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Conserved domains on  [gi|611961114|gb|AHW83344|]
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APN2, partial [Metarhizium globosum]

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 ...
 1-305 2.83e-120

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 cd09088:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 309  Bit Score: 348.15  E-value: 2.83e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114   1 PFGYQPWREQRTFQAMFDILESDIVVMQETKIQRKDLQDDMVLVPGWDVFFSLPKHKKGYSGVAIYTRNASCAPIRAEEG 80
Cdd:cd09088   13 RLQYQPWNKENSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGVATYCRDSAATPVAAEEG 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  81 ITGVLCPPKSttkFRDLPSDQQIGGYPRPGQLSGIVEDTVLDSEGRCVILEFPAFVLLGVYCPANRDES--RVEFRTSFF 158
Cdd:cd09088   93 LTGVLSSPNQ---KNELSENDDIGCYGEMLEFTDSKELLELDSEGRCVLTDHGTFVLINVYCPRADPEKeeRLEFKLDFY 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 159 EALDVRIRNLVAEGKEVILAGDLNVIRSEMDSTNVVENLRKenmTIDEWISLPTRRIFNQLifegsiVGDRDE--GRETP 236
Cdd:cd09088  170 RLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDF---GGESFEDNPSRQWLDQL------LGDSGEggGSPGG 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 611961114 237 VLWDLCRCFHPSRLGMNTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMGSDHCPVFATI 305
Cdd:cd09088  241 LLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYADL 309
 
Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 1-305 2.83e-120

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: 348.15  E-value: 2.83e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114   1 PFGYQPWREQRTFQAMFDILESDIVVMQETKIQRKDLQDDMVLVPGWDVFFSLPKHKKGYSGVAIYTRNASCAPIRAEEG 80
Cdd:cd09088   13 RLQYQPWNKENSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGVATYCRDSAATPVAAEEG 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  81 ITGVLCPPKSttkFRDLPSDQQIGGYPRPGQLSGIVEDTVLDSEGRCVILEFPAFVLLGVYCPANRDES--RVEFRTSFF 158
Cdd:cd09088   93 LTGVLSSPNQ---KNELSENDDIGCYGEMLEFTDSKELLELDSEGRCVLTDHGTFVLINVYCPRADPEKeeRLEFKLDFY 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 159 EALDVRIRNLVAEGKEVILAGDLNVIRSEMDSTNVVENLRKenmTIDEWISLPTRRIFNQLifegsiVGDRDE--GRETP 236
Cdd:cd09088  170 RLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDF---GGESFEDNPSRQWLDQL------LGDSGEggGSPGG 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 611961114 237 VLWDLCRCFHPSRLGMNTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMGSDHCPVFATI 305
Cdd:cd09088  241 LLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYADL 309
XthA COG0708
Exonuclease III [Replication, recombination and repair];
16-306 3.22e-41

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 144.06  E-value: 3.22e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  16 MFDILES---DIVVMQETKIQRKDLQDDMVLVPGWDVFFSlpkHKKGYSGVAIYTRNascapiraeegitgvlcPPKSTT 92
Cdd:COG0708   18 LLDWLAEedpDVLCLQETKAQDEQFPLEAFEAAGYHVYFH---GQKGYNGVAILSRL-----------------PPEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  93 kfRDLPSDqqiggyprpgqlsgivedtVLDSEGRCVILEFPAFVLLGVYCPA--NRDESRVEFRTSFFEALDVRIRNLVA 170
Cdd:COG0708   78 --RGLGGD-------------------EFDAEGRYIEADFGGVRVVSLYVPNggSVGSEKFDYKLRFLDALRAYLAELLA 136

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 171 EGKEVILAGDLNVIRSEMDSTNVVENLRKENMTIDEwislptRRIFNQLIfegsivgdrDEGretpvLWDLCRCFHPSRL 250
Cdd:COG0708  137 PGRPLILCGDFNIAPTEIDVKNPKANLKNAGFLPEE------RAWFDRLL---------ELG-----LVDAFRALHPDVE 196

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 251 GMNTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANI----QEGLMGSDHCPVFATIA 306
Cdd:COG0708  197 GQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIdrepRGDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 18-306 4.88e-36

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: 130.48  E-value: 4.88e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114   18 DILES---DIVVMQETKIQRKDLQDDMVLVPGWDVFFSlpKHKKGYSGVAIYTRNascapiraeegitgvlcPPKSTTKf 94
Cdd:TIGR00633  21 DWLKEeqpDVLCLQETKVADEQFPAELFEELGYHVFFH--GAKKGYSGVAILSKV-----------------EPLDVRY- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114   95 rdlpsdqqiggyprpgqlsGIVEDTvLDSEGRCVILEFPAFVLLGVYCP--ANRDESRVEFRTSFFEALDVRIRNLVAEG 172
Cdd:TIGR00633  81 -------------------GFGGEP-HDEEGRVITAEFDGFTVVNVYVPngGSRDLERLEYKLQFWDALFQYLEKELDAG 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  173 KEVILAGDLNVIRSEMDSTNVVENLRKENMTIDEwislptRRIFNQLIFEGsivgdrdegretpvLWDLCRCFHPSRLGM 252
Cdd:TIGR00633 141 KPVVICGDMNVAHTEIDLGNPKENKGNAGFTPEE------REWFDELLEAG--------------FVDTFRHFNPDTGDA 200

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 611961114  253 NTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMGSDHCPVFATIA 306
Cdd:TIGR00633 201 YTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDSEIRGSDHCPIVLELD 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 11-301 6.60e-25

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 100.92  E-value: 6.60e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  11 RTFQAMFDILESDIVVMQETKIQRkdlQDDMVLVPGWDVFFSLPKhKKGYSGVAIYTRNAscaPIRAEEGITgvlcppks 90
Cdd:PRK13911  17 KGFMDFFNSVDADVFCIQESKMQQ---EQNTFEFKGYFDFWNCAI-KKGYSGVVTFTKKE---PLSVSYGIN-------- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  91 ttkfrdlpsdqqiggyprpgqlsgiVEDTvlDSEGRCVILEFPAFVLLGVYCPANRDE-SRVEFRTS-------FFEALD 162
Cdd:PRK13911  82 -------------------------IEEH--DKEGRVITCEFESFYLVNVYTPNSQQAlSRLSYRMSwevefkkFLKALE 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 163 VRirnlvaegKEVILAGDLNVIRSEMDSTNVVENLRKENMTIDEwislptRRIFNQLIFEGSIvgdrdegretpvlwDLC 242
Cdd:PRK13911 135 LK--------KPVIVCGDLNVAHNEIDLENPKTNRKNAGFSDEE------RGKFSELLNAGFI--------------DTF 186

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 611961114 243 RCFHPSRLGMNTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMGSDHCPV 301
Cdd:PRK13911 187 RYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDILGSDHCPV 245
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 23-183 1.44e-06

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: 47.99  E-value: 1.44e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114   23 DIVVMQETKIQRKDLQDDMVLVPGWDVFFSLPKHKKGYSGVAIYTRnascapiraeegitgvlcppksttkfrdlpsdqq 102
Cdd:pfam03372  32 DVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSR---------------------------------- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  103 iggYPRPGQLSGIVEDTVLDSEGRCVILEFPAFVLLGVYCPANRDESRVEFRTSFFEALDVRIRNLVAEGKEVILAGDLN 182
Cdd:pfam03372  78 ---YPLSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN 154


                  .
gi 611961114  183 V 183
Cdd:pfam03372 155 A 155
 
Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 1-305 2.83e-120

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: 348.15  E-value: 2.83e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114   1 PFGYQPWREQRTFQAMFDILESDIVVMQETKIQRKDLQDDMVLVPGWDVFFSLPKHKKGYSGVAIYTRNASCAPIRAEEG 80
Cdd:cd09088   13 RLQYQPWNKENSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGVATYCRDSAATPVAAEEG 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  81 ITGVLCPPKSttkFRDLPSDQQIGGYPRPGQLSGIVEDTVLDSEGRCVILEFPAFVLLGVYCPANRDES--RVEFRTSFF 158
Cdd:cd09088   93 LTGVLSSPNQ---KNELSENDDIGCYGEMLEFTDSKELLELDSEGRCVLTDHGTFVLINVYCPRADPEKeeRLEFKLDFY 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 159 EALDVRIRNLVAEGKEVILAGDLNVIRSEMDSTNVVENLRKenmTIDEWISLPTRRIFNQLifegsiVGDRDE--GRETP 236
Cdd:cd09088  170 RLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDF---GGESFEDNPSRQWLDQL------LGDSGEggGSPGG 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 611961114 237 VLWDLCRCFHPSRLGMNTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMGSDHCPVFATI 305
Cdd:cd09088  241 LLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYADL 309
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 13-305 7.05e-51

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: 169.01  E-value: 7.05e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  13 FQAMFDILESDIVVMQETKIQRKDLQDDMVLVPGWDVFFSlPKHKKGYSGVAIYTRNAscaPIRAEEGItgvlcppkstt 92
Cdd:cd09073   18 VLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWS-PARKKGYSGVATLSKEE---PLDVSYGI----------- 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  93 kfrdlPSDQqiggyprpgqlsgivedtvLDSEGRCVILEFPAFVLLGVYCP-ANRDESRVEFRTSFFEALDVRIRNLVAE 171
Cdd:cd09073   83 -----GGEE-------------------FDSEGRVITAEFDDFYLINVYFPnGGRGLERLDYKLRFYEAFLEFLEKLRKR 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 172 GKEVILAGDLNVIRSEMDSTNVVENLRKENMTIDEwislptRRIFNQLIFEGSIvgdrdegretpvlwDLCRCFHPSRlG 251
Cdd:cd09073  139 GKPVVICGDFNVAHEEIDLARPKKNEKNAGFTPEE------RAWFDKLLSLGYV--------------DTFRHFHPEP-G 197

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 611961114 252 MNTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMGSDHCPVFATI 305
Cdd:cd09073  198 AYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILSKVKGSDHAPVTLEL 251
XthA COG0708
Exonuclease III [Replication, recombination and repair];
16-306 3.22e-41

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 144.06  E-value: 3.22e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  16 MFDILES---DIVVMQETKIQRKDLQDDMVLVPGWDVFFSlpkHKKGYSGVAIYTRNascapiraeegitgvlcPPKSTT 92
Cdd:COG0708   18 LLDWLAEedpDVLCLQETKAQDEQFPLEAFEAAGYHVYFH---GQKGYNGVAILSRL-----------------PPEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  93 kfRDLPSDqqiggyprpgqlsgivedtVLDSEGRCVILEFPAFVLLGVYCPA--NRDESRVEFRTSFFEALDVRIRNLVA 170
Cdd:COG0708   78 --RGLGGD-------------------EFDAEGRYIEADFGGVRVVSLYVPNggSVGSEKFDYKLRFLDALRAYLAELLA 136

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 171 EGKEVILAGDLNVIRSEMDSTNVVENLRKENMTIDEwislptRRIFNQLIfegsivgdrDEGretpvLWDLCRCFHPSRL 250
Cdd:COG0708  137 PGRPLILCGDFNIAPTEIDVKNPKANLKNAGFLPEE------RAWFDRLL---------ELG-----LVDAFRALHPDVE 196

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 251 GMNTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANI----QEGLMGSDHCPVFATIA 306
Cdd:COG0708  197 GQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIdrepRGDERPSDHAPVVVELD 256
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 23-305 6.53e-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: 143.08  E-value: 6.53e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  23 DIVVMQETKIQRKDLQDD-MVLVPGWDVFFSLPKhKKGYSGVAIYTRNAscaPIRAEEGItgvlcppksttkfrdlpsdq 101
Cdd:cd09087   29 DILCLQETKLQEGDVPKElKELLKGYHQYWNAAE-KKGYSGTAILSKKK---PLSVTYGI-------------------- 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 102 qiggyprpgqlsGIVEDtvlDSEGRCVILEFPAFVLLGVYCP-ANRDESRVEFRTSFfealDVRIRNLVAE---GKEVIL 177
Cdd:cd09087   85 ------------GIEEH---DQEGRVITAEFENFYLVNTYVPnSGRGLERLDRRKEW----DVDFRAYLKKldsKKPVIW 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 178 AGDLNVIRSEMDSTNVVENLRKENMTIDEwislptRRIFNQLIFEGSIvgdrdegretpvlwDLCRCFHPSRLGMNTCWD 257
Cdd:cd09087  146 CGDLNVAHEEIDLANPKTNKKSAGFTPEE------RESFTELLEAGFV--------------DTFRHLHPDKEGAYTFWS 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 611961114 258 TKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMGSDHCPVFATI 305
Cdd:cd09087  206 YRGNARAKNVGWRLDYFLVSERLKDRVVDSFIRSDIMGSDHCPIGLEL 253
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 23-305 2.51e-38

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: 136.25  E-value: 2.51e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  23 DIVVMQETKIQRKDLQDDMVLVPGWDVFFSlPKHKKGYSGVAIYTRNAscaPIRAEEGItgvlcppksttkfrdlpsdqq 102
Cdd:cd09085   29 DILCLQETKAQPEQLPEDLRNIEGYHSYFN-SAERKGYSGVALYSKIE---PDSVREGL--------------------- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 103 iggyprpgqlsGIVEdtvLDSEGRCVILEFPAFVLLGVYCP-ANRDESRVEFRTSFFEALDVRIRNLVAEGKEVILAGDL 181
Cdd:cd09085   84 -----------GVEE---FDNEGRILIADFDDFTLFNIYFPnGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDF 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 182 NVIRSEMDSTNVVEN------LRKENMTIDEWIS---LPTRRIFNQlifegsivgdrDEGRETpvlWdlcrcfhpsrlgm 252
Cdd:cd09085  150 NTAHKEIDLARPKENekvsgfLPEERAWMDKFIEngyVDTFRMFNK-----------EPGQYT---W------------- 202

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 611961114 253 ntcWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMGSDHCPVFATI 305
Cdd:cd09085  203 ---WSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPDVMGSDHCPVSLEL 252
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 18-306 4.88e-36

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: 130.48  E-value: 4.88e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114   18 DILES---DIVVMQETKIQRKDLQDDMVLVPGWDVFFSlpKHKKGYSGVAIYTRNascapiraeegitgvlcPPKSTTKf 94
Cdd:TIGR00633  21 DWLKEeqpDVLCLQETKVADEQFPAELFEELGYHVFFH--GAKKGYSGVAILSKV-----------------EPLDVRY- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114   95 rdlpsdqqiggyprpgqlsGIVEDTvLDSEGRCVILEFPAFVLLGVYCP--ANRDESRVEFRTSFFEALDVRIRNLVAEG 172
Cdd:TIGR00633  81 -------------------GFGGEP-HDEEGRVITAEFDGFTVVNVYVPngGSRDLERLEYKLQFWDALFQYLEKELDAG 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  173 KEVILAGDLNVIRSEMDSTNVVENLRKENMTIDEwislptRRIFNQLIFEGsivgdrdegretpvLWDLCRCFHPSRLGM 252
Cdd:TIGR00633 141 KPVVICGDMNVAHTEIDLGNPKENKGNAGFTPEE------REWFDELLEAG--------------FVDTFRHFNPDTGDA 200

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 611961114  253 NTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMGSDHCPVFATIA 306
Cdd:TIGR00633 201 YTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDSEIRGSDHCPIVLELD 254
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 16-301 1.24e-31

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: 118.87  E-value: 1.24e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  16 MFDILE---SDIVVMQETKIQRKDLQDDMVLVPGWDVFFsLPKHKKGYSGVAIYTRNascapiraeegitgvlcPPKSTT 92
Cdd:cd10281   19 FLEWLAaqdADVVCLQEVRAQEEQLDDDFFEPEGYNAYF-FDAEKKGYAGVAIYSRT-----------------QPKAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  93 KFRDLPSDqqiggyprpgqlsgivedtvlDSEGRCVILEFPAFVLLGVYCP-ANRDESRVEFRTSFFEALDVRIRNLVAE 171
Cdd:cd10281   81 YGLGFEEF---------------------DDEGRYIEADFDNVSVASLYVPsGSSGDERQEAKMAFLDAFLEHLKELRRK 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 172 GKEVILAGDLNVIRSEMDSTNVVENLRKENMtidewisLPTRRI-FNQLIFEgsiVGDRDEGRETpvlwdlcrcfHPSrL 250
Cdd:cd10281  140 RREFIVCGDFNIAHTEIDIKNWKANQKNSGF-------LPEERAwLDQVFGE---LGYVDAFREL----------NPD-E 198

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 611961114 251 GMNTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMGSDHCPV 301
Cdd:cd10281  199 GQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYREERFSDHAPL 249
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 14-305 1.11e-30

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: 116.33  E-value: 1.11e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114   14 QAMFDILES---DIVVMQETKIQRKDLQDDMVLVPGWDVFFSlpkHKKGYSGVAIYTRNascapiraeegitgvlcPPKS 90
Cdd:TIGR00195  16 HKGLAWLKEnqpDVLCLQETKVQDEQFPLEPFHKEGYHVFFS---GQKGYSGVAIFSKE-----------------EPIS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114   91 TTkfRDLPSDQQiggyprpgqlsgivedtvlDSEGRCVILEFPAFVLLGVYCP--ANRDESRVEFRTSFFEALDVRIRNL 168
Cdd:TIGR00195  76 VR--RGFGVEEE-------------------DAEGRIIMAEFDSFLVINGYFPngSRDDSEKLPYKLQWLEALQNYLEKL 134

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  169 VAEGKEVILAGDLNVIRSEMDSTNVVENLRKENMTIDEwislptRRIFNQLIFEGsivgdrdegretpvLWDLCRCFHPS 248
Cdd:TIGR00195 135 VDKDKPVLICGDMNIAPTEIDLHIPDENRNHTGFLPEE------REWLDRLLEAG--------------LVDTFRKFNPD 194

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 611961114  249 RlGMNTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMG----SDHCPVFATI 305
Cdd:TIGR00195 195 E-GAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDYDIRGsekpSDHCPVVLEF 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 11-301 6.60e-25

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 100.92  E-value: 6.60e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  11 RTFQAMFDILESDIVVMQETKIQRkdlQDDMVLVPGWDVFFSLPKhKKGYSGVAIYTRNAscaPIRAEEGITgvlcppks 90
Cdd:PRK13911  17 KGFMDFFNSVDADVFCIQESKMQQ---EQNTFEFKGYFDFWNCAI-KKGYSGVVTFTKKE---PLSVSYGIN-------- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  91 ttkfrdlpsdqqiggyprpgqlsgiVEDTvlDSEGRCVILEFPAFVLLGVYCPANRDE-SRVEFRTS-------FFEALD 162
Cdd:PRK13911  82 -------------------------IEEH--DKEGRVITCEFESFYLVNVYTPNSQQAlSRLSYRMSwevefkkFLKALE 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 163 VRirnlvaegKEVILAGDLNVIRSEMDSTNVVENLRKENMTIDEwislptRRIFNQLIFEGSIvgdrdegretpvlwDLC 242
Cdd:PRK13911 135 LK--------KPVIVCGDLNVAHNEIDLENPKTNRKNAGFSDEE------RGKFSELLNAGFI--------------DTF 186

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 611961114 243 RCFHPSRLGMNTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMGSDHCPV 301
Cdd:PRK13911 187 RYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDILGSDHCPV 245
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 23-305 1.71e-17

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: 80.64  E-value: 1.71e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  23 DIVVMQETKIQRKDLQDDMVLVPGWDVFFSlpkHKKGYSGVAIYTRNascapiraeegitgvlcPPKSTtkFRDLPSDQQ 102
Cdd:cd09086   28 DVLCLQETKVEDDQFPADAFEALGYHVAVH---GQKAYNGVAILSRL-----------------PLEDV--RTGFPGDPD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 103 iggyprpgqlsgivedtvlDSEGRCVILEFPAFVLLGVYCPA--NRDESRVEFRTSFFEALDVRIRNLVAEGKEVILAGD 180
Cdd:cd09086   86 -------------------DDQARLIAARVGGVRVINLYVPNggDIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGD 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 181 LNVIRSEMDSTNVvENLRKENMTidewiSLPTRRIFNQLIFEGsivgdrdegretpvLWDLCRCFHPSRlGMNTCWDTKK 260
Cdd:cd09086  147 FNIAPEDIDVWDP-KQLLGKVLF-----TPEEREALRALLDLG--------------FVDAFRALHPDE-KLFTWWDYRA 205

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 611961114 261 NTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMG----SDHCPVFATI 305
Cdd:cd09086  206 GAFERNRGLRIDHILASPALADRLKDVGIDREPRGwekpSDHAPVVAEL 254
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 122-305 1.81e-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: 68.92  E-value: 1.81e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 122 DSEGRCVILEF----PAFVLLGVYCPANRDEsrvEFRTSFFEALDVRIRNlVAEGKEVILAGDLNVIRSEMDSTNVVENL 197
Cdd:cd09076   83 VVSGRIIMVRFkikgKRLTIINVYAPTARDE---EEKEEFYDQLQDVLDK-VPRHDTLIIGGDFNAVLGPKDDGRKGLDK 158

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 198 RKENmtidewislpTRRIFNQLIfegsivgdrdegrETPVLWDLCRCFHPSRlgmnTCWdTKKNTRPaNNGSRIDYILCS 277
Cdd:cd09076  159 RNEN----------GERALSALI-------------EEHDLVDVWRENNPKT----REY-TWRSPDH-GSRSRIDRILVS 209

                        170       180
                 ....*....|....*....|....*...
gi 611961114 278 NGLKDWFTSANIQEGLmGSDHCPVFATI 305
Cdd:cd09076  210 KRLRVKVKKTKITPGA-GSDHRLVTLKL 236
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 23-305 4.74e-11

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: 61.73  E-value: 4.74e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  23 DIVVMQETKI-QRKDLQDDMVLVPGWDVFFSLPKHKKGYSGVAIYTRNASCAPIraeegitgvlcpPKSTTKFrdlpsdq 101
Cdd:cd08372   28 DIVCLQEVKDsQYSAVALNQLLPEGYHQYQSGPSRKEGYEGVAILSKTPKFKIV------------EKHQYKF------- 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 102 qiggyprpgqlsgiveDTVLDSEGRCVILEFPA----FVLLGVYCPANRDESRVEFRtSFFEALDVRIRNLVAEGKEVIL 177
Cdd:cd08372   89 ----------------GEGDSGERRAVVVKFDVhdkeLCVVNAHLQAGGTRADVRDA-QLKEVLEFLKRLRQPNSAPVVI 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 178 AGDLNVirsemDSTNVVENLRKEnmtideWISLPTRRIFnqlifegsivgdrdegretpvlwdlcrCFHPSRLGMNTCWD 257
Cdd:cd08372  152 CGDFNV-----RPSEVDSENPSS------MLRLFVALNL---------------------------VDSFETLPHAYTFD 193

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 611961114 258 TKkntrPANNGSRIDYILCSNGLKDWFTSANI----QEGLMGSDHCPVFATI 305
Cdd:cd08372  194 TY----MHNVKSRLDYIFVSKSLLPSVKSSKIlsdaARARIPSDHYPIEVTL 241
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 23-183 1.44e-06

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: 47.99  E-value: 1.44e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114   23 DIVVMQETKIQRKDLQDDMVLVPGWDVFFSLPKHKKGYSGVAIYTRnascapiraeegitgvlcppksttkfrdlpsdqq 102
Cdd:pfam03372  32 DVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSR---------------------------------- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  103 iggYPRPGQLSGIVEDTVLDSEGRCVILEFPAFVLLGVYCPANRDESRVEFRTSFFEALDVRIRNLVAEGKEVILAGDLN 182
Cdd:pfam03372  78 ---YPLSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN 154


                  .
gi 611961114  183 V 183
Cdd:pfam03372 155 A 155
PRK11756 PRK11756
exonuclease III; Provisional
 14-304 6.64e-06

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 46.81  E-value: 6.64e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  14 QAMFDILESDIVVMQETKIQRKDLQDDMVLVPGWDVFFslpkH-KKGYSGVAIYTRNascapiraeegitgvlcPPKSTT 92
Cdd:PRK11756  19 EAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFY----HgQKGHYGVALLSKQ-----------------TPIAVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114  93 KfrdlpsdqqigGYPRPGQlsgivedtvlDSEGRCVILEFP-AFVLLGV---YCPA--NRD-ESRVEFRTSFFEALDVRI 165
Cdd:PRK11756  78 K-----------GFPTDDE----------EAQRRIIMATIPtPNGNLTVingYFPQgeSRDhPTKFPAKRQFYQDLQNYL 136

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 611961114 166 RNLVAEGKEVILAGDLNVIRSEMDsTNVVENLRKEnmtideWIS------LPTRRIFNQLIFEGSIVgdrdegretpvlw 239
Cdd:PRK11756 137 ETELSPDNPLLIMGDMNISPTDLD-IGIGEENRKR------WLRtgkcsfLPEEREWLDRLMDWGLV------------- 196

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 611961114 240 DLCRCFHPSRLGMNTCWDTKKNTRPANNGSRIDYILCSNGLKDWFTSANIQEGLMG----SDHCPVFAT 304
Cdd:PRK11756 197 DTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAERCVETGIDYDIRGmekpSDHAPIWAT 265
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 263-305 4.97e-04

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: 41.05  E-value: 4.97e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 611961114 263 RPANNGSRIDYILCSNGLK--DWFTSANIQEGLMGSDHCPVFATI 305
Cdd:cd09083  208 KGPPGGSRIDYIFVSPGVKvlSYEILTDRYDGRYPSDHFPVVADL 252
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 271-305 1.59e-03

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 38.74  E-value: 1.59e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 611961114 271 IDYILCSNGLKdwFTSANI---QEGLMGSDHCPVFATI 305
Cdd:COG3568  129 IDYILVSPGLR--VLSAEVldsPLGRAASDHLPVVADL 164
 
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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