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Conserved domains on  [gi|492539053|ref|WP_005878231|]
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exodeoxyribonuclease III [Oxalobacter paraformigenes]

Protein Classification

exodeoxyribonuclease III( domain architecture ID 10178908)

exodeoxyribonuclease III is a Mg-dependent 3' to 5' exonuclease acting on dsDNA, which releases 5' phosphomononucleotides as degradation products

CATH:  3.60.10.10
EC:  3.1.11.2
Gene Ontology:  GO:0003677|GO:0046872|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
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 4-256 3.17e-146

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: 408.92  E-value: 3.17e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   4 ITTANLNGIRSAVRKGFLEWMHQSGSHFVCVQEIKAQPDDIVPAIASPDLFHGHFGCAEKKGYSGVGIYSKTKPDKVIRG 83
Cdd:cd10281    3 VISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVIYG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  84 FGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSPERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAHKEIDLKNWK 163
Cdd:cd10281   83 LGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKNWK 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 164 SNQKNSGFLPEERAWLSRILDELGLIDVYRCLHPDttDASYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYKE 243
Cdd:cd10281  163 ANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPD--EGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYRE 240

                        250
                 ....*....|...
gi 492539053 244 TRFSDHAPLTIWY 256
Cdd:cd10281  241 ERFSDHAPLIVDY 253
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 4-256 3.17e-146

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: 408.92  E-value: 3.17e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   4 ITTANLNGIRSAVRKGFLEWMHQSGSHFVCVQEIKAQPDDIVPAIASPDLFHGHFGCAEKKGYSGVGIYSKTKPDKVIRG 83
Cdd:cd10281    3 VISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVIYG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  84 FGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSPERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAHKEIDLKNWK 163
Cdd:cd10281   83 LGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKNWK 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 164 SNQKNSGFLPEERAWLSRILDELGLIDVYRCLHPDttDASYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYKE 243
Cdd:cd10281  163 ANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPD--EGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYRE 240

                        250
                 ....*....|...
gi 492539053 244 TRFSDHAPLTIWY 256
Cdd:cd10281  241 ERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
4-257 1.73e-127

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 361.70  E-value: 1.73e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   4 ITTANLNGIRSAVRKgFLEWMHQSGSHFVCVQEIKAQPDDIVPAIASPDLFHGHFgcAEKKGYSGVGIYSKTKPDKVIRG 83
Cdd:COG0708    3 IASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYF--HGQKGYNGVAILSRLPPEDVRRG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  84 FGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSP-ERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAHKEIDLKNW 162
Cdd:COG0708   80 LGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSVGsEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVKNP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 163 KSNQKNSGFLPEERAWLSRILDeLGLIDVYRCLHPDTTDAsYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYK 242
Cdd:COG0708  160 KANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPDVEGQ-YTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDR 237

                        250
                 ....*....|....*....
gi 492539053 243 ETR----FSDHAPLTIWYD 257
Cdd:COG0708  238 EPRgderPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 4-257 1.97e-86

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: 257.59  E-value: 1.97e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053    4 ITTANLNGIRSAVRKGFLEWMHQSGSHFVCVQEIKAQPDDIVPAIASPDLFHGHFGCAeKKGYSGVGIYSKTKPDKVIRG 83
Cdd:TIGR00633   3 IISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGA-KKGYSGVAILSKVEPLDVRYG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   84 FGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSS-SPERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAHKEIDLKNW 162
Cdd:TIGR00633  82 FGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSrDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLGNP 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  163 KSNQKNSGFLPEERAWLSRILDElGLIDVYRCLHPDTTDAsYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYK 242
Cdd:TIGR00633 162 KENKGNAGFTPEEREWFDELLEA-GFVDTFRHFNPDTGDA-YTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS 239

                         250
                  ....*....|....*
gi 492539053  243 ETRFSDHAPLTIWYD 257
Cdd:TIGR00633 240 EIRGSDHCPIVLELD 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 8-252 7.41e-54

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 174.50  E-value: 7.41e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   8 NLNGIRSAVRKGFLEWMHQSGSHFVCVQEIKAQPDDivpaiaSPDLFHGHF---GCAEKKGYSGVGIYSKTKPDKVIRGF 84
Cdd:PRK13911   7 NVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQ------NTFEFKGYFdfwNCAIKKGYSGVVTFTKKEPLSVSYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  85 GCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSPERQEAKFRFMDHFFPFLEKLkESEREFIICGDWNIAHKEIDLKNWKS 164
Cdd:PRK13911  81 NIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKAL-ELKKPVIVCGDLNVAHNEIDLENPKT 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 165 NQKNSGFLPEERAWLSRILDElGLIDVYRCLHPDTTDAsYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYKET 244
Cdd:PRK13911 160 NRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEKA-YTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDI 237


                 ....*...
gi 492539053 245 RFSDHAPL 252
Cdd:PRK13911 238 LGSDHCPV 245
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 6-152 4.05e-16

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: 74.18  E-value: 4.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053    6 TANLNGIRS------AVRKGFLEWMHQSGSHFVCVQEIKAQPDDIVP-AIASPDLFHGHFGCAEKKGYSGVGIYSKTKPD 78
Cdd:pfam03372   2 TWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASRLLlALLAYGGFLSYGGPGGGGGGGGVAILSRYPLS 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492539053   79 KVIRGFGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSPERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNI 152
Cdd:pfam03372  82 SVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 4-256 3.17e-146

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: 408.92  E-value: 3.17e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   4 ITTANLNGIRSAVRKGFLEWMHQSGSHFVCVQEIKAQPDDIVPAIASPDLFHGHFGCAEKKGYSGVGIYSKTKPDKVIRG 83
Cdd:cd10281    3 VISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVIYG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  84 FGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSPERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAHKEIDLKNWK 163
Cdd:cd10281   83 LGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKNWK 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 164 SNQKNSGFLPEERAWLSRILDELGLIDVYRCLHPDttDASYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYKE 243
Cdd:cd10281  163 ANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPD--EGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYRE 240

                        250
                 ....*....|...
gi 492539053 244 TRFSDHAPLTIWY 256
Cdd:cd10281  241 ERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
4-257 1.73e-127

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 361.70  E-value: 1.73e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   4 ITTANLNGIRSAVRKgFLEWMHQSGSHFVCVQEIKAQPDDIVPAIASPDLFHGHFgcAEKKGYSGVGIYSKTKPDKVIRG 83
Cdd:COG0708    3 IASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYF--HGQKGYNGVAILSRLPPEDVRRG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  84 FGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSP-ERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAHKEIDLKNW 162
Cdd:COG0708   80 LGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSVGsEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVKNP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 163 KSNQKNSGFLPEERAWLSRILDeLGLIDVYRCLHPDTTDAsYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYK 242
Cdd:COG0708  160 KANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPDVEGQ-YTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDR 237

                        250
                 ....*....|....*....
gi 492539053 243 ETR----FSDHAPLTIWYD 257
Cdd:COG0708  238 EPRgderPSDHAPVVVELD 256
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 4-254 5.63e-110

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: 317.31  E-value: 5.63e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   4 ITTANLNGIRSAVRKGFLEWMHQSGSHFVCVQEIKAQPDDIVPAIASPDLFHGHFGCAEKKGYSGVGIYSKTKPDKVIRG 83
Cdd:cd09073    2 IISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPARKKGYSGVATLSKEEPLDVSYG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  84 FGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSPERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAHKEIDLKNWK 163
Cdd:cd09073   82 IGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEIDLARPK 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 164 SNQKNSGFLPEERAWLSRILdELGLIDVYRCLHPDttDASYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYKE 243
Cdd:cd09073  162 KNEKNAGFTPEERAWFDKLL-SLGYVDTFRHFHPE--PGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILSK 238

                        250
                 ....*....|.
gi 492539053 244 TRFSDHAPLTI 254
Cdd:cd09073  239 VKGSDHAPVTL 249
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 8-254 9.82e-99

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: 288.79  E-value: 9.82e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   8 NLNGIRSAVRKGFLEWMHQSGSHFVCVQEIKAQPDDIVPAIASPDLFHGHFGCAEKKGYSGVGIYSKTKPDKVIRGFGCP 87
Cdd:cd09085    7 NVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAERKGYSGVALYSKIEPDSVREGLGVE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  88 EFDAEGRYLQCDYKDFSLVSLYAPSGSSSPERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAHKEIDLKNWKSNQK 167
Cdd:cd09085   87 EFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLARPKENEK 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 168 NSGFLPEERAWLSRILDElGLIDVYRCLHPDttDASYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYKETRFS 247
Cdd:cd09085  167 VSGFLPEERAWMDKFIEN-GYVDTFRMFNKE--PGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPDVMGS 243


                 ....*..
gi 492539053 248 DHAPLTI 254
Cdd:cd09085  244 DHCPVSL 250
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 2-255 1.25e-86

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: 258.25  E-value: 1.25e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   2 FSITTANLNGIRSAVRKGFLEWMHQSGSHFVCVQEIKAQPDDIVPAIAS-PDLFHGHFGCAEKKGYSGVGIYSKTKPDKV 80
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKElLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  81 IRGFGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSPERQEAKFRFMDHFFPFLEKLkESEREFIICGDWNIAHKEIDLK 160
Cdd:cd09087   81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKL-DSKKPVIWCGDLNVAHEEIDLA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 161 NWKSNQKNSGFLPEERAWLSRILDElGLIDVYRCLHPDTTDAsYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASI 240
Cdd:cd09087  160 NPKTNKKSAGFTPEERESFTELLEA-GFVDTFRHLHPDKEGA-YTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFI 237

                        250
                 ....*....|....*
gi 492539053 241 YKETRFSDHAPLTIW 255
Cdd:cd09087  238 RSDIMGSDHCPIGLE 252
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 4-257 1.97e-86

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: 257.59  E-value: 1.97e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053    4 ITTANLNGIRSAVRKGFLEWMHQSGSHFVCVQEIKAQPDDIVPAIASPDLFHGHFGCAeKKGYSGVGIYSKTKPDKVIRG 83
Cdd:TIGR00633   3 IISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGA-KKGYSGVAILSKVEPLDVRYG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   84 FGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSS-SPERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAHKEIDLKNW 162
Cdd:TIGR00633  82 FGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSrDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLGNP 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  163 KSNQKNSGFLPEERAWLSRILDElGLIDVYRCLHPDTTDAsYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYK 242
Cdd:TIGR00633 162 KENKGNAGFTPEEREWFDELLEA-GFVDTFRHFNPDTGDA-YTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS 239

                         250
                  ....*....|....*
gi 492539053  243 ETRFSDHAPLTIWYD 257
Cdd:TIGR00633 240 EIRGSDHCPIVLELD 254
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 4-252 8.95e-79

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: 238.05  E-value: 8.95e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053    4 ITTANLNGIRSAVRKGfLEWMHQSGSHFVCVQEIKAQPDDIVPAIASPDLFHGHFGCAekKGYSGVGIYSKTKPDKVIRG 83
Cdd:TIGR00195   3 IISWNVNGLRARPHKG-LAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQ--KGYSGVAIFSKEEPISVRRG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   84 FGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSS-SPERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAHKEIDLKNW 162
Cdd:TIGR00195  80 FGVEEEDAEGRIIMAEFDSFLVINGYFPNGSRdDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDLHIP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  163 KSNQKNSGFLPEERAWLSRILdELGLIDVYRCLHPDTtdASYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYK 242
Cdd:TIGR00195 160 DENRNHTGFLPEEREWLDRLL-EAGLVDTFRKFNPDE--GAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDY 236

                         250
                  ....*....|....
gi 492539053  243 ETR----FSDHAPL 252
Cdd:TIGR00195 237 DIRgsekPSDHCPV 250
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 2-254 7.05e-66

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: 205.44  E-value: 7.05e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   2 FSITTANLNGIRSavRKGFLE-WMHQSGSHFVCVQEIKAqPDDIVPAIASPDL-----FHGhfgcaeKKGYSGVGIYSKT 75
Cdd:cd09086    1 MKIATWNVNSIRA--RLEQVLdWLKEEDPDVLCLQETKV-EDDQFPADAFEALgyhvaVHG------QKAYNGVAILSRL 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  76 KPDKVIRGFGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSP-ERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAH 154
Cdd:cd09086   72 PLEDVRTGFPGDPDDDQARLIAARVGGVRVINLYVPNGGDIGsPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAP 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 155 KEIDLKNWKSNQKNSGFLPEERAWLSRILDeLGLIDVYRCLHPDTTdaSYTWWSNRGQAWQKNVGWRIDYQIATPGIAGK 234
Cdd:cd09086  152 EDIDVWDPKQLLGKVLFTPEEREALRALLD-LGFVDAFRALHPDEK--LFTWWDYRAGAFERNRGLRIDHILASPALADR 228

                        250       260
                 ....*....|....*....|....
gi 492539053 235 AVSASIYKETRF----SDHAPLTI 254
Cdd:cd09086  229 LKDVGIDREPRGwekpSDHAPVVA 252
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 8-252 7.41e-54

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 174.50  E-value: 7.41e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   8 NLNGIRSAVRKGFLEWMHQSGSHFVCVQEIKAQPDDivpaiaSPDLFHGHF---GCAEKKGYSGVGIYSKTKPDKVIRGF 84
Cdd:PRK13911   7 NVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQ------NTFEFKGYFdfwNCAIKKGYSGVVTFTKKEPLSVSYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  85 GCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSPERQEAKFRFMDHFFPFLEKLkESEREFIICGDWNIAHKEIDLKNWKS 164
Cdd:PRK13911  81 NIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKAL-ELKKPVIVCGDLNVAHNEIDLENPKT 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 165 NQKNSGFLPEERAWLSRILDElGLIDVYRCLHPDTTDAsYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYKET 244
Cdd:PRK13911 160 NRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEKA-YTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDI 237


                 ....*...
gi 492539053 245 RFSDHAPL 252
Cdd:PRK13911 238 LGSDHCPV 245
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 3-251 8.68e-41

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: 142.46  E-value: 8.68e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   3 SITTANLNGIRsAVRKGFLEWMHQSGSHF--------VCVQEIKAQPDDIVPAIASPDLFHGHFG-CAEKKGYSGVGIYS 73
Cdd:cd09088    1 RIVTWNVNGIR-TRLQYQPWNKENSLKSFldsldadiICLQETKLTRDELDEPSAIVEGYDSFFSfSRGRKGYSGVATYC 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  74 KTKPDKVIR---GF-------------------GC-------------PEFDAEGRYLQCDYKDFSLVSLYAPS-GSSSP 117
Cdd:cd09088   80 RDSAATPVAaeeGLtgvlsspnqknelsenddiGCygemleftdskelLELDSEGRCVLTDHGTFVLINVYCPRaDPEKE 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 118 ERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNIAHKEIDLKNWKSNQKNSGFLPEE---RAWLSRILDELG------- 187
Cdd:cd09088  160 ERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLGDSGegggspg 239

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492539053 188 --LIDVYRCLHPDTTDAsYTWWSNRGQAWQKNVGWRIDYQIATPGIAGKAVSASIYKETRFSDHAP 251
Cdd:cd09088  240 glLIDSFRYFHPTRKGA-YTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCP 304
PRK11756 PRK11756
exonuclease III; Provisional
 8-255 4.38e-38

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 134.25  E-value: 4.38e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   8 NLNGIRSavRkgflewMHQ----SGSH---FVCVQEIKAQpDDIVPAIASPDL-----FHGhfgcaeKKGYSGVGIYSKT 75
Cdd:PRK11756   7 NINGLRA--R------PHQleaiIEKHqpdVIGLQETKVH-DEMFPLEEVEALgyhvfYHG------QKGHYGVALLSKQ 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  76 KPDKVIRGFGCPEFDAEGRYLQCDYKD-FSLVSL---YAPSGSS--SPERQEAKFRFMDHFFPFLEKLKESEREFIICGD 149
Cdd:PRK11756  72 TPIAVRKGFPTDDEEAQRRIIMATIPTpNGNLTVingYFPQGESrdHPTKFPAKRQFYQDLQNYLETELSPDNPLLIMGD 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 150 WNIAHKEIDL-------KNWKSNQKNSgFLPEERAWLSRILDeLGLIDVYRCLHPDTTDaSYTWWSNRGQAWQKNVGWRI 222
Cdd:PRK11756 152 MNISPTDLDIgigeenrKRWLRTGKCS-FLPEEREWLDRLMD-WGLVDTFRQLNPDVND-RFSWFDYRSKGFDDNRGLRI 228

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 492539053 223 DYQIATPGIAGKAVSASIYKETRF----SDHAPltIW 255
Cdd:PRK11756 229 DLILATQPLAERCVETGIDYDIRGmekpSDHAP--IW 263
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 4-254 7.51e-24

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: 96.01  E-value: 7.51e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   4 ITTANLNGIRSAVR-KGFLEWMHQSGSHFVCVQEIK-AQPDDIVPAIASPDLFHGHF-GCAEKKGYSGVGIYSKT---KP 77
Cdd:cd08372    1 VASYNVNGLNAATRaSGIARWVRELDPDIVCLQEVKdSQYSAVALNQLLPEGYHQYQsGPSRKEGYEGVAILSKTpkfKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  78 DKVIRGFGCPEFDAEGRYL----QCDYKDFSLVSLYAPSGsssPERQEAKFRFMDHFFPFL-EKLKESEREFIICGDWNI 152
Cdd:cd08372   81 VEKHQYKFGEGDSGERRAVvvkfDVHDKELCVVNAHLQAG---GTRADVRDAQLKEVLEFLkRLRQPNSAPVVICGDFNV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 153 AHKEIDLKNWKSnqknsgflpeerawLSRILDELGLIDVYR-CLHPdttdasYTWWSNRgqawqKNVGWRIDYQIATPGI 231
Cdd:cd08372  158 RPSEVDSENPSS--------------MLRLFVALNLVDSFEtLPHA------YTFDTYM-----HNVKSRLDYIFVSKSL 212

                        250       260
                 ....*....|....*....|....*..
gi 492539053 232 AGKAVSASI---YKETRF-SDHAPLTI 254
Cdd:cd08372  213 LPSVKSSKIlsdAARARIpSDHYPIEV 239
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 4-254 3.45e-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: 78.16  E-value: 3.45e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   4 ITTANLNGIRSAV-RKGFLEWMHQSGSHFVCVQEIKAQPDDIVPAIASPD--LFHGHfgcaEKKGYSGVGI-YSKTKPDK 79
Cdd:cd09076    1 IGTLNVRGLRSPGkRAQLLEELKRKKLDILGLQETHWTGEGELKKKREGGtiLYSGS----DSGKSRGVAIlLSKTAANK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  80 VIRGfgcpEFDAEGRYLQCD----YKDFSLVSLYAPSGSSSPERQEakfrfmdhffpFLEKL-----KESEREFIIC-GD 149
Cdd:cd09076   77 LLEY----TKVVSGRIIMVRfkikGKRLTIINVYAPTARDEEEKEE-----------FYDQLqdvldKVPRHDTLIIgGD 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 150 WNIAHKEIDLKNWKSNQKNSGflpEERAWLSRIlDELGLIDVYRCLHPDTTDasYTWWSNRGQAWQknvgwRIDYQIATP 229
Cdd:cd09076  142 FNAVLGPKDDGRKGLDKRNEN---GERALSALI-EEHDLVDVWRENNPKTRE--YTWRSPDHGSRS-----RIDRILVSK 210

                        250       260
                 ....*....|....*....|....*
gi 492539053 230 GIAGKAVSASIYkETRFSDHAPLTI 254
Cdd:cd09076  211 RLRVKVKKTKIT-PGAGSDHRLVTL 234
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 6-152 4.05e-16

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: 74.18  E-value: 4.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053    6 TANLNGIRS------AVRKGFLEWMHQSGSHFVCVQEIKAQPDDIVP-AIASPDLFHGHFGCAEKKGYSGVGIYSKTKPD 78
Cdd:pfam03372   2 TWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASRLLlALLAYGGFLSYGGPGGGGGGGGVAILSRYPLS 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492539053   79 KVIRGFGCPEFDAEGRYLQCDYKDFSLVSLYAPSGSSSPERQEAKFRFMDHFFPFLEKLKESEREFIICGDWNI 152
Cdd:pfam03372  82 SVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 4-254 1.74e-07

Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-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. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-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: 197311 [Multi-domain]  Cd Length: 205  Bit Score: 50.37  E-value: 1.74e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053   4 ITTANLNGIRSAVRkGFLEWMHQSGSHFVCVQEikaqpddivpaiasPDLFHGHFGCAEKKGYSGVGIY-SKTKPDKVIR 82
Cdd:cd09077    3 ILQINLNRCKAAQD-LLLQTAREEGADIALIQE--------------PYLVPVNNPNWVTDESGRAAIVvSDRLPRKPIQ 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053  83 GFGcpefdaEGRYLQC-DYKDFSLVSLYAPSGSSSPErqeakfrfmdhFFPFLEKLKE----SEREFIICGDWNIAHKEi 157
Cdd:cd09077   68 RLS------LGLGIVAaRVGGITVVSCYAPPSESLEE-----------FEEYLENLVRivrgLSRPVIIGGDFNAWSPA- 129

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492539053 158 dlknWKSNQKNS-GFLpeerawLSRILDELGLIDVyrclhpdTTDASYTWWSNRGQAWqknvgwrIDYQIATPGIAGKAV 236
Cdd:cd09077  130 ----WGSKRTDRrGRL------LEDWIANLGLVLL-------NDGNSPTFVRPRGTSI-------IDVTFCSPSLARRIS 185

                        250
                 ....*....|....*...
gi 492539053 237 SASIYKETRFSDHAPLTI 254
Cdd:cd09077  186 NWRVLEDETLSDHRYIRF 203
 
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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