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Conserved domains on  [gi|491649545|ref|WP_005506814|]
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MULTISPECIES: exodeoxyribonuclease III [Rothia]

Protein Classification

exodeoxyribonuclease III( domain architecture ID 10178908)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 15-287 5.35e-128

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: 364.24  E-value: 5.35e-128
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKKDMAAWLASRDIDILCLQEVRAPDAIVRELLDESQ-WHILHAEAAAKGRAGVLVATRRtpnsag 93
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEgYNAYFFDAEKKGYAGVAIYSRT------ 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  94 evlenQPVATRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYVHSGEVGTQKQDDKYRFLERMLVRMPELAKHSDHVL 173
Cdd:cd10281   75 -----QPKAVIYGLGFEEFDDEGRYIEADF-----DNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFI 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 174 IVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFGDIGYRDVARELAGQvPGPYTWWSYRGKAFDNDAGWRIDYHM 253
Cdd:cd10281  145 VCGDFNIAHTEIDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPD-EGQYTWWSNRGQARANNVGWRIDYQI 223

                        250       260       270
                 ....*....|....*....|....*....|....
gi 491649545 254 ATPALAESAVEAVVDRaasyDERFSDHAPLVVDY 287
Cdd:cd10281  224 ATPGLASKVVSAWIYR----EERFSDHAPLIVDY 253
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 15-287 5.35e-128

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: 364.24  E-value: 5.35e-128
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKKDMAAWLASRDIDILCLQEVRAPDAIVRELLDESQ-WHILHAEAAAKGRAGVLVATRRtpnsag 93
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEgYNAYFFDAEKKGYAGVAIYSRT------ 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  94 evlenQPVATRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYVHSGEVGTQKQDDKYRFLERMLVRMPELAKHSDHVL 173
Cdd:cd10281   75 -----QPKAVIYGLGFEEFDDEGRYIEADF-----DNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFI 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 174 IVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFGDIGYRDVARELAGQvPGPYTWWSYRGKAFDNDAGWRIDYHM 253
Cdd:cd10281  145 VCGDFNIAHTEIDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPD-EGQYTWWSNRGQARANNVGWRIDYQI 223

                        250       260       270
                 ....*....|....*....|....*....|....
gi 491649545 254 ATPALAESAVEAVVDRaasyDERFSDHAPLVVDY 287
Cdd:cd10281  224 ATPGLASKVVSAWIYR----EERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
15-288 6.33e-113

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 326.26  E-value: 6.33e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKKdMAAWLASRDIDILCLQEVRAPDAIV-RELLDESQWHILHAeaAAKGRAGVLVATRRtpnsag 93
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFpLEAFEAAGYHVYFH--GQKGYNGVAILSRL------ 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  94 evlenQPVATRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYVHSGE-VGTQKQDDKYRFLERMLVRMPELAKHSDHV 172
Cdd:COG0708   72 -----PPEDVRRGLGGDEFDAEGRYIEADF-----GGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELLAPGRPL 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 173 LIVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFgDIGYRDVARELAGQVPGPYTWWSYRGKAFDNDAGWRIDYH 252
Cdd:COG0708  142 ILCGDFNIAPTEIDVKNPKANLKNAGFLPEERAWFDRLL-ELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYI 220

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 491649545 253 MATPALAESAVEAVVDRAASYDERFSDHAPLVVDYR 288
Cdd:COG0708  221 LASPALADRLKDAGIDREPRGDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 15-288 5.42e-68

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: 211.75  E-value: 5.42e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   15 LRVASVNVNGIRAAYKKDMAAWLASRDIDILCLQEVRAPD-----AIVRELLDESQWHilhaeAAAKGRAGVLVATRRTP 89
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADeqfpaELFEELGYHVFFH-----GAKKGYSGVAILSKVEP 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   90 NSagevlenqpvaTRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYV-HSGEVGTQKQDDKYRFLERMLVRMPELAKH 168
Cdd:TIGR00633  76 LD-----------VRYGFGGEPHDEEGRVITAEF-----DGFTVVNVYVpNGGSRDLERLEYKLQFWDALFQYLEKELDA 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  169 SDHVLIVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFgDIGYRDVARELAGQVPGPYTWWSYRGKAFDNDAGWR 248
Cdd:TIGR00633 140 GKPVVICGDMNVAHTEIDLGNPKENKGNAGFTPEEREWFDELL-EAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWR 218

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 491649545  249 IDYHMATPALAESAVEAVVDRaasyDERFSDHAPLVVDYR 288
Cdd:TIGR00633 219 IDYFLVSEPLAERVVDSYIDS----EIRGSDHCPIVLELD 254
PRK11756 PRK11756
exonuclease III; Provisional
 15-289 6.63e-32

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 118.84  E-value: 6.63e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKKdMAAWLASRDIDILCLQEVRAPDAIV-RELLDESQWHILHAeaAAKGRAGVLVATRrtpnsag 93
Cdd:PRK11756   1 MKFVSFNINGLRARPHQ-LEAIIEKHQPDVIGLQETKVHDEMFpLEEVEALGYHVFYH--GQKGHYGVALLSK------- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  94 evleNQPVATRSNIGEEYFDDSGRWVEADYVLPNGkTLTVVSAYVHSGEvgTQKQDDKY----RFLERMLVRMPELAKHS 169
Cdd:PRK11756  71 ----QTPIAVRKGFPTDDEEAQRRIIMATIPTPNG-NLTVINGYFPQGE--SRDHPTKFpakrQFYQDLQNYLETELSPD 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 170 DHVLIVGDLNVGHTELDIKNWKANQKR------AGFLPEERAYFDRFFgDIGYRDVARELAGQVPGPYTWWSYRGKAFDN 243
Cdd:PRK11756 144 NPLLIMGDMNISPTDLDIGIGEENRKRwlrtgkCSFLPEEREWLDRLM-DWGLVDTFRQLNPDVNDRFSWFDYRSKGFDD 222

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 491649545 244 DAGWRIDYHMATPALAESAVEAVVDraasYD----ERFSDHAPLVVDYRI 289
Cdd:PRK11756 223 NRGLRIDLILATQPLAERCVETGID----YDirgmEKPSDHAPIWATFKL 268
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 18-180 8.53e-10

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: 56.85  E-value: 8.53e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   18 ASVNVNGIRAAYKKDM------AAWLASRDIDILCLQEVRAPDA--IVRELLDESQWHILHAEAAAKGRAGVLVATRRTP 89
Cdd:pfam03372   1 LTWNVNGGNADAAGDDrkldalAALIRAYDPDVVALQETDDDDAsrLLLALLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   90 NSAgevlenqpvatrsnigEEYFDDSGRWVEADYVLPNGKTLTVVSAYVHSGEVGTQKQDDKYRFLERMLVRMPELAKHS 169
Cdd:pfam03372  81 SSV----------------ILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRS 144

                         170
                  ....*....|.
gi 491649545  170 DHVLIVGDLNV 180
Cdd:pfam03372 145 EPVILAGDFNA 155
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 15-287 5.35e-128

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: 364.24  E-value: 5.35e-128
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKKDMAAWLASRDIDILCLQEVRAPDAIVRELLDESQ-WHILHAEAAAKGRAGVLVATRRtpnsag 93
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEgYNAYFFDAEKKGYAGVAIYSRT------ 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  94 evlenQPVATRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYVHSGEVGTQKQDDKYRFLERMLVRMPELAKHSDHVL 173
Cdd:cd10281   75 -----QPKAVIYGLGFEEFDDEGRYIEADF-----DNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFI 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 174 IVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFGDIGYRDVARELAGQvPGPYTWWSYRGKAFDNDAGWRIDYHM 253
Cdd:cd10281  145 VCGDFNIAHTEIDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPD-EGQYTWWSNRGQARANNVGWRIDYQI 223

                        250       260       270
                 ....*....|....*....|....*....|....
gi 491649545 254 ATPALAESAVEAVVDRaasyDERFSDHAPLVVDY 287
Cdd:cd10281  224 ATPGLASKVVSAWIYR----EERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
15-288 6.33e-113

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 326.26  E-value: 6.33e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKKdMAAWLASRDIDILCLQEVRAPDAIV-RELLDESQWHILHAeaAAKGRAGVLVATRRtpnsag 93
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFpLEAFEAAGYHVYFH--GQKGYNGVAILSRL------ 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  94 evlenQPVATRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYVHSGE-VGTQKQDDKYRFLERMLVRMPELAKHSDHV 172
Cdd:COG0708   72 -----PPEDVRRGLGGDEFDAEGRYIEADF-----GGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELLAPGRPL 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 173 LIVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFgDIGYRDVARELAGQVPGPYTWWSYRGKAFDNDAGWRIDYH 252
Cdd:COG0708  142 ILCGDFNIAPTEIDVKNPKANLKNAGFLPEERAWFDRLL-ELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYI 220

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 491649545 253 MATPALAESAVEAVVDRAASYDERFSDHAPLVVDYR 288
Cdd:COG0708  221 LASPALADRLKDAGIDREPRGDERPSDHAPVVVELD 256
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 16-287 1.36e-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: 231.02  E-value: 1.36e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  16 RVASVNVNGIRAAYKKDMAAWLASRDIDILCLQEVRA-PDAIVRELLDESQWHILHAEAAAKGRAGVLVATRRTPNSAge 94
Cdd:cd09073    1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKAdEDKLPEELQHVEGYHSYWSPARKKGYSGVATLSKEEPLDV-- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  95 vlenqpvatRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYVHSGEVGTQKQDDKYRFLERMLVRMPELAKHSDHVLI 174
Cdd:cd09073   79 ---------SYGIGGEEFDSEGRVITAEF-----DDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRGKPVVI 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 175 VGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFgDIGYRDVARELAGQvPGPYTWWSYRGKAFDNDAGWRIDYHMA 254
Cdd:cd09073  145 CGDFNVAHEEIDLARPKKNEKNAGFTPEERAWFDKLL-SLGYVDTFRHFHPE-PGAYTWWSYRGNARERNVGWRIDYFLV 222

                        250       260       270
                 ....*....|....*....|....*....|...
gi 491649545 255 TPALAESAVEAVVDraasYDERFSDHAPLVVDY 287
Cdd:cd09073  223 SEELAEKVKDSGIL----SKVKGSDHAPVTLEL 251
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 15-288 5.42e-68

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: 211.75  E-value: 5.42e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   15 LRVASVNVNGIRAAYKKDMAAWLASRDIDILCLQEVRAPD-----AIVRELLDESQWHilhaeAAAKGRAGVLVATRRTP 89
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADeqfpaELFEELGYHVFFH-----GAKKGYSGVAILSKVEP 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   90 NSagevlenqpvaTRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYV-HSGEVGTQKQDDKYRFLERMLVRMPELAKH 168
Cdd:TIGR00633  76 LD-----------VRYGFGGEPHDEEGRVITAEF-----DGFTVVNVYVpNGGSRDLERLEYKLQFWDALFQYLEKELDA 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  169 SDHVLIVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFgDIGYRDVARELAGQVPGPYTWWSYRGKAFDNDAGWR 248
Cdd:TIGR00633 140 GKPVVICGDMNVAHTEIDLGNPKENKGNAGFTPEEREWFDELL-EAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWR 218

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 491649545  249 IDYHMATPALAESAVEAVVDRaasyDERFSDHAPLVVDYR 288
Cdd:TIGR00633 219 IDYFLVSEPLAERVVDSYIDS----EIRGSDHCPIVLELD 254
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 15-287 2.08e-64

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: 202.51  E-value: 2.08e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKKDMAAWLASRDIDILCLQEVRA-PDAIVRELLDESQWHILHAEAAAKGRAGVLVATRRTPNSag 93
Cdd:cd09085    1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAqPEQLPEDLRNIEGYHSYFNSAERKGYSGVALYSKIEPDS-- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  94 evlenqpvaTRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYVHSGEVGTQKQDDKYRFLERMLVRMPELAKHSDHVL 173
Cdd:cd09085   79 ---------VREGLGVEEFDNEGRILIADF-----DDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVI 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 174 IVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFgDIGYRDVARELAGQvPGPYTWWSYRGKAFDNDAGWRIDYHM 253
Cdd:cd09085  145 ICGDFNTAHKEIDLARPKENEKVSGFLPEERAWMDKFI-ENGYVDTFRMFNKE-PGQYTWWSYRTRARERNVGWRIDYFF 222

                        250       260       270
                 ....*....|....*....|....*....|....
gi 491649545 254 ATpalaESAVEAVVDRAASYDERFSDHAPLVVDY 287
Cdd:cd09085  223 VN----EEFKPKVKDAGILPDVMGSDHCPVSLEL 252
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 15-285 8.11e-62

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: 196.06  E-value: 8.11e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   15 LRVASVNVNGIRAAYKKdMAAWLASRDIDILCLQEVRA-PDAIVRELLDESQWHILHAeaAAKGRAGVLVATRRTPNSag 93
Cdd:TIGR00195   1 MKIISWNVNGLRARPHK-GLAWLKENQPDVLCLQETKVqDEQFPLEPFHKEGYHVFFS--GQKGYSGVAIFSKEEPIS-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   94 evlenqpvaTRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYVHSG-EVGTQKQDDKYRFLERMLVRMPELAKHSDHV 172
Cdd:TIGR00195  76 ---------VRRGFGVEEEDAEGRIIMAEF-----DSFLVINGYFPNGsRDDSEKLPYKLQWLEALQNYLEKLVDKDKPV 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  173 LIVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFgDIGYRDVARELAGQvPGPYTWWSYRGKAFDNDAGWRIDYH 252
Cdd:TIGR00195 142 LICGDMNIAPTEIDLHIPDENRNHTGFLPEEREWLDRLL-EAGLVDTFRKFNPD-EGAYSWWDYRTKARDRNRGWRIDYF 219

                         250       260       270
                  ....*....|....*....|....*....|...
gi 491649545  253 MATPALAESAVEAVVDRAASYDERFSDHAPLVV 285
Cdd:TIGR00195 220 LVSEPLKERCVDCGIDYDIRGSEKPSDHCPVVL 252
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 15-286 1.49e-57

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: 185.03  E-value: 1.49e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKkDMAAWLASRDIDILCLQEVRAPD-----AIVRELLDESQWHilhaeaAAKGRAGVLVATRRtp 89
Cdd:cd09086    1 MKIATWNVNSIRARLE-QVLDWLKEEDPDVLCLQETKVEDdqfpaDAFEALGYHVAVH------GQKAYNGVAILSRL-- 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  90 nsagevlenQPVATRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYV-HSGEVGTQKQDDKYRFLERMLVRMPELAKH 168
Cdd:cd09086   72 ---------PLEDVRTGFPGDPDDDQARLIAARV-----GGVRVINLYVpNGGDIGSPKFAYKLDWLDRLIRYLQKLLKP 137

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 169 SDHVLIVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFgDIGYRDVARELAGQvPGPYTWWSYRGKAFDNDAGWR 248
Cdd:cd09086  138 DDPLVLVGDFNIAPEDIDVWDPKQLLGKVLFTPEEREALRALL-DLGFVDAFRALHPD-EKLFTWWDYRAGAFERNRGLR 215

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 491649545 249 IDYHMATPALAESAVEAVVDRAASYDERFSDHAPLVVD 286
Cdd:cd09086  216 IDHILASPALADRLKDVGIDREPRGWEKPSDHAPVVAE 253
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 15-286 1.16e-52

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: 172.35  E-value: 1.16e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKKDMAAWLASRDIDILCLQEVRAPDAIVRELLDE--SQWHILHAEAAAKGRAGVLVATRRTPNSa 92
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKEllKGYHQYWNAAEKKGYSGTAILSKKKPLS- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  93 gevlenqpvaTRSNIGEEYFDDSGRWVEADYvlpngKTLTVVSAYV-HSGE-----VGTQKQDDKYR-FLERMLVRMPel 165
Cdd:cd09087   80 ----------VTYGIGIEEHDQEGRVITAEF-----ENFYLVNTYVpNSGRglerlDRRKEWDVDFRaYLKKLDSKKP-- 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 166 akhsdhVLIVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFgDIGYRDVARELAGQVPGPYTWWSYRGKAFDNDA 245
Cdd:cd09087  143 ------VIWCGDLNVAHEEIDLANPKTNKKSAGFTPEERESFTELL-EAGFVDTFRHLHPDKEGAYTFWSYRGNARAKNV 215

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 491649545 246 GWRIDYHMATPALAESaveaVVDRAASYDERFSDHAPLVVD 286
Cdd:cd09087  216 GWRLDYFLVSERLKDR----VVDSFIRSDIMGSDHCPIGLE 252
PRK11756 PRK11756
exonuclease III; Provisional
 15-289 6.63e-32

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 118.84  E-value: 6.63e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKKdMAAWLASRDIDILCLQEVRAPDAIV-RELLDESQWHILHAeaAAKGRAGVLVATRrtpnsag 93
Cdd:PRK11756   1 MKFVSFNINGLRARPHQ-LEAIIEKHQPDVIGLQETKVHDEMFpLEEVEALGYHVFYH--GQKGHYGVALLSK------- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  94 evleNQPVATRSNIGEEYFDDSGRWVEADYVLPNGkTLTVVSAYVHSGEvgTQKQDDKY----RFLERMLVRMPELAKHS 169
Cdd:PRK11756  71 ----QTPIAVRKGFPTDDEEAQRRIIMATIPTPNG-NLTVINGYFPQGE--SRDHPTKFpakrQFYQDLQNYLETELSPD 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 170 DHVLIVGDLNVGHTELDIKNWKANQKR------AGFLPEERAYFDRFFgDIGYRDVARELAGQVPGPYTWWSYRGKAFDN 243
Cdd:PRK11756 144 NPLLIMGDMNISPTDLDIGIGEENRKRwlrtgkCSFLPEEREWLDRLM-DWGLVDTFRQLNPDVNDRFSWFDYRSKGFDD 222

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 491649545 244 DAGWRIDYHMATPALAESAVEAVVDraasYD----ERFSDHAPLVVDYRI 289
Cdd:PRK11756 223 NRGLRIDLILATQPLAERCVETGID----YDirgmEKPSDHAPIWATFKL 268
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 15-283 4.30e-29

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 111.32  E-value: 4.30e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKKDMAAWLASRDIDILCLQEVRAPDAivRELLDESQWHILHAEAAAKGRAGVLVATRRtpnsage 94
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQE--QNTFEFKGYFDFWNCAIKKGYSGVVTFTKK------- 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  95 vlenQPVATRSNIGEEYFDDSGRWVEADY--------VLPNGKTLTVVSAYVHSGEVGTQKqddkyrFLERMLVRMPela 166
Cdd:PRK13911  72 ----EPLSVSYGINIEEHDKEGRVITCEFesfylvnvYTPNSQQALSRLSYRMSWEVEFKK------FLKALELKKP--- 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 167 khsdhVLIVGDLNVGHTELDIKNWKANQKRAGFLPEERAYFDRFFgDIGYRDVARELAGQVPGPYTWWSYRGKAFDNDAG 246
Cdd:PRK13911 139 -----VIVCGDLNVAHNEIDLENPKTNRKNAGFSDEERGKFSELL-NAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIG 212

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 491649545 247 WRIDYHMATPALAESAVEAVVDRaasyDERFSDHAPL 283
Cdd:PRK13911 213 WRIDYFLCSNPLKTRLKDALIYK----DILGSDHCPV 245
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 17-285 1.67e-20

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: 87.92  E-value: 1.67e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  17 VASVNVNGIRAAYK-KDMAAWLASRDIDILCLQEVRAP--DAIVRELLDESQWHILHAEA-AAKGRAGVLVATRRTpnsa 92
Cdd:cd08372    1 VASYNVNGLNAATRaSGIARWVRELDPDIVCLQEVKDSqySAVALNQLLPEGYHQYQSGPsRKEGYEGVAILSKTP---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  93 gevlENQPVATRSNIGEEYFDDSGR--WVEADYvlpNGKTLTVVSAYVHSGEvgtQKQDDKYRFLERMLVRMPELAKH-S 169
Cdd:cd08372   77 ----KFKIVEKHQYKFGEGDSGERRavVVKFDV---HDKELCVVNAHLQAGG---TRADVRDAQLKEVLEFLKRLRQPnS 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 170 DHVLIVGDLNVGHTELDIKNWKAnqkragflpeerayFDRFFGDIGYRDVARELagqvPGPYTWWSYrgkafDNDAGWRI 249
Cdd:cd08372  147 APVVICGDFNVRPSEVDSENPSS--------------MLRLFVALNLVDSFETL----PHAYTFDTY-----MHNVKSRL 203

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 491649545 250 DYHMATPALAESAVEA-VVDRAASYDErFSDHAPLVV 285
Cdd:cd08372  204 DYIFVSKSLLPSVKSSkILSDAARARI-PSDHYPIEV 239
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 16-286 1.05e-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: 78.51  E-value: 1.05e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  16 RVASVNVNGIRA-------AYKKDMAAWLASRDIDILCLQEVRapdaIVRELLDE--------SQWHILHAeaAAKGRAG 80
Cdd:cd09088    1 RIVTWNVNGIRTrlqyqpwNKENSLKSFLDSLDADIICLQETK----LTRDELDEpsaivegyDSFFSFSR--GRKGYSG 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  81 VLVATRR---TPNSAGE----VLENQPVATR----SNIG----EEYFDDSGRWVEADY----VLPNGKTLTVVSAYVHSG 141
Cdd:cd09088   75 VATYCRDsaaTPVAAEEgltgVLSSPNQKNElsenDDIGcygeMLEFTDSKELLELDSegrcVLTDHGTFVLINVYCPRA 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 142 EVGTQKQDD-KYRFLERMLVRMPELAKHSDHVLIVGDLNVGHTELDIKNWKANQKRAGFLPEE---RAYFDRFFGDIGYR 217
Cdd:cd09088  155 DPEKEERLEfKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLGDSGEG 234

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491649545 218 ---------DVARELAGQVPGPYTWWSYRGKAFDNDAGWRIDYHMATPALAESAVEAVVDRaasyDERFSDHAPLVVD 286
Cdd:cd09088  235 ggspgglliDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILP----EVEGSDHCPVYAD 308
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 17-287 6.99e-13

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: 66.61  E-value: 6.99e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  17 VASVNVNGIRAAYKKDM-AAWLASRDIDILCLQEVRAPDAIVRELLDESqWHILHAEAAAKGRAGVLVATRRTPNSAgeV 95
Cdd:cd09076    1 IGTLNVRGLRSPGKRAQlLEELKRKKLDILGLQETHWTGEGELKKKREG-GTILYSGSDSGKSRGVAILLSKTAANK--L 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  96 LENQPVatrsnigeeyfdDSGRWVEADyVLPNGKTLTVVSAYVHSgevgTQKQDDKYRFLERMLVRMPELAKHsDHVLIV 175
Cdd:cd09076   78 LEYTKV------------VSGRIIMVR-FKIKGKRLTIINVYAPT----ARDEEEKEEFYDQLQDVLDKVPRH-DTLIIG 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 176 GDLN-------VGHTELDIKNwKANQKRAGFLPEERAYFdrffgdigyrDVARELAGQVPGpYTWWSYRGKAFDndagwR 248
Cdd:cd09076  140 GDFNavlgpkdDGRKGLDKRN-ENGERALSALIEEHDLV----------DVWRENNPKTRE-YTWRSPDHGSRS-----R 202

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 491649545 249 IDYHMATpalaeSAVEAVVDRAASYDERFSDHAPLVVDY 287
Cdd:cd09076  203 IDRILVS-----KRLRVKVKKTKITPGAGSDHRLVTLKL 236
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 3-289 1.79e-12

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 66.56  E-value: 1.79e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   3 FSNTPAPRPSGLLRVASVNVNGIRAAYKKdMAAWLASRDIDILCLQEV-RAPDAIVRELLDESQWHILHAEAaakGRAGV 81
Cdd:COG3021   83 PAPKSAPAGGPDLRVLTANVLFGNADAEA-LAALVREEDPDVLVLQETtPAWEEALAALEADYPYRVLCPLD---NAYGM 158

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  82 LVATRRtPNSAGEVLENQPVATRSnigeeyfddsgrwVEADYVLPnGKTLTVVSAYVHSGEVGTQKQDDKYRFLERmlvr 161
Cdd:COG3021  159 ALLSRL-PLTEAEVVYLVGDDIPS-------------IRATVELP-GGPVRLVAVHPAPPVGGSAERDAELAALAK---- 219

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 162 mpELAKHSDHVLIVGDLN--VGHteldiknwkanqkragflpeerAYFDRFFGDIGYRDvARELAGQVPgpyTWWSYRGK 239
Cdd:COG3021  220 --AVAALDGPVIVAGDFNatPWS----------------------PTLRRLLRASGLRD-ARAGRGLGP---TWPANLPF 271

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 491649545 240 afdndAGWRIDYHMATPALAesAVEAVVDRAASyderfSDHAPLVVDYRI 289
Cdd:COG3021  272 -----LRLPIDHVLVSRGLT--VVDVRVLPVIG-----SDHRPLLAELAL 309
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 18-180 8.53e-10

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: 56.85  E-value: 8.53e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   18 ASVNVNGIRAAYKKDM------AAWLASRDIDILCLQEVRAPDA--IVRELLDESQWHILHAEAAAKGRAGVLVATRRTP 89
Cdd:pfam03372   1 LTWNVNGGNADAAGDDrkldalAALIRAYDPDVVALQETDDDDAsrLLLALLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   90 NSAgevlenqpvatrsnigEEYFDDSGRWVEADYVLPNGKTLTVVSAYVHSGEVGTQKQDDKYRFLERMLVRMPELAKHS 169
Cdd:pfam03372  81 SSV----------------ILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRS 144

                         170
                  ....*....|.
gi 491649545  170 DHVLIVGDLNV 180
Cdd:pfam03372 145 EPVILAGDFNA 155
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
3-289 5.60e-08

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 53.10  E-value: 5.60e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   3 FSNT-PAPRPSGLLRVASVNV----NGIRAAYKKDMAAW---------------LASRDIDILCLQEVRAPDAIVRELLD 62
Cdd:COG2374   56 FVNPrPEAPVGGDLRVATFNVenlfDTDDDDDDFGRGADtpeeyerklakiaaaIAALDADIVGLQEVENNGSALQDLVA 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  63 E-----SQWHILHAEAAAKGRA---GVLVATRRTPnsagevlenqPVATRS-NIGEEYFDDSGRW----VEADYVLPNGK 129
Cdd:COG2374  136 AlnlagGTYAFVHPPDGPDGDGirvALLYRPDRVT----------LVGSATiADLPDSPGNPDRFsrppLAVTFELANGE 205

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 130 TLTVVSayVH------SGEVGTQKQDDKYRFLE----RMLVRMPELAKHSDHVLIVGDLNVGhteldiknwkanqkragf 199
Cdd:COG2374  206 PFTVIV--NHfkskgsDDPGDGQGASEAKRTAQaealRAFVDSLLAADPDAPVIVLGDFNDY------------------ 265

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 200 lPEERAYfDRFFGDIGYRDVARELAGQVPgpytwWSYrgkAFDNDAGwRIDYHMATPALAESAVEA--VVDRAASYDE-- 275
Cdd:COG2374  266 -PFEDPL-RALLGAGGLTNLAEKLPAAER-----YSY---VYDGNSG-LLDHILVSPALAARVTGAdiWHINADIYNDdf 334

                        330       340
                 ....*....|....*....|....*.
gi 491649545 276 ------------RFSDHAPLVVDYRI 289
Cdd:COG2374  335 kpdfrtyaddpgRASDHDPVVVGLRL 360
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 17-287 8.51e-06

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: 46.14  E-value: 8.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  17 VASVNVNG----IRAAYKKDMAAWLASRDIDILCLQE----VRAPDAIVRELLDESQWHILHaEAAAKGRAGVLVATRrt 88
Cdd:cd09084    1 VMSYNVRSfnryKWKDDPDKILDFIKKQDPDILCLQEyygsEGDKDDDLRLLLKGYPYYYVV-YKSDSGGTGLAIFSK-- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  89 pnsagevlenQPVATRSNIGEEYFDDSGRWVEadyVLPNGKTLTVVSAYVHS----------GEVGTQKQDDKYRFLERM 158
Cdd:cd09084   78 ----------YPILNSGSIDFPNTNNNAIFAD---IRVGGDTIRVYNVHLESfritpsdkelYKEEKKAKELSRNLLRKL 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 159 LVRMPELAKHSDH-----------VLIVGDLN---VGHTeldiknwkanqkragflpeerayfdrffgdigYRDVAREL- 223
Cdd:cd09084  145 AEAFKRRAAQADLlaadiaaspypVIVCGDFNdtpASYV--------------------------------YRTLKKGLt 192

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491649545 224 -----AGQVPGpytwWSYRGKAFdndaGWRIDYHMATPALaesaveaVVDRAASYDERFSDHAPLVVDY 287
Cdd:cd09084  193 dafveAGSGFG----YTFNGLFF----PLRIDYILTSKGF-------KVLRYRVDPGKYSDHYPIVATL 246
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 15-199 1.09e-05

Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197314 [Multi-domain]  Cd Length: 248  Bit Score: 45.80  E-value: 1.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  15 LRVASVNVNGIRAAYKKD--MAAW--LASRDIDILCLQEVraPDAIVRELLDE----SQWHILHAEAAAKGRA-GVLVAT 85
Cdd:cd09080    1 LKVLTWNVDFLDDVNLAErmRAILklLEELDPDVIFLQEV--TPPFLAYLLSQpwvrKNYYFSEGPPSPAVDPyGVLILS 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  86 RRTPnsageVLENQPVATRSnigeeyfddSGR-WVEADYVLPNGKTLTVVSAYVHSGevgtqKQDDKYRF--LERMLVRM 162
Cdd:cd09080   79 KKSL-----VVRRVPFTSTR---------MGRnLLAAEINLGSGEPLRLATTHLESL-----KSHSSERTaqLEEIAKKL 139

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 491649545 163 PELAKHSDhVLIVGDLN-------VGHTELDIKN-WKA--NQKRAGF 199
Cdd:cd09080  140 KKPPGAAN-VILGGDFNlrdkeddTGGLPNGFVDaWEElgPPGEPGY 185
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 8-180 3.14e-03

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 37.58  E-value: 3.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545   8 APRPSGLLRVASVNV-NGIRAAYKKD---MAAWLASRDIDILCLQEVrapdAIVrelldeSQWHILHAEAAAkgragvLV 83
Cdd:COG3568    1 AAAAAATLRVMTYNIrYGLGTDGRADlerIARVIRALDPDVVALQEN----AIL------SRYPIVSSGTFD------LP 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545  84 ATRRTPNSAgevlenqpvatrsnigeeyfddsgrwVEADYVLPnGKTLTVVSA-YVHSGEVGTQKQddkyrfLERMLVRM 162
Cdd:COG3568   65 DPGGEPRGA--------------------------LWADVDVP-GKPLRVVNThLDLRSAAARRRQ------ARALAELL 111

                        170
                 ....*....|....*...
gi 491649545 163 PELAKHsDHVLIVGDLNV 180
Cdd:COG3568  112 AELPAG-APVILAGDFND 128
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 172-287 5.91e-03

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: 37.58  E-value: 5.91e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491649545 172 VLIVGDLNVGhteldiknwkanqkragflPEERAYfdRFFGDIGYRDvARELAGQVPGP--YTWWSYRGKAFDNdagwRI 249
Cdd:cd09083  163 VILTGDFNAE-------------------PDSEPY--KTLTSGGLKD-ARDTAATTDGGpeGTFHGFKGPPGGS----RI 216

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 491649545 250 DYHMATPALAESAVEAVVDRaasYDERF-SDHAPLVVDY 287
Cdd:cd09083  217 DYIFVSPGVKVLSYEILTDR---YDGRYpSDHFPVVADL 252
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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