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Conserved domains on  [gi|643712261|ref|WP_025252010|]
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exodeoxyribonuclease III [Corynebacterium vitaeruminis]

Protein Classification

exonuclease/endonuclease/phosphatase family protein( domain architecture ID 662)

exonuclease/endonuclease/phosphatase (EEP) family protein may cleave phosphodiester bonds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EEP super family cl00490
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 1-298 5.20e-100

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.


The actual alignment was detected with superfamily member cd10281:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 253  Bit Score: 293.75  E-value: 5.20e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   1 MQITTVNVNGIRAAVKQrseantGFLPWLEASGSDVVLLQEVRASEKDsLTALAPAIDaGWHYVGAPAAAKGRAGVGILS 80
Cdd:cd10281    1 MRVISVNVNGIRAAAKK------GFLEWLAAQDADVVCLQEVRAQEEQ-LDDDFFEPE-GYNAYFFDAEKKGYAGVAIYS 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  81 RTPLTDVTIG--IDGFEESGRYIAGTFDDggqaVTVASLYLPSGSAGTDKQDEKYRFLDSFEGYLADQGALDQQMVIGGD 158
Cdd:cd10281   73 RTQPKAVIYGlgFEEFDDEGRYIEADFDN----VSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGD 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 159 WNICHREQDLKNFKTNRNKSGFLPDEREFMDSVFGAFPdeapqakpggawagavdyesdrrraaatdpvWFDAARRLAPD 238
Cdd:cd10281  149 FNIAHTEIDIKNWKANQKNSGFLPEERAWLDQVFGELG-------------------------------YVDAFRELNPD 197

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 239 EDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKATghdmRWSDHAPMTVVY 298
Cdd:cd10281  198 EGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYREE----RFSDHAPLIVDY 253
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-298 5.20e-100

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: 293.75  E-value: 5.20e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   1 MQITTVNVNGIRAAVKQrseantGFLPWLEASGSDVVLLQEVRASEKDsLTALAPAIDaGWHYVGAPAAAKGRAGVGILS 80
Cdd:cd10281    1 MRVISVNVNGIRAAAKK------GFLEWLAAQDADVVCLQEVRAQEEQ-LDDDFFEPE-GYNAYFFDAEKKGYAGVAIYS 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  81 RTPLTDVTIG--IDGFEESGRYIAGTFDDggqaVTVASLYLPSGSAGTDKQDEKYRFLDSFEGYLADQGALDQQMVIGGD 158
Cdd:cd10281   73 RTQPKAVIYGlgFEEFDDEGRYIEADFDN----VSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGD 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 159 WNICHREQDLKNFKTNRNKSGFLPDEREFMDSVFGAFPdeapqakpggawagavdyesdrrraaatdpvWFDAARRLAPD 238
Cdd:cd10281  149 FNIAHTEIDIKNWKANQKNSGFLPEERAWLDQVFGELG-------------------------------YVDAFRELNPD 197

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 239 EDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKATghdmRWSDHAPMTVVY 298
Cdd:cd10281  198 EGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYREE----RFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-298 4.21e-97

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 286.20  E-value: 4.21e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   1 MQITTVNVNGIRAAVKQrseantgFLPWLEASGSDVVLLQEVRASekDSLTALAPAIDAGWHYVGAPAaaKGRAGVGILS 80
Cdd:COG0708    1 MKIASWNVNGIRARLPK-------LLDWLAEEDPDVLCLQETKAQ--DEQFPLEAFEAAGYHVYFHGQ--KGYNGVAILS 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  81 RTPLTDVTIGIDG--FEESGRYIAGTFDDggqaVTVASLYLPSGSA-GTDKQDEKYRFLDSFEGYLADQGALDQQMVIGG 157
Cdd:COG0708   70 RLPPEDVRRGLGGdeFDAEGRYIEADFGG----VRVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLAPGRPLILCG 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 158 DWNICHREQDLKNFKTNRNKSGFLPDEREFMDSVFgafpdeapqakpggaWAGavdyesdrrraaatdpvWFDAARRLAP 237
Cdd:COG0708  146 DFNIAPTEIDVKNPKANLKNAGFLPEERAWFDRLL---------------ELG-----------------LVDAFRALHP 193

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 643712261 238 D-EDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKATGHDMRWSDHAPMTVVY 298
Cdd:COG0708  194 DvEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDREPRGDERPSDHAPVVVEL 255
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-298 7.74e-61

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: 193.65  E-value: 7.74e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261    1 MQITTVNVNGIRAAVKQrseantGFLPWLEASGSDVVLLQEVRASEKDslTALAPAIDAGWH--YVGAPaaaKGRAGVGI 78
Cdd:TIGR00633   1 MKIISWNVNGLRARLHK------LFLDWLKEEQPDVLCLQETKVADEQ--FPAELFEELGYHvfFHGAK---KGYSGVAI 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   79 LSRTPLTDVTIGIDG--FEESGRYIAGTFDDggqaVTVASLYLPSGSA-GTDKQDEKYRFLDSFEGYLADQGALDQQMVI 155
Cdd:TIGR00633  70 LSKVEPLDVRYGFGGepHDEEGRVITAEFDG----FTVVNVYVPNGGSrDLERLEYKLQFWDALFQYLEKELDAGKPVVI 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  156 GGDWNICHREQDLKNFKTNRNKSGFLPDEREFMDSVFGafpdeapqakpggawAGAVdyesdrrraaatdpvwfDAARRL 235
Cdd:TIGR00633 146 CGDMNVAHTEIDLGNPKENKGNAGFTPEEREWFDELLE---------------AGFV-----------------DTFRHF 193

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 643712261  236 APD-EDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKatghDMRWSDHAPMTVVY 298
Cdd:TIGR00633 194 NPDtGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS----EIRGSDHCPIVLEL 253
PRK11756 PRK11756
exonuclease III; Provisional
 1-293 2.41e-27

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 107.29  E-value: 2.41e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   1 MQITTVNVNGIRAAVKQrseantgflpwLEA----SGSDVVLLQEVRASekDSLTALApAIDA-GWH--YVGApaaaKGR 73
Cdd:PRK11756   1 MKFVSFNINGLRARPHQ-----------LEAiiekHQPDVIGLQETKVH--DEMFPLE-EVEAlGYHvfYHGQ----KGH 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  74 AGVGILSRTPLTDVTIGI--DGFEESGRYIAGTFDDGGQAVTVASLYLPSGSAGT--DKQDEKYRFLDSFEGYLADQGAL 149
Cdd:PRK11756  63 YGVALLSKQTPIAVRKGFptDDEEAQRRIIMATIPTPNGNLTVINGYFPQGESRDhpTKFPAKRQFYQDLQNYLETELSP 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 150 DQQMVIGGDWNICHREQDLKNFKTNRN---KSG---FLPDEREFMDSVFGafpdeapqakpggaWaGAVdyesdrrraaa 223
Cdd:PRK11756 143 DNPLLIMGDMNISPTDLDIGIGEENRKrwlRTGkcsFLPEEREWLDRLMD--------------W-GLV----------- 196

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 643712261 224 tdpvwfDAARRLAPD-EDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDkatgHDMRW----SDHAP 293
Cdd:PRK11756 197 ------DTFRQLNPDvNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAERCVETGID----YDIRGmekpSDHAP 261
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 5-161 1.00e-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: 68.02  E-value: 1.00e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261    5 TVNVNGIRAAVKQRSEANTGFLPWLEASGSDVVLLQEVRASEKDSLTALAPAIDAGWHYVGaPAAAKGRAGVGILSRTPL 84
Cdd:pfam03372   2 TWNVNGGNADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGG-PGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 643712261   85 TDVTIGIdgFEESGRYIAGTFDDGGQAVTVASLYLPSGSAGTDKQDEKYRFLDSFEGYLADQGALDQQMVIGGDWNI 161
Cdd:pfam03372  81 SSVILVD--LGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-298 5.20e-100

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: 293.75  E-value: 5.20e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   1 MQITTVNVNGIRAAVKQrseantGFLPWLEASGSDVVLLQEVRASEKDsLTALAPAIDaGWHYVGAPAAAKGRAGVGILS 80
Cdd:cd10281    1 MRVISVNVNGIRAAAKK------GFLEWLAAQDADVVCLQEVRAQEEQ-LDDDFFEPE-GYNAYFFDAEKKGYAGVAIYS 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  81 RTPLTDVTIG--IDGFEESGRYIAGTFDDggqaVTVASLYLPSGSAGTDKQDEKYRFLDSFEGYLADQGALDQQMVIGGD 158
Cdd:cd10281   73 RTQPKAVIYGlgFEEFDDEGRYIEADFDN----VSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGD 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 159 WNICHREQDLKNFKTNRNKSGFLPDEREFMDSVFGAFPdeapqakpggawagavdyesdrrraaatdpvWFDAARRLAPD 238
Cdd:cd10281  149 FNIAHTEIDIKNWKANQKNSGFLPEERAWLDQVFGELG-------------------------------YVDAFRELNPD 197

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 239 EDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKATghdmRWSDHAPMTVVY 298
Cdd:cd10281  198 EGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYREE----RFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-298 4.21e-97

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 286.20  E-value: 4.21e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   1 MQITTVNVNGIRAAVKQrseantgFLPWLEASGSDVVLLQEVRASekDSLTALAPAIDAGWHYVGAPAaaKGRAGVGILS 80
Cdd:COG0708    1 MKIASWNVNGIRARLPK-------LLDWLAEEDPDVLCLQETKAQ--DEQFPLEAFEAAGYHVYFHGQ--KGYNGVAILS 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  81 RTPLTDVTIGIDG--FEESGRYIAGTFDDggqaVTVASLYLPSGSA-GTDKQDEKYRFLDSFEGYLADQGALDQQMVIGG 157
Cdd:COG0708   70 RLPPEDVRRGLGGdeFDAEGRYIEADFGG----VRVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLAPGRPLILCG 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 158 DWNICHREQDLKNFKTNRNKSGFLPDEREFMDSVFgafpdeapqakpggaWAGavdyesdrrraaatdpvWFDAARRLAP 237
Cdd:COG0708  146 DFNIAPTEIDVKNPKANLKNAGFLPEERAWFDRLL---------------ELG-----------------LVDAFRALHP 193

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 643712261 238 D-EDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKATGHDMRWSDHAPMTVVY 298
Cdd:COG0708  194 DvEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDREPRGDERPSDHAPVVVEL 255
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 3-298 9.96e-75

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: 229.10  E-value: 9.96e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   3 ITTVNVNGIRAAVKqrseanTGFLPWLEASGSDVVLLQEVRASEKDSLTALAPAIdaGWHYVGAPAAAKGRAGVGILSRT 82
Cdd:cd09073    2 IISWNVNGLRARLK------KGVLKWLKEEKPDILCLQETKADEDKLPEELQHVE--GYHSYWSPARKKGYSGVATLSKE 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  83 PLTDVTIGIDG--FEESGRYIAGTFDDggqaVTVASLYLPSGSAGTDKQDEKYRFLDSFEGYLADQGALDQQMVIGGDWN 160
Cdd:cd09073   74 EPLDVSYGIGGeeFDSEGRVITAEFDD----FYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFN 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 161 ICHREQDLKNFKTNRNKSGFLPDEREFMDSVFgafpdEAPqakpggawagavdyesdrrraaatdpvWFDAARRLAPDED 240
Cdd:cd09073  150 VAHEEIDLARPKKNEKNAGFTPEERAWFDKLL-----SLG---------------------------YVDTFRHFHPEPG 197

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 643712261 241 IYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKatghDMRWSDHAPMTVVY 298
Cdd:cd09073  198 AYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILS----KVKGSDHAPVTLEL 251
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-298 7.74e-61

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: 193.65  E-value: 7.74e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261    1 MQITTVNVNGIRAAVKQrseantGFLPWLEASGSDVVLLQEVRASEKDslTALAPAIDAGWH--YVGAPaaaKGRAGVGI 78
Cdd:TIGR00633   1 MKIISWNVNGLRARLHK------LFLDWLKEEQPDVLCLQETKVADEQ--FPAELFEELGYHvfFHGAK---KGYSGVAI 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   79 LSRTPLTDVTIGIDG--FEESGRYIAGTFDDggqaVTVASLYLPSGSA-GTDKQDEKYRFLDSFEGYLADQGALDQQMVI 155
Cdd:TIGR00633  70 LSKVEPLDVRYGFGGepHDEEGRVITAEFDG----FTVVNVYVPNGGSrDLERLEYKLQFWDALFQYLEKELDAGKPVVI 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  156 GGDWNICHREQDLKNFKTNRNKSGFLPDEREFMDSVFGafpdeapqakpggawAGAVdyesdrrraaatdpvwfDAARRL 235
Cdd:TIGR00633 146 CGDMNVAHTEIDLGNPKENKGNAGFTPEEREWFDELLE---------------AGFV-----------------DTFRHF 193

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 643712261  236 APD-EDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKatghDMRWSDHAPMTVVY 298
Cdd:TIGR00633 194 NPDtGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS----EIRGSDHCPIVLEL 253
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-297 1.85e-59

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: 190.42  E-value: 1.85e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   1 MQITTVNVNGIRAAVKQrseantgFLPWLEASGSDVVLLQEVRASEKD-SLTALApaiDAGWH--YVGApaaaKGRAGVG 77
Cdd:cd09086    1 MKIATWNVNSIRARLEQ-------VLDWLKEEDPDVLCLQETKVEDDQfPADAFE---ALGYHvaVHGQ----KAYNGVA 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  78 ILSRTPLTDVTIGIDGFEESG--RYIAGTFDDggqaVTVASLYLPSG-SAGTDKQDEKYRFLDSFEGYLADQGALDQQMV 154
Cdd:cd09086   67 ILSRLPLEDVRTGFPGDPDDDqaRLIAARVGG----VRVINLYVPNGgDIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLV 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 155 IGGDWNICHREQDLKNFKTNRNKSGFLPDEREFMDSVFgafpdeapqakpggaWAGavdyesdrrraaatdpvWFDAARR 234
Cdd:cd09086  143 LVGDFNIAPEDIDVWDPKQLLGKVLFTPEEREALRALL---------------DLG-----------------FVDAFRA 190

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 643712261 235 LAPDEDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKATGHDMRWSDHAPMTVV 297
Cdd:cd09086  191 LHPDEKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGIDREPRGWEKPSDHAPVVAE 253
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-297 1.51e-55

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: 180.27  E-value: 1.51e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261    1 MQITTVNVNGIRAAVKQrseantgFLPWLEASGSDVVLLQEVRASEKDslTALAPAIDAGWHYVGAPAaaKGRAGVGILS 80
Cdd:TIGR00195   1 MKIISWNVNGLRARPHK-------GLAWLKENQPDVLCLQETKVQDEQ--FPLEPFHKEGYHVFFSGQ--KGYSGVAIFS 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   81 RTPLTDVTIGIDG--FEESGRYIAGTFDDggqaVTVASLYLPSGSA-GTDKQDEKYRFLDSFEGYLADQGALDQQMVIGG 157
Cdd:TIGR00195  70 KEEPISVRRGFGVeeEDAEGRIIMAEFDS----FLVINGYFPNGSRdDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICG 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  158 DWNICHREQDLKNFKTNRNKSGFLPDEREFMDSVFGafpdeapqakpggawAGAVdyesdrrraaatdpvwfDAARRLAP 237
Cdd:TIGR00195 146 DMNIAPTEIDLHIPDENRNHTGFLPEEREWLDRLLE---------------AGLV-----------------DTFRKFNP 193

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  238 DEDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKATGHDMRWSDHAPMTVV 297
Cdd:TIGR00195 194 DEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDYDIRGSEKPSDHCPVVLE 253
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-298 7.03e-55

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: 178.62  E-value: 7.03e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   1 MQITTVNVNGIRAAVKQrseantGFLPWLEASGSDVVLLQEVRASE---KDSLTALApaidaGWHYVGAPAAAKGRAGVG 77
Cdd:cd09085    1 MKIISWNVNGLRAVHKK------GFLDWFKEEKPDILCLQETKAQPeqlPEDLRNIE-----GYHSYFNSAERKGYSGVA 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  78 ILSRTPLTDVT--IGIDGFEESGRYIAGTFDDggqaVTVASLYLPSGSAGTDKQDEKYRFLDSFEGYLADQGALDQQMVI 155
Cdd:cd09085   70 LYSKIEPDSVRegLGVEEFDNEGRILIADFDD----FTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVII 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 156 GGDWNICHREQDLKNFKTNRNKSGFLPDEREFMDSVFGAfpdeapqakpggawaGavdyesdrrraaatdpvWFDAARRL 235
Cdd:cd09085  146 CGDFNTAHKEIDLARPKENEKVSGFLPEERAWMDKFIEN---------------G-----------------YVDTFRMF 193

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 643712261 236 APDEDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKatghDMRWSDHAPMTVVY 298
Cdd:cd09085  194 NKEPGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILP----DVMGSDHCPVSLEL 252
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-297 1.08e-41

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: 144.23  E-value: 1.08e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   1 MQITTVNVNGIRAAVKqrseanTGFLPWLEASGSDVVLLQEVRASEKDsLTALAPAIDAGWHYVGAPAAAKGRAGVGILS 80
Cdd:cd09087    1 LKIISWNVNGLRALLK------KGLLDYVKKEDPDILCLQETKLQEGD-VPKELKELLKGYHQYWNAAEKKGYSGTAILS 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  81 RTPLTDVT--IGIDGFEESGRYIAGTFDDggqaVTVASLYLPSGSAGTDKQDEKYRFLDSFEGYLADqgaLDQQ--MVIG 156
Cdd:cd09087   74 KKKPLSVTygIGIEEHDQEGRVITAEFEN----FYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKK---LDSKkpVIWC 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 157 GDWNICHREQDLKNFKTNRNKSGFLPDEREfmdsVFGAFPDeapqakpggawAGAVdyesdrrraaatdpvwfDAARRLA 236
Cdd:cd09087  147 GDLNVAHEEIDLANPKTNKKSAGFTPEERE----SFTELLE-----------AGFV-----------------DTFRHLH 194

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 643712261 237 PD-EDIYTWWTYRGQAFDNNAGWRIDYQAVTapllaraeRSWVDKATGHDMR----WSDHAPMTVV 297
Cdd:cd09087  195 PDkEGAYTFWSYRGNARAKNVGWRLDYFLVS--------ERLKDRVVDSFIRsdimGSDHCPIGLE 252
PRK11756 PRK11756
exonuclease III; Provisional
 1-293 2.41e-27

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 107.29  E-value: 2.41e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   1 MQITTVNVNGIRAAVKQrseantgflpwLEA----SGSDVVLLQEVRASekDSLTALApAIDA-GWH--YVGApaaaKGR 73
Cdd:PRK11756   1 MKFVSFNINGLRARPHQ-----------LEAiiekHQPDVIGLQETKVH--DEMFPLE-EVEAlGYHvfYHGQ----KGH 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  74 AGVGILSRTPLTDVTIGI--DGFEESGRYIAGTFDDGGQAVTVASLYLPSGSAGT--DKQDEKYRFLDSFEGYLADQGAL 149
Cdd:PRK11756  63 YGVALLSKQTPIAVRKGFptDDEEAQRRIIMATIPTPNGNLTVINGYFPQGESRDhpTKFPAKRQFYQDLQNYLETELSP 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 150 DQQMVIGGDWNICHREQDLKNFKTNRN---KSG---FLPDEREFMDSVFGafpdeapqakpggaWaGAVdyesdrrraaa 223
Cdd:PRK11756 143 DNPLLIMGDMNISPTDLDIGIGEENRKrwlRTGkcsFLPEEREWLDRLMD--------------W-GLV----------- 196

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 643712261 224 tdpvwfDAARRLAPD-EDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDkatgHDMRW----SDHAP 293
Cdd:PRK11756 197 ------DTFRQLNPDvNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAERCVETGID----YDIRGmekpSDHAP 261
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-294 1.68e-24

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 99.00  E-value: 1.68e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   1 MQITTVNVNGIRAAVKQrseantGFLPWLEASGSDVVLLQEVRASEKDSLTALAPAIDAgWHYvgapAAAKGRAGVGILS 80
Cdd:PRK13911   1 MKLISWNVNGLRACMTK------GFMDFFNSVDADVFCIQESKMQQEQNTFEFKGYFDF-WNC----AIKKGYSGVVTFT 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  81 RTPLTDVTIGIDGFE--ESGRYIAGTFddggQAVTVASLYLPSGSAGTDKQDEKYRFLDSFEGYLADQgALDQQMVIGGD 158
Cdd:PRK13911  70 KKEPLSVSYGINIEEhdKEGRVITCEF----ESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKAL-ELKKPVIVCGD 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 159 WNICHREQDLKNFKTNRNKSGFLPDEREFMDSVFGAFpdeapqakpggawagavdyesdrrraaatdpvWFDAARRLAPD 238
Cdd:PRK13911 145 LNVAHNEIDLENPKTNRKNAGFSDEERGKFSELLNAG--------------------------------FIDTFRYFYPN 192

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 643712261 239 -EDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAERSWVDKatghDMRWSDHAPM 294
Cdd:PRK13911 193 kEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYK----DILGSDHCPV 245
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-191 1.40e-16

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: 77.01  E-value: 1.40e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   3 ITTVNVNGIRAAVKQRSEANtgflpWLEASGSDVVLLQEVRASEKDSLTALapaiDAGWHYVGAPAAAKGRAGVGILSRT 82
Cdd:cd09076    1 IGTLNVRGLRSPGKRAQLLE-----ELKRKKLDILGLQETHWTGEGELKKK----REGGTILYSGSDSGKSRGVAILLSK 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  83 PLTDVTIGIDgFEESGRYIAGTFDDGGQAVTVASLYLPSgsagTDKQDEKYRFLDSFEGYLADQGALDqQMVIGGDWNIC 162
Cdd:cd09076   72 TAANKLLEYT-KVVSGRIIMVRFKIKGKRLTIINVYAPT----ARDEEEKEEFYDQLQDVLDKVPRHD-TLIIGGDFNAV 145

                        170       180       190
                 ....*....|....*....|....*....|..
gi 643712261 163 HREQDLKNF---KTNRNKSGFLPDEREFMDSV 191
Cdd:cd09076  146 LGPKDDGRKgldKRNENGERALSALIEEHDLV 177
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-296 3.29e-16

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: 76.37  E-value: 3.29e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   3 ITTVNVNGIRAAVKQRseantGFLPWLEASGSDVVLLQEVRASEKDSLTALAPAIDAGWHYVGAPAAAKGRAGVGILSRT 82
Cdd:cd08372    1 VASYNVNGLNAATRAS-----GIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGYHQYQSGPSRKEGYEGVAILSKT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  83 PLTDVTIGIDGF-----EESGRYIAGTFDDGGQAVTVASLYLPsgsAGTDKQDEKYRFLDSF-EGYLADQGALDQQMVIG 156
Cdd:cd08372   76 PKFKIVEKHQYKfgegdSGERRAVVVKFDVHDKELCVVNAHLQ---AGGTRADVRDAQLKEVlEFLKRLRQPNSAPVVIC 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 157 GDWNICHREQDLKNfktnrnksgflpdeREFMDSVFGAFPdeapqakpggawagAVDyesdrrraaatdpVWFDAArrla 236
Cdd:cd08372  153 GDFNVRPSEVDSEN--------------PSSMLRLFVALN--------------LVD-------------SFETLP---- 187

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 643712261 237 pdeDIYTWWTYrgqafDNNAGWRIDYQAVTAPLLARAERSWV--DKATGHDMrwSDHAPMTV 296
Cdd:cd08372  188 ---HAYTFDTY-----MHNVKSRLDYIFVSKSLLPSVKSSKIlsDAARARIP--SDHYPIEV 239
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 3-293 9.17e-16

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: 76.20  E-value: 9.17e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   3 ITTVNVNGIRAaVKQRSEANT-----GFLPWLEAsgsDVVLLQEVRaSEKDSLTAlAPAIDAGWH-YVGAPAAAKGRAGV 76
Cdd:cd09088    2 IVTWNVNGIRT-RLQYQPWNKenslkSFLDSLDA---DIICLQETK-LTRDELDE-PSAIVEGYDsFFSFSRGRKGYSGV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  77 GILSRTPLT----------------------DVTIGIDGF----EESGRYIAGTFDDGGQAV-------TVASLYLPSgs 123
Cdd:cd09088   76 ATYCRDSAAtpvaaeegltgvlsspnqknelSENDDIGCYgemlEFTDSKELLELDSEGRCVltdhgtfVLINVYCPR-- 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 124 AGTDKQdEKYRFLDSFEGYLADQG-ALDQ---QMVIGGDWNICHREQDLKNFKTNRNKSGFLPDE---REFMDSVFGafP 196
Cdd:cd09088  154 ADPEKE-ERLEFKLDFYRLLEERVeALLKagrRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLG--D 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261 197 DEAPQAKPGGawagavdyesdrrraaatdpVWFDAARRLAPD-EDIYTWWTYRGQAFDNNAGWRIDYQAVTAPLLARAER 275
Cdd:cd09088  231 SGEGGGSPGG--------------------LLIDSFRYFHPTrKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKA 290

                        330
                 ....*....|....*...
gi 643712261 276 SWVDkatgHDMRWSDHAP 293
Cdd:cd09088  291 ADIL----PEVEGSDHCP 304
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 5-161 1.00e-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: 68.02  E-value: 1.00e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261    5 TVNVNGIRAAVKQRSEANTGFLPWLEASGSDVVLLQEVRASEKDSLTALAPAIDAGWHYVGaPAAAKGRAGVGILSRTPL 84
Cdd:pfam03372   2 TWNVNGGNADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGG-PGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 643712261   85 TDVTIGIdgFEESGRYIAGTFDDGGQAVTVASLYLPSGSAGTDKQDEKYRFLDSFEGYLADQGALDQQMVIGGDWNI 161
Cdd:pfam03372  81 SSVILVD--LGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 28-160 1.15e-09

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 58.08  E-value: 1.15e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261  28 WLEASGSDVVLLQEVrasEKDSLTALApAIDAGW-HYVGAPAAakGRAGVGILSRTPLTDVTIgIDGFEESGRYIAGTFD 106
Cdd:COG3021  115 LVREEDPDVLVLQET---TPAWEEALA-ALEADYpYRVLCPLD--NAYGMALLSRLPLTEAEV-VYLVGDDIPSIRATVE 187

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 643712261 107 DGGQAVTVASLYLPSGSAGTDKQDEKYRfldsfegYLADQ-GALDQQMVIGGDWN 160
Cdd:COG3021  188 LPGGPVRLVAVHPAPPVGGSAERDAELA-------ALAKAvAALDGPVIVAGDFN 235
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 5-121 1.40e-03

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: 39.59  E-value: 1.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 643712261   5 TVNVNGIRAAVKQRSEANtgFLPWLEASGSDVVLLQEVRASEKDSLTALAPAIdAGW-HYVGAPAAAKGRAGVGILSRTP 83
Cdd:cd09084    3 SYNVRSFNRYKWKDDPDK--ILDFIKKQDPDILCLQEYYGSEGDKDDDLRLLL-KGYpYYYVVYKSDSGGTGLAIFSKYP 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 643712261  84 LTDVtiG-IDGFEESGRYIAGTFDDGGQAVTVASLYLPS 121
Cdd:cd09084   80 ILNS--GsIDFPNTNNNAIFADIRVGGDTIRVYNVHLES 116
 
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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