VQAFLTRHDVDVLAVQETKCKDE-QFPYLafeELGYEVAHFGLNQW--NGVAIISRVGIEDVA 77
Cdd:cd09076    1 IGTLNVRGLRSPGKRaqLLEELKRKKLDILGLQETHWTGEgELKKK---REGGTILYSGSDSGksRGVAILLSKTAANKL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  78 TSFPGQPGfnkdpGKKQAIEARALGATcggVRVWSLYVPNGREiaDPHYDYklrwLYA-LSCYVGAAPDERM-VLLGDYN 155
Cdd:cd09076   78 LEYTKVVS-----GRIIMVRFKIKGKR---LTIINVYAPTARD--EEEKEE----FYDqLQDVLDKVPRHDTlIIGGDFN 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 156 --IAPRDQDVW--DIRAFEGKTHVTEPERQafESLLDAGLDITSPLEGYSYwdYKGGRFQRGQgmlIDFQLSRGlRPTNS 231
Cdd:cd09076  144 avLGPKDDGRKglDKRNENGERALSALIEE--HDLVDVWRENNPKTREYTW--RSPDHGSRSR---IDRILVSK-RLRVK 215

                        250       260
                 ....*....|....*....|..
gi 643730857 232 FIDVDERRGTGaSDHAPVVVDY 253
Cdd:cd09076  216 VKKTKITPGAG-SDHRLVTLKL 236
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-256 1.36e-05

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 44.13  E-value: 1.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   1 MRIVNWNVNSM-----RTRVERVQAFLTRHDVDVLAVQEtkckdeqfpylafeelgyevahfglnqwngVAIISRVGIED 75
Cdd:COG3568    8 LRVMTYNIRYGlgtdgRADLERIARVIRALDPDVVALQE------------------------------NAILSRYPIVS 57

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  76 VATSFPGQPGFNKdpgkKQAIEARaLGATCGGVRVWSLyvpngreiadpHYDYK-----LRWLYALSCYV-GAAPDERMV 149
Cdd:COG3568   58 SGTFDLPDPGGEP----RGALWAD-VDVPGKPLRVVNT-----------HLDLRsaaarRRQARALAELLaELPAGAPVI 121

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 150 LLGDYNIaprdqdvwdirafegkthvteperqafeslldaglditsplegysywdykggrfqrgqgmlIDFQL-SRGLRP 228
Cdd:COG3568  122 LAGDFND-------------------------------------------------------------IDYILvSPGLRV 140

                        250       260
                 ....*....|....*....|....*...
gi 643730857 229 TNSFIdVDERRGTGASDHAPVVVDYELA 256
Cdd:COG3568  141 LSAEV-LDSPLGRAASDHLPVVADLELP 167
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 5-253 3.57e-05

Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.


Pssm-ID: 197317 [Multi-domain]  Cd Length: 252  Bit Score: 43.74  E-value: 3.57e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857   5 NWNVNSMRTRVERVQAFLTRHDVDVLAVQEtkCKDEQFPYLAfEEL-GYEVAHFG----LNQWNGVAII---SRVGIEDV 76
Cdd:cd09083   13 SDGENSWENRKDLVAELIKFYDPDIIGTQE--ALPHQLADLE-ELLpEYDWIGVGrddgKEKGEFSAIFyrkDRFELLDS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857  77 ATSFpgqpgFNKDPgkkQAIEARALGATCggVRV--WSL--YVPNGREI--ADPHYDYK------------LRWLYALsc 138
Cdd:cd09083   90 GTFW-----LSETP---DVVGSKGWDAAL--PRIctWARfkDKKTGKEFyvFNTHLDHVgeeareesakliLERIKEI-- 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643730857 139 yvgaAPDERMVLLGDYNiaprdqdvwdirafegkthvTEPERQAFESLLDAGL-------DITSPLEGYSYWDYKGGRfq 211
Cdd:cd09083  158 ----AGDLPVILTGDFN--------------------AEPDSEPYKTLTSGGLkdardtaATTDGGPEGTFHGFKGPP-- 211

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 643730857 212 rgQGMLIDFQL-SRGLRPTNSFIDVDERRGTGASDHAPVVVDY 253
Cdd:cd09083  212 --GGSRIDYIFvSPGVKVLSYEILTDRYDGRYPSDHFPVVADL 252
 
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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