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Conserved domains on  [gi|1894882849|ref|WP_185982635|]
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exodeoxyribonuclease III [Aureimonas mangrovi]

Protein Classification

exodeoxyribonuclease III( domain architecture ID 10173387)

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:0046872|GO:0008853
PubMed:  7885481
SCOP:  4002213

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-255 7.13e-130

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: 367.61  E-value: 7.13e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWKGQRQWNGVAILGRGKtPILTRDQ 80
Cdd:cd09086     1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHGQKAYNGVAILSRLP-LEDVRTG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  81 LPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPGPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDLDIYPT 160
Cdd:cd09086    80 FPGDPDDDQARLIAARVGGVRVINLYVPNGGDIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDVWDP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 161 KSWNDDALTQPEPRSAFRSLTDAGWTDAIRKLHPAEPMFSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGGVDRDVR 240
Cdd:cd09086   160 KQLLGKVLFTPEEREALRALLDLGFVDAFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGIDREPR 239

                         250
                  ....*....|....*
gi 1894882849 241 GEEGASDHAPVWIEL 255
Cdd:cd09086   240 GWEKPSDHAPVVAEL 254
 
Name Accession Description Interval E-value
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-255 7.13e-130

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: 367.61  E-value: 7.13e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWKGQRQWNGVAILGRGKtPILTRDQ 80
Cdd:cd09086     1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHGQKAYNGVAILSRLP-LEDVRTG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  81 LPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPGPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDLDIYPT 160
Cdd:cd09086    80 FPGDPDDDQARLIAARVGGVRVINLYVPNGGDIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDVWDP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 161 KSWNDDALTQPEPRSAFRSLTDAGWTDAIRKLHPAEPMFSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGGVDRDVR 240
Cdd:cd09086   160 KQLLGKVLFTPEEREALRALLDLGFVDAFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGIDREPR 239

                         250
                  ....*....|....*
gi 1894882849 241 GEEGASDHAPVWIEL 255
Cdd:cd09086   240 GWEKPSDHAPVVAEL 254
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-256 1.17e-120

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 344.37  E-value: 1.17e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWKGQRQWNGVAILGRGKtPILTRDQ 80
Cdd:COG0708     1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLP-PEDVRRG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  81 LPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPGPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDLDIYPT 160
Cdd:COG0708    80 LGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVKNP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 161 KSWNDDALTQPEPRSAFRSLTDAGWTDAIRKLHPAEP-MFSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGGVDRDV 239
Cdd:COG0708   160 KANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEgQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDREP 239

                         250
                  ....*....|....*..
gi 1894882849 240 RGEEGASDHAPVWIELA 256
Cdd:COG0708   240 RGDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-256 1.64e-78

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: 237.56  E-value: 1.64e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPNL-LAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWKGQ-RQWNGVAILGRgKTPILTR 78
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLfLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAkKGYSGVAILSK-VEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  79 DQLPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPGPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDLDIY 158
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 159 PTKSWNDDALTQPEPRSAFRSLTDAGWTDAIRKLHPAEPM-FSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGGVDR 237
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS 239

                         250
                  ....*....|....*....
gi 1894882849 238 DVRGeegaSDHAPVWIELA 256
Cdd:TIGR00633 240 EIRG----SDHCPIVLELD 254
PRK11756 PRK11756
exonuclease III; Provisional
 1-255 3.86e-54

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 175.47  E-value: 3.86e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWKGQRQWNGVAILGRgKTPILTRDQ 80
Cdd:PRK11756    1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVALLSK-QTPIAVRKG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  81 LPGGDSDTQSRYIEAAYD----GVIVASIYLPNGNPRPGP-KFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDL 155
Cdd:PRK11756   80 FPTDDEEAQRRIIMATIPtpngNLTVINGYFPQGESRDHPtKFPAKRQFYQDLQNYLETELSPDNPLLIMGDMNISPTDL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 156 DI----YPTKSWNDDALT--QPEPRSAFRSLTDAGWTDAIRKLHP-AEPMFSFWDYKRQRWPQGKGLRLDHLLLSPQIVP 228
Cdd:PRK11756  160 DIgigeENRKRWLRTGKCsfLPEEREWLDRLMDWGLVDTFRQLNPdVNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAE 239

                         250       260
                  ....*....|....*....|....*..
gi 1894882849 229 RLMAGGVDRDVRGEEGASDHAPVWIEL 255
Cdd:PRK11756  240 RCVETGIDYDIRGMEKPSDHAPIWATF 266
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-179 1.61e-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: 66.86  E-value: 1.61e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   4 ATFNINNVN-------RRLPNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWK---GQRQWNGVAILGRgkT 73
Cdd:pfam03372   1 LTWNVNGGNadaagddRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGgpgGGGGGGGVAILSR--Y 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  74 PILTRDQLPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPGPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNvvpT 153
Cdd:pfam03372  79 PLSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN---A 155

                         170       180
                  ....*....|....*....|....*..
gi 1894882849 154 DLdIYPTKSWN-DDALTQPEPRSAFRS 179
Cdd:pfam03372 156 DY-ILVSGGLTvLSVGVLPDLGPRTGS 181
 
Name Accession Description Interval E-value
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-255 7.13e-130

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: 367.61  E-value: 7.13e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWKGQRQWNGVAILGRGKtPILTRDQ 80
Cdd:cd09086     1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHGQKAYNGVAILSRLP-LEDVRTG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  81 LPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPGPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDLDIYPT 160
Cdd:cd09086    80 FPGDPDDDQARLIAARVGGVRVINLYVPNGGDIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDVWDP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 161 KSWNDDALTQPEPRSAFRSLTDAGWTDAIRKLHPAEPMFSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGGVDRDVR 240
Cdd:cd09086   160 KQLLGKVLFTPEEREALRALLDLGFVDAFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGIDREPR 239

                         250
                  ....*....|....*
gi 1894882849 241 GEEGASDHAPVWIEL 255
Cdd:cd09086   240 GWEKPSDHAPVVAEL 254
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-256 1.17e-120

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 344.37  E-value: 1.17e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWKGQRQWNGVAILGRGKtPILTRDQ 80
Cdd:COG0708     1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLP-PEDVRRG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  81 LPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPGPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDLDIYPT 160
Cdd:COG0708    80 LGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVKNP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 161 KSWNDDALTQPEPRSAFRSLTDAGWTDAIRKLHPAEP-MFSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGGVDRDV 239
Cdd:COG0708   160 KANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEgQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDREP 239

                         250
                  ....*....|....*..
gi 1894882849 240 RGEEGASDHAPVWIELA 256
Cdd:COG0708   240 RGDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-256 1.64e-78

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: 237.56  E-value: 1.64e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPNL-LAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWKGQ-RQWNGVAILGRgKTPILTR 78
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLfLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAkKGYSGVAILSK-VEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  79 DQLPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPGPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDLDIY 158
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 159 PTKSWNDDALTQPEPRSAFRSLTDAGWTDAIRKLHPAEPM-FSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGGVDR 237
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS 239

                         250
                  ....*....|....*....
gi 1894882849 238 DVRGeegaSDHAPVWIELA 256
Cdd:TIGR00633 240 EIRG----SDHCPIVLELD 254
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-255 2.44e-73

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: 224.18  E-value: 2.44e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWKGQRQWNGVAILGRgKTPILTRDQ 80
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQKGYSGVAIFSK-EEPISVRRG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  81 LPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPGPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDLDIYPT 160
Cdd:TIGR00195  80 FGVEEEDAEGRIIMAEFDSFLVINGYFPNGSRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDLHIP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 161 KSWNDDALTQPEPRSAFRSLTDAGWTDAIRKLHPAEPMFSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGGVDRDVR 240
Cdd:TIGR00195 160 DENRNHTGFLPEEREWLDRLLEAGLVDTFRKFNPDEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDYDIR 239

                         250
                  ....*....|....*
gi 1894882849 241 GEEGASDHAPVWIEL 255
Cdd:TIGR00195 240 GSEKPSDHCPVVLEF 254
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-255 4.48e-67

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: 208.30  E-value: 4.48e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   2 KIATFNINNVNRRLPN-LLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWKGQRQ--WNGVAILGRgKTPILTR 78
Cdd:cd09073     1 KIISWNVNGLRARLKKgVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPARKkgYSGVATLSK-EEPLDVS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  79 DQLPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPgPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDLDIY 158
Cdd:cd09073    80 YGIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGL-ERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEIDLA 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 159 PTKSWNDDALTQPEPRSAFRSLTDAGWTDAIRKLHPAEPMFSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGGVDRD 238
Cdd:cd09073   159 RPKKNEKNAGFTPEERAWFDKLLSLGYVDTFRHFHPEPGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILSK 238

                         250
                  ....*....|....*..
gi 1894882849 239 VRGeegaSDHAPVWIEL 255
Cdd:cd09073   239 VKG----SDHAPVTLEL 251
PRK11756 PRK11756
exonuclease III; Provisional
 1-255 3.86e-54

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 175.47  E-value: 3.86e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWKGQRQWNGVAILGRgKTPILTRDQ 80
Cdd:PRK11756    1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVALLSK-QTPIAVRKG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  81 LPGGDSDTQSRYIEAAYD----GVIVASIYLPNGNPRPGP-KFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDL 155
Cdd:PRK11756   80 FPTDDEEAQRRIIMATIPtpngNLTVINGYFPQGESRDHPtKFPAKRQFYQDLQNYLETELSPDNPLLIMGDMNISPTDL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 156 DI----YPTKSWNDDALT--QPEPRSAFRSLTDAGWTDAIRKLHP-AEPMFSFWDYKRQRWPQGKGLRLDHLLLSPQIVP 228
Cdd:PRK11756  160 DIgigeENRKRWLRTGKCsfLPEEREWLDRLMDWGLVDTFRQLNPdVNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAE 239

                         250       260
                  ....*....|....*....|....*..
gi 1894882849 229 RLMAGGVDRDVRGEEGASDHAPVWIEL 255
Cdd:PRK11756  240 RCVETGIDYDIRGMEKPSDHAPIWATF 266
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-255 3.14e-47

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: 157.33  E-value: 3.14e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPN-LLAWLEAAEPDLVCLQELKAAQDAFPQKALSSA-GYEAVW-----KGqrqWNGVAILGRGKt 73
Cdd:cd09087     1 LKIISWNVNGLRALLKKgLLDYVKKEDPDILCLQETKLQEGDVPKELKELLkGYHQYWnaaekKG---YSGTAILSKKK- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  74 PILTRDQLPGGDSDTQSRYIEAAYDGVIVASIYLPNgNPRPGPKFDYKLAWFDRLVRHAGELmDAKVPVVLAGDYNVVPT 153
Cdd:cd09087    77 PLSVTYGIGIEEHDQEGRVITAEFENFYLVNTYVPN-SGRGLERLDRRKEWDVDFRAYLKKL-DSKKPVIWCGDLNVAHE 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 154 DLDIYPTKSWNDDALTQPEPRSAFRSLTDAGWTDAIRKLHP-AEPMFSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLma 232
Cdd:cd09087   155 EIDLANPKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPdKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRV-- 232

                         250       260
                  ....*....|....*....|...
gi 1894882849 233 ggVDRDVRGEEGASDHAPVWIEL 255
Cdd:cd09087   233 --VDSFIRSDIMGSDHCPIGLEL 253
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-254 7.19e-45

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: 151.23  E-value: 7.19e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPN-LLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWK--GQRQWNGVAILGRgKTPILT 77
Cdd:cd10281     1 MRVISVNVNGIRAAAKKgFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFdaEKKGYAGVAIYSR-TQPKAV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  78 RDQLPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPgPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDLDI 157
Cdd:cd10281    80 IYGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGD-ERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 158 YPTKSWNDDALTQPEPRSAF-RSLTDAGWTDAIRKLHPAEPMFSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGGVD 236
Cdd:cd10281   159 KNWKANQKNSGFLPEERAWLdQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIY 238

                         250
                  ....*....|....*...
gi 1894882849 237 RDVRGeegaSDHAPVWIE 254
Cdd:cd10281   239 REERF----SDHAPLIVD 252
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-255 2.53e-42

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: 144.73  E-value: 2.53e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRL-PNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVW-----KGQrqwNGVAILGRGKtP 74
Cdd:cd09085     1 MKIISWNVNGLRAVHkKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFnsaerKGY---SGVALYSKIE-P 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  75 ILTRDQLPGGDSDTQSRYIEAAYDGVIVASIYLPNGNpRPGPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTD 154
Cdd:cd09085    77 DSVREGLGVEEFDNEGRILIADFDDFTLFNIYFPNGQ-MSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKE 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 155 LDIYPTKSWNDDALTQPEPRSAFRSLTDAGWTDAIRKLHPAEPMFSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGG 234
Cdd:cd09085   156 IDLARPKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKEPGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAG 235

                         250       260
                  ....*....|....*....|.
gi 1894882849 235 VDRDVRGeegaSDHAPVWIEL 255
Cdd:cd09085   236 ILPDVMG----SDHCPVSLEL 252
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-255 3.29e-18

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: 81.98  E-value: 3.29e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   2 KIATFNINNVNRRL--------PNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVW---KGQRQWNGVAILGR 70
Cdd:cd09088     1 RIVTWNVNGIRTRLqyqpwnkeNSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFsfsRGRKGYSGVATYCR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  71 -----------GKTPILTRDQLP------------GGDSDTQSRYIEAAYD-----------GVIVASIYLPNGNPRPGP 116
Cdd:cd09088    81 dsaatpvaaeeGLTGVLSSPNQKnelsenddigcyGEMLEFTDSKELLELDsegrcvltdhgTFVLINVYCPRADPEKEE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 117 KFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNVVPTDLDIYPTKSWNDDALTQPEP---RSAFRSL---TDAGWT---- 186
Cdd:cd09088   161 RLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLlgdSGEGGGspgg 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1894882849 187 ---DAIRKLHPAEP-MFSFWDYKRQRWPQGKGLRLDHLLLSPQIVPRLMAGGVDRDVRGeegaSDHAPVWIEL 255
Cdd:cd09088   241 lliDSFRYFHPTRKgAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEG----SDHCPVYADL 309
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-179 1.61e-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: 66.86  E-value: 1.61e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   4 ATFNINNVN-------RRLPNLLAWLEAAEPDLVCLQELKAAQDAFPQKALSSAGYEAVWK---GQRQWNGVAILGRgkT 73
Cdd:pfam03372   1 LTWNVNGGNadaagddRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGgpgGGGGGGGVAILSR--Y 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  74 PILTRDQLPGGDSDTQSRYIEAAYDGVIVASIYLPNGNPRPGPKFDYKLAWFDRLVRHAGELMDAKVPVVLAGDYNvvpT 153
Cdd:pfam03372  79 PLSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN---A 155

                         170       180
                  ....*....|....*....|....*..
gi 1894882849 154 DLdIYPTKSWN-DDALTQPEPRSAFRS 179
Cdd:pfam03372 156 DY-ILVSGGLTvLSVGVLPDLGPRTGS 181
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-256 1.26e-12

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 66.17  E-value: 1.26e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINNVNRRLPNLLAWLEAAEPDLVCLQELkaaqDAFPQKALSSAGYE---AVWKGQRQWNGVAILGRgkTPILT 77
Cdd:COG3021    95 LRVLTANVLFGNADAEALAALVREEDPDVLVLQET----TPAWEEALAALEADypyRVLCPLDNAYGMALLSR--LPLTE 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  78 RDQLPGGDSDTQSryieaaydgvIVASIYLPNGNPR-----PGPKFDYKLAWfDRLVRHAGELMDA-KVPVVLAGDYNVV 151
Cdd:COG3021   169 AEVVYLVGDDIPS----------IRATVELPGGPVRlvavhPAPPVGGSAER-DAELAALAKAVAAlDGPVIVAGDFNAT 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 152 PTDldiyptkswnddaltqpeprSAFRSLTDA-GWTDAIRklhpAEPMFSFWDykrQRWPqGKGLRLDHLLLSPQIVPRL 230
Cdd:COG3021   238 PWS--------------------PTLRRLLRAsGLRDARA----GRGLGPTWP---ANLP-FLRLPIDHVLVSRGLTVVD 289

                         250       260
                  ....*....|....*....|....*.
gi 1894882849 231 MAggvdrdvRGEEGASDHAPVWIELA 256
Cdd:COG3021   290 VR-------VLPVIGSDHRPLLAELA 308
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-255 2.67e-12

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: 64.42  E-value: 2.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   3 IATFNIN--NVNRRLPNLLAWLEAAEPDLVCLQELKAAQ-DAFPQKALSSAGYEAVWKGQRQWN---GVAILGRGKT-PI 75
Cdd:cd08372     1 VASYNVNglNAATRASGIARWVRELDPDIVCLQEVKDSQySAVALNQLLPEGYHQYQSGPSRKEgyeGVAILSKTPKfKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  76 LTRDQLPGGDSDTQSRYIEAA-----YDGVIVASIYLPNGNPRpgpkFDYKLAW-------FDRLVRHAGElmdakvPVV 143
Cdd:cd08372    81 VEKHQYKFGEGDSGERRAVVVkfdvhDKELCVVNAHLQAGGTR----ADVRDAQlkevlefLKRLRQPNSA------PVV 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 144 LAGDYNVVPTDLDIYPTKSWNDdaLTQPEPRSafrsltdagwtDAIRKLHPAEPMFSFWDYkrqrwpqgKGLRLDHLLLS 223
Cdd:cd08372   151 ICGDFNVRPSEVDSENPSSMLR--LFVALNLV-----------DSFETLPHAYTFDTYMHN--------VKSRLDYIFVS 209

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1894882849 224 PQIVPRLMAGGVDRDVRGEEGASDHAPVWIEL 255
Cdd:cd08372   210 KSLLPSVKSSKILSDAARARIPSDHYPIEVTL 241
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-255 3.78e-11

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: 61.21  E-value: 3.78e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   3 IATFNIN--NVNRRLPNLLAWLEAAEPDLVCLQELKAAQdafpqkalSSAGYEAVWKGQRQWNGVAILGRGKTPILTRDQ 80
Cdd:cd09076     1 IGTLNVRglRSPGKRAQLLEELKRKKLDILGLQETHWTG--------EGELKKKREGGTILYSGSDSGKSRGVAILLSKT 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  81 LPGG----DSDTQSRYIEAAYDG----VIVASIYLPNGNPrpgPKFdyKLAWFDRLVRHAgELMDAKVPVVLAGDYNVV- 151
Cdd:cd09076    73 AANKlleyTKVVSGRIIMVRFKIkgkrLTIINVYAPTARD---EEE--KEEFYDQLQDVL-DKVPRHDTLIIGGDFNAVl 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 152 -PTDLDIYPTKSWNDDALTQPEPRSAFRSLTDAGwtdaiRKLHPAEPMFSFwdykrqRWPQGKGL-RLDHLLLSPQIVPR 229
Cdd:cd09076   147 gPKDDGRKGLDKRNENGERALSALIEEHDLVDVW-----RENNPKTREYTW------RSPDHGSRsRIDRILVSKRLRVK 215

                         250       260
                  ....*....|....*....|....*..
gi 1894882849 230 lmaggvDRDVRGEEGA-SDHAPVWIEL 255
Cdd:cd09076   216 ------VKKTKITPGAgSDHRLVTLKL 236
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 3-255 7.67e-09

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.


Pssm-ID: 197318 [Multi-domain]  Cd Length: 246  Bit Score: 54.61  E-value: 7.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   3 IATFNINNVNRR-----LPNLLAWLEAAEPDLVCLQE-LKAAQDAFPQKALSSAGYE--AVWKGQRQWN-GVAILgrGKT 73
Cdd:cd09084     1 VMSYNVRSFNRYkwkddPDKILDFIKKQDPDILCLQEyYGSEGDKDDDLRLLLKGYPyyYVVYKSDSGGtGLAIF--SKY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  74 PILTRDQLPGGDSDTQSRYIEAAYDG--VIVASIYLP----NGNPRPGPKFDYKLAW-----FDRL----VRHAG--ELM 136
Cdd:cd09084    79 PILNSGSIDFPNTNNNAIFADIRVGGdtIRVYNVHLEsfriTPSDKELYKEEKKAKElsrnlLRKLaeafKRRAAqaDLL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 137 DAKV-----PVVLAGDYNVVPTDLdIYPT--KSWNDdaltqpeprsAFRsltDAGWTdairklhpaePMFSFWDYKRqrw 209
Cdd:cd09084   159 AADIaaspyPVIVCGDFNDTPASY-VYRTlkKGLTD----------AFV---EAGSG----------FGYTFNGLFF--- 211

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1894882849 210 pqgkGLRLDHLLLSPQIVPRlmAGGVDRDVrgeegASDHAPVWIEL 255
Cdd:cd09084   212 ----PLRIDYILTSKGFKVL--RYRVDPGK-----YSDHYPIVATL 246
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 2-255 1.11e-08

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: 54.15  E-value: 1.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   2 KIATFNI---------NNVNRRLPNLLAWLEAAEPDLVCLQELKAAQDAFPQKALssAGYEAVwkgqrqwnGVailGR-- 70
Cdd:cd09083     1 RVMTFNIrydnpsdgeNSWENRKDLVAELIKFYDPDIIGTQEALPHQLADLEELL--PEYDWI--------GV---GRdd 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  71 GK-----TPILTRDQ----LPGGD---SDTQ----SRYIEAAYdgvivasiylpngnPRP-----------GPKFDY--- 120
Cdd:cd09083    68 GKekgefSAIFYRKDrfelLDSGTfwlSETPdvvgSKGWDAAL--------------PRIctwarfkdkktGKEFYVfnt 133

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 121 ------KLAwfdR------LVRHAGELMDaKVPVVLAGDYNVVPTDldiyptkswnddaltqpeprSAFRSLTDAGWTDA 188
Cdd:cd09083   134 hldhvgEEA---ReesaklILERIKEIAG-DLPVILTGDFNAEPDS--------------------EPYKTLTSGGLKDA 189

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1894882849 189 --IRKLHPAEPMFSFWDYKrqrwPQGKGLRLDHLLLSPQIVPRLMAggVDRDVRGEEGASDHAPVWIEL 255
Cdd:cd09083   190 rdTAATTDGGPEGTFHGFK----GPPGGSRIDYIFVSPGVKVLSYE--ILTDRYDGRYPSDHFPVVADL 252
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
1-255 2.46e-07

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 50.79  E-value: 2.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNINN--------------------VNRRLPNLLAWLEAAEPDLVCLQEL----KAAQDAFPQKALSSAGYEAVW 56
Cdd:COG2374    69 LRVATFNVENlfdtddddddfgrgadtpeeYERKLAKIAAAIAALDADIVGLQEVenngSALQDLVAALNLAGGTYAFVH 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  57 KGQRQWNG---VAILGRGKT-PILTRDQLPG-----GDSDTQSRYIeaaydgvIVASIYLPNGNP-----------RPGP 116
Cdd:COG2374   149 PPDGPDGDgirVALLYRPDRvTLVGSATIADlpdspGNPDRFSRPP-------LAVTFELANGEPftvivnhfkskGSDD 221

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 117 KFDYKLAWFDRLVRHAGEL---------MDAKVPVVLAGDYNvvptdldiyptkswnDDALTQPeprsaFRSLTDA-GWT 186
Cdd:COG2374   222 PGDGQGASEAKRTAQAEALrafvdsllaADPDAPVIVLGDFN---------------DYPFEDP-----LRALLGAgGLT 281

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849 187 DAIRKLHPAEPmFSFWdYkrqrwpQGKGLRLDHLLLSPQIVPRLMAGGV----------------DRDVRGEEGASDHAP 250
Cdd:COG2374   282 NLAEKLPAAER-YSYV-Y------DGNSGLLDHILVSPALAARVTGADIwhinadiynddfkpdfRTYADDPGRASDHDP 353


                  ....*
gi 1894882849 251 VWIEL 255
Cdd:COG2374   354 VVVGL 358
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-163 5.52e-07

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 48.37  E-value: 5.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849   1 MKIATFNI---NNVNRR--LPNLLAWLEAAEPDLVCLQElkaaqdafpqkalssagyeavwkgqrqwngVAILGRgkTPI 75
Cdd:COG3568     8 LRVMTYNIrygLGTDGRadLERIARVIRALDPDVVALQE------------------------------NAILSR--YPI 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894882849  76 LTRDQLPGGDSDTQSRY-----IEAAYDGVIVASIYLPNGNPRpgpkfdYKLAWFDRLVRHAGELmDAKVPVVLAGDYNv 150
Cdd:COG3568    56 VSSGTFDLPDPGGEPRGalwadVDVPGKPLRVVNTHLDLRSAA------ARRRQARALAELLAEL-PAGAPVILAGDFN- 127

                         170
                  ....*....|....
gi 1894882849 151 vptDLD-IYPTKSW 163
Cdd:COG3568   128 ---DIDyILVSPGL 138
 
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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