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Conserved domains on  [gi|490389715|ref|WP_004269170|]
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MULTISPECIES: exodeoxyribonuclease III [Bifidobacterium]

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 ...
 3-284 4.33e-112

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


The actual alignment was detected with superfamily member cd10281:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 253  Bit Score: 323.80  E-value: 4.33e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   3 LTITTSNLNGIRAAKRKGFDHWAKAHTPNVWCMQETRAPQEIIADIYGElaadyvhagkiasPEELHTLVDVCRIKGRAG 82
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFE-------------PEGYNAYFFDAEKKGYAG 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  83 VGMISDMPVLETRVGLpGLEEDVDSGRWIEADVRTeqgyvITVVCVYVHAGgLVDDPKEAQKYRFLDTMTERMQQLQDEa 162
Cdd:cd10281   68 VAIYSRTQPKAVIYGL-GFEEFDDEGRYIEADFDN-----VSVASLYVPSG-SSGDERQEAKMAFLDAFLEHLKELRRK- 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 163 asgGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDQMDYVDVMRDLAGDiQGPYTWWSQRGRAFDNDS 242
Cdd:cd10281  140 ---RREFIVCGDFNIAHTEIDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPD-EGQYTWWSNRGQARANNV 215

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 490389715 243 GWRLDYQFATPELAQQARGFVVDRassyDSRWSDHAPLTISY 284
Cdd:cd10281  216 GWRIDYQIATPGLASKVVSAWIYR----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) ...
 3-284 4.33e-112

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: 323.80  E-value: 4.33e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   3 LTITTSNLNGIRAAKRKGFDHWAKAHTPNVWCMQETRAPQEIIADIYGElaadyvhagkiasPEELHTLVDVCRIKGRAG 82
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFE-------------PEGYNAYFFDAEKKGYAG 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  83 VGMISDMPVLETRVGLpGLEEDVDSGRWIEADVRTeqgyvITVVCVYVHAGgLVDDPKEAQKYRFLDTMTERMQQLQDEa 162
Cdd:cd10281   68 VAIYSRTQPKAVIYGL-GFEEFDDEGRYIEADFDN-----VSVASLYVPSG-SSGDERQEAKMAFLDAFLEHLKELRRK- 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 163 asgGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDQMDYVDVMRDLAGDiQGPYTWWSQRGRAFDNDS 242
Cdd:cd10281  140 ---RREFIVCGDFNIAHTEIDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPD-EGQYTWWSNRGQARANNV 215

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 490389715 243 GWRLDYQFATPELAQQARGFVVDRassyDSRWSDHAPLTISY 284
Cdd:cd10281  216 GWRIDYQIATPGLASKVVSAWIYR----EERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
3-285 4.25e-95

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 280.81  E-value: 4.25e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   3 LTITTSNLNGIRAAKRKgFDHWAKAHTPNVWCMQETRAPQEIIADIYGElAADY--VHAGKiaspeelhtlvdvcriKGR 80
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAFE-AAGYhvYFHGQ----------------KGY 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  81 AGVGMISDMPVLETRVGLPGLEEDvDSGRWIEADVRTeqgyvITVVCVYVHAGGLVDDPKEAQKYRFLDTMTERMQQLQD 160
Cdd:COG0708   63 NGVAILSRLPPEDVRRGLGGDEFD-AEGRYIEADFGG-----VRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLA 136

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 161 EaasgGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDqMDYVDVMRDLAGDIQGPYTWWSQRGRAFDN 240
Cdd:COG0708  137 P----GRPLILCGDFNIAPTEIDVKNPKANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPDVEGQYTWWSYRAGAFAR 211

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 490389715 241 DSGWRLDYQFATPELAQQARGFVVDRASSYDSRWSDHAPLTISYD 285
Cdd:COG0708  212 NRGWRIDYILASPALADRLKDAGIDREPRGDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 3-285 4.63e-59

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: 188.64  E-value: 4.63e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715    3 LTITTSNLNGIRAAKRKGFDHWAKAHTPNVWCMQETRAPQE-IIADIYGELAADYVHagkiaspeelhtlvdVCRIKGRA 81
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEqFPAELFEELGYHVFF---------------HGAKKGYS 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   82 GVGMISDMPVLETRVGLPGLEEDvDSGRWIEADVRTeqgyvITVVCVYVHAGGLVDDPKEAQKYRFLDtmteRMQQLQDE 161
Cdd:TIGR00633  66 GVAILSKVEPLDVRYGFGGEPHD-EEGRVITAEFDG-----FTVVNVYVPNGGSRDLERLEYKLQFWD----ALFQYLEK 135

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  162 AASGGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDQmDYVDVMRDLAGDIQGPYTWWSQRGRAFDND 241
Cdd:TIGR00633 136 ELDAGKPVVICGDMNVAHTEIDLGNPKENKGNAGFTPEEREWFDELLEA-GFVDTFRHFNPDTGDAYTWWDYRSGARDRN 214

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 490389715  242 SGWRLDYQFATPELAQQargfVVDRASSYDSRWSDHAPLTISYD 285
Cdd:TIGR00633 215 RGWRIDYFLVSEPLAER----VVDSYIDSEIRGSDHCPIVLELD 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 3-280 1.97e-22

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 93.22  E-value: 1.97e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   3 LTITTSNLNGIRAAKRKGFDHWAKAHTPNVWCMQETRAPQEiiadiygelaadyvhagkiASPEELHTLVDV--CRIK-G 79
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQE-------------------QNTFEFKGYFDFwnCAIKkG 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  80 RAGVGMISDMPVLETRVGLpGLEEDVDSGRWIEADVrtEQGYVITVVCvyvhagglvddPKEAQKyrfLDTMTERMQQLQ 159
Cdd:PRK13911  62 YSGVVTFTKKEPLSVSYGI-NIEEHDKEGRVITCEF--ESFYLVNVYT-----------PNSQQA---LSRLSYRMSWEV 124

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 160 D-----EAASGGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDQmDYVDVMRDLAGDIQGPYTWWSQR 234
Cdd:PRK13911 125 EfkkflKALELKKPVIVCGDLNVAHNEIDLENPKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEKAYTWWSYM 203

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 490389715 235 GRAFDNDSGWRLDYQFATPELAQQARGFVVDRassyDSRWSDHAPL 280
Cdd:PRK13911 204 QQARDKNIGWRIDYFLCSNPLKTRLKDALIYK----DILGSDHCPV 245
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 7-177 1.89e-07

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: 50.30  E-value: 1.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715    7 TSNLNGIRA------AKRKGFDHWAKAHTPNVWCMQETRAPQEIIADIYGELAADYVHAgkiaspeelhtlVDVCRIKGR 80
Cdd:pfam03372   2 TWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSY------------GGPGGGGGG 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   81 AGVGMISDMPVLETRVGLPGLEEDVDSGRWIEADVRTeqgyvitVVCVYVHAGGLVDDPKEAQKYRFLDtmteRMQQLQD 160
Cdd:pfam03372  70 GGVAILSRYPLSSVILVDLGEFGDPALRGAIAPFAGV-------LVVPLVLTLAPHASPRLARDEQRAD----LLLLLLA 138

                         170
                  ....*....|....*..
gi 490389715  161 EAASGGRQAVVCGDFNI 177
Cdd:pfam03372 139 LLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 3-284 4.33e-112

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: 323.80  E-value: 4.33e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   3 LTITTSNLNGIRAAKRKGFDHWAKAHTPNVWCMQETRAPQEIIADIYGElaadyvhagkiasPEELHTLVDVCRIKGRAG 82
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFE-------------PEGYNAYFFDAEKKGYAG 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  83 VGMISDMPVLETRVGLpGLEEDVDSGRWIEADVRTeqgyvITVVCVYVHAGgLVDDPKEAQKYRFLDTMTERMQQLQDEa 162
Cdd:cd10281   68 VAIYSRTQPKAVIYGL-GFEEFDDEGRYIEADFDN-----VSVASLYVPSG-SSGDERQEAKMAFLDAFLEHLKELRRK- 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 163 asgGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDQMDYVDVMRDLAGDiQGPYTWWSQRGRAFDNDS 242
Cdd:cd10281  140 ---RREFIVCGDFNIAHTEIDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPD-EGQYTWWSNRGQARANNV 215

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 490389715 243 GWRLDYQFATPELAQQARGFVVDRassyDSRWSDHAPLTISY 284
Cdd:cd10281  216 GWRIDYQIATPGLASKVVSAWIYR----EERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
3-285 4.25e-95

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 280.81  E-value: 4.25e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   3 LTITTSNLNGIRAAKRKgFDHWAKAHTPNVWCMQETRAPQEIIADIYGElAADY--VHAGKiaspeelhtlvdvcriKGR 80
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAFE-AAGYhvYFHGQ----------------KGY 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  81 AGVGMISDMPVLETRVGLPGLEEDvDSGRWIEADVRTeqgyvITVVCVYVHAGGLVDDPKEAQKYRFLDTMTERMQQLQD 160
Cdd:COG0708   63 NGVAILSRLPPEDVRRGLGGDEFD-AEGRYIEADFGG-----VRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLA 136

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 161 EaasgGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDqMDYVDVMRDLAGDIQGPYTWWSQRGRAFDN 240
Cdd:COG0708  137 P----GRPLILCGDFNIAPTEIDVKNPKANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPDVEGQYTWWSYRAGAFAR 211

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 490389715 241 DSGWRLDYQFATPELAQQARGFVVDRASSYDSRWSDHAPLTISYD 285
Cdd:COG0708  212 NRGWRIDYILASPALADRLKDAGIDREPRGDERPSDHAPVVVELD 256
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 3-282 1.42e-62

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: 197.88  E-value: 1.42e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   3 LTITTSNLNGIRAAKRKGFDHWAKAHTPNVWCMQETRAPQEIIADiygelaadyvhagKIASPEELHTLVDVCRIKGRAG 82
Cdd:cd09085    1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPE-------------DLRNIEGYHSYFNSAERKGYSG 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  83 VGMISDMPVLETRVGLpGLEEDVDSGRWIEADVRTeqgyvITVVCVYVHAGGlVDDPKEAQKYRFLDTMTERMQQLQDEa 162
Cdd:cd09085   68 VALYSKIEPDSVREGL-GVEEFDNEGRILIADFDD-----FTLFNIYFPNGQ-MSEERLDYKLEFYDAFLEYLNELRDS- 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 163 asgGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDqMDYVDVMRDLAGDiQGPYTWWSQRGRAFDNDS 242
Cdd:cd09085  140 ---GKNVIICGDFNTAHKEIDLARPKENEKVSGFLPEERAWMDKFIE-NGYVDTFRMFNKE-PGQYTWWSYRTRARERNV 214

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 490389715 243 GWRLDYQFATPElaqqARGFVVDRASSYDSRWSDHAPLTI 282
Cdd:cd09085  215 GWRIDYFFVNEE----FKPKVKDAGILPDVMGSDHCPVSL 250
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 5-284 4.73e-60

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: 191.35  E-value: 4.73e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   5 ITTSNLNGIRAAKRKGFDHWAKAHTPNVWCMQETRAPQEiiadiygELAADYVHagkiasPEELHTLVDVCRIKGRAGVG 84
Cdd:cd09073    2 IISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADED-------KLPEELQH------VEGYHSYWSPARKKGYSGVA 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  85 MISDMPVLETRVGLPGLEEDvDSGRWIEADVRTeqgyvITVVCVYVHAGGlvDDPKEAQ-KYRFLDTMTERMQQLQDEaa 163
Cdd:cd09073   69 TLSKEEPLDVSYGIGGEEFD-SEGRVITAEFDD-----FYLINVYFPNGG--RGLERLDyKLRFYEAFLEFLEKLRKR-- 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 164 sgGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDqMDYVDVMRDLAGDiQGPYTWWSQRGRAFDNDSG 243
Cdd:cd09073  139 --GKPVVICGDFNVAHEEIDLARPKKNEKNAGFTPEERAWFDKLLS-LGYVDTFRHFHPE-PGAYTWWSYRGNARERNVG 214

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 490389715 244 WRLDYQFATPELAQQargfVVDRASSYDSRWSDHAPLTISY 284
Cdd:cd09073  215 WRIDYFLVSEELAEK----VKDSGILSKVKGSDHAPVTLEL 251
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 3-285 4.63e-59

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: 188.64  E-value: 4.63e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715    3 LTITTSNLNGIRAAKRKGFDHWAKAHTPNVWCMQETRAPQE-IIADIYGELAADYVHagkiaspeelhtlvdVCRIKGRA 81
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEqFPAELFEELGYHVFF---------------HGAKKGYS 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   82 GVGMISDMPVLETRVGLPGLEEDvDSGRWIEADVRTeqgyvITVVCVYVHAGGLVDDPKEAQKYRFLDtmteRMQQLQDE 161
Cdd:TIGR00633  66 GVAILSKVEPLDVRYGFGGEPHD-EEGRVITAEFDG-----FTVVNVYVPNGGSRDLERLEYKLQFWD----ALFQYLEK 135

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  162 AASGGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDQmDYVDVMRDLAGDIQGPYTWWSQRGRAFDND 241
Cdd:TIGR00633 136 ELDAGKPVVICGDMNVAHTEIDLGNPKENKGNAGFTPEEREWFDELLEA-GFVDTFRHFNPDTGDAYTWWDYRSGARDRN 214

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 490389715  242 SGWRLDYQFATPELAQQargfVVDRASSYDSRWSDHAPLTISYD 285
Cdd:TIGR00633 215 RGWRIDYFLVSEPLAER----VVDSYIDSEIRGSDHCPIVLELD 254
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 3-283 7.05e-53

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: 173.08  E-value: 7.05e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   3 LTITTSNLNGIRAakRKGF-DHWAKAHTPNVWCMQETRAPQEIIAdiYGELAADYVHagkiaspeelhtlVDVCRIKGRA 81
Cdd:cd09086    1 MKIATWNVNSIRA--RLEQvLDWLKEEDPDVLCLQETKVEDDQFP--ADAFEALGYH-------------VAVHGQKAYN 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  82 GVGMISDMPVLETRVGLPGLEEDVDSgRWIEADVRTeqgyvITVVCVYVHAGGLVDDPKEAQKYRFLDTMTERMQQLQDE 161
Cdd:cd09086   64 GVAILSRLPLEDVRTGFPGDPDDDQA-RLIAARVGG-----VRVINLYVPNGGDIGSPKFAYKLDWLDRLIRYLQKLLKP 137

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 162 aasgGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDqMDYVDVMRDLAGDiQGPYTWWSQRGRAFDND 241
Cdd:cd09086  138 ----DDPLVLVGDFNIAPEDIDVWDPKQLLGKVLFTPEEREALRALLD-LGFVDAFRALHPD-EKLFTWWDYRAGAFERN 211

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 490389715 242 SGWRLDYQFATPELAQQARGFVVDRASSYDSRWSDHAPLTIS 283
Cdd:cd09086  212 RGLRIDHILASPALADRLKDVGIDREPRGWEKPSDHAPVVAE 253
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 3-280 1.46e-52

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: 172.18  E-value: 1.46e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715    3 LTITTSNLNGIRAAKRKGFDhWAKAHTPNVWCMQETRAPQEIIADIYGELAADYVHAgkiaSPEelhtlvdvcriKGRAG 82
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGLA-WLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFF----SGQ-----------KGYSG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   83 VGMISDMPVLETRVGLPGLEEDVDsGRWIEADVRTeqgyvITVVCVYVHAGGLVDDPKEAQKYRFLDTMTERMQQLQDEa 162
Cdd:TIGR00195  65 VAIFSKEEPISVRRGFGVEEEDAE-GRIIMAEFDS-----FLVINGYFPNGSRDDSEKLPYKLQWLEALQNYLEKLVDK- 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  163 asgGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDqMDYVDVMRDLAGDiQGPYTWWSQRGRAFDNDS 242
Cdd:TIGR00195 138 ---DKPVLICGDMNIAPTEIDLHIPDENRNHTGFLPEEREWLDRLLE-AGLVDTFRKFNPD-EGAYSWWDYRTKARDRNR 212

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 490389715  243 GWRLDYQFATPELAQQARGFVVDRASSYDSRWSDHAPL 280
Cdd:TIGR00195 213 GWRIDYFLVSEPLKERCVDCGIDYDIRGSEKPSDHCPV 250
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 3-282 1.54e-42

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: 146.16  E-value: 1.54e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   3 LTITTSNLNGIRAAKRKGFDHWAKAHTPNVWCMQETRAPQEIIADIYGELAADYvhagkiaspeelHTLVDVCRIKGRAG 82
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGY------------HQYWNAAEKKGYSG 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  83 VGMISDMPVLETRVGLPGLEEDvDSGRWIEADVrtEQGYVITVvcvYV-HAG-GLVDDPKeaqKYRFLDTMTERMQQLQD 160
Cdd:cd09087   69 TAILSKKKPLSVTYGIGIEEHD-QEGRVITAEF--ENFYLVNT---YVpNSGrGLERLDR---RKEWDVDFRAYLKKLDS 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 161 eaasgGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIdQMDYVDVMRDLAGDIQGPYTWWSQRGRAFDN 240
Cdd:cd09087  140 -----KKPVIWCGDLNVAHEEIDLANPKTNKKSAGFTPEERESFTELL-EAGFVDTFRHLHPDKEGAYTFWSYRGNARAK 213

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 490389715 241 DSGWRLDYQFATPELAQQargfVVDRASSYDSRWSDHAPLTI 282
Cdd:cd09087  214 NVGWRLDYFLVSERLKDR----VVDSFIRSDIMGSDHCPIGL 251
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 3-280 1.97e-22

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 93.22  E-value: 1.97e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   3 LTITTSNLNGIRAAKRKGFDHWAKAHTPNVWCMQETRAPQEiiadiygelaadyvhagkiASPEELHTLVDV--CRIK-G 79
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQE-------------------QNTFEFKGYFDFwnCAIKkG 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  80 RAGVGMISDMPVLETRVGLpGLEEDVDSGRWIEADVrtEQGYVITVVCvyvhagglvddPKEAQKyrfLDTMTERMQQLQ 159
Cdd:PRK13911  62 YSGVVTFTKKEPLSVSYGI-NIEEHDKEGRVITCEF--ESFYLVNVYT-----------PNSQQA---LSRLSYRMSWEV 124

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 160 D-----EAASGGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRERAYMDKWIDQmDYVDVMRDLAGDIQGPYTWWSQR 234
Cdd:PRK13911 125 EfkkflKALELKKPVIVCGDLNVAHNEIDLENPKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEKAYTWWSYM 203

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 490389715 235 GRAFDNDSGWRLDYQFATPELAQQARGFVVDRassyDSRWSDHAPL 280
Cdd:PRK13911 204 QQARDKNIGWRIDYFLCSNPLKTRLKDALIYK----DILGSDHCPV 245
PRK11756 PRK11756
exonuclease III; Provisional
 9-286 3.49e-16

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 76.47  E-value: 3.49e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   9 NLNGIRAakRKgfdHWAKA----HTPNVWCMQETRA-----PQEIIADiYGELAadYVHAGKiaspeelhtlvdvcrikG 79
Cdd:PRK11756   7 NINGLRA--RP---HQLEAiiekHQPDVIGLQETKVhdemfPLEEVEA-LGYHV--FYHGQK-----------------G 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  80 RAGVGMISDMPVLETRVGLPGLEEDVDSgRWIEADVRTEQGyVITVVCVYVHAGGLVDDP-KEAQKYRFLdtmtERMQQL 158
Cdd:PRK11756  62 HYGVALLSKQTPIAVRKGFPTDDEEAQR-RIIMATIPTPNG-NLTVINGYFPQGESRDHPtKFPAKRQFY----QDLQNY 135

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 159 QDEAASGGRQAVVCGDFNIAHNPID-----------LKNPKSNennngYFPRERAYMDKWidqMDY--VDVMRDLAGDIQ 225
Cdd:PRK11756 136 LETELSPDNPLLIMGDMNISPTDLDigigeenrkrwLRTGKCS-----FLPEEREWLDRL---MDWglVDTFRQLNPDVN 207

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490389715 226 GPYTWWSQRGRAFDNDSGWRLDYQFATPELAQQargfVVDRASSYDSRW----SDHAPLTISYDV 286
Cdd:PRK11756 208 DRFSWFDYRSKGFDDNRGLRIDLILATQPLAER----CVETGIDYDIRGmekpSDHAPIWATFKL 268
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 5-284 7.71e-16

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


Pssm-ID: 197306 [Multi-domain]  Cd Length: 241  Bit Score: 74.83  E-value: 7.71e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   5 ITTSNLNGIRAA-KRKGFDHWAKAHTPNVWCMQETRAPQeiiADIYGELAADYVHAGKIASPEElhtlvdvcRIKGRAGV 83
Cdd:cd08372    1 VASYNVNGLNAAtRASGIARWVRELDPDIVCLQEVKDSQ---YSAVALNQLLPEGYHQYQSGPS--------RKEGYEGV 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  84 GMIS---DMPVLETRVGLPGlEEDVDSGRWIEADVrTEQGYVITVVCVYVHAGGLVDDPKEAQKYRFLDTMtermqqlQD 160
Cdd:cd08372   70 AILSktpKFKIVEKHQYKFG-EGDSGERRAVVVKF-DVHDKELCVVNAHLQAGGTRADVRDAQLKEVLEFL-------KR 140

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 161 EAASGGRQAVVCGDFNIAHNPIDLKNPKSnennNGYFPRERAymdkwidqmdYVDVMRDLAgdiqGPYTWWSqrgraFDN 240
Cdd:cd08372  141 LRQPNSAPVVICGDFNVRPSEVDSENPSS----MLRLFVALN----------LVDSFETLP----HAYTFDT-----YMH 197

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 490389715 241 DSGWRLDYQFATPELAQQARGFvvdrASSYDSRW----SDHAPLTISY 284
Cdd:cd08372  198 NVKSRLDYIFVSKSLLPSVKSS----KILSDAARaripSDHYPIEVTL 241
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 5-279 3.84e-15

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: 73.89  E-value: 3.84e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   5 ITTSNLNGIRAakRKGFDHWAKAHT---------PNVWCMQETRA-PQEIIADIygelaadyvhagkiASPEELHTLVDV 74
Cdd:cd09088    2 IVTWNVNGIRT--RLQYQPWNKENSlksfldsldADIICLQETKLtRDELDEPS--------------AIVEGYDSFFSF 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  75 CRI-KGRAGVGM---ISDMPVLETRVGLPGL----------------------EEDVDSGRWIEAD-----VRTEQGyVI 123
Cdd:cd09088   66 SRGrKGYSGVATycrDSAATPVAAEEGLTGVlsspnqknelsenddigcygemLEFTDSKELLELDsegrcVLTDHG-TF 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 124 TVVCVYVHAGGLVDDPKEAQKYRFLDTMTERMQQLQDEaasgGRQAVVCGDFNIAHNPIDLKNPKSNENNNGYFPRE--- 200
Cdd:cd09088  145 VLINVYCPRADPEKEERLEFKLDFYRLLEERVEALLKA----GRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnps 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 201 RaymdKWIDQM-------------DYVDVMRDLAGDIQGPYTWWSQRGRAFDNDSGWRLDYQFATPELAQQARGFVVDRa 267
Cdd:cd09088  221 R----QWLDQLlgdsgegggspggLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILP- 295

                        330
                 ....*....|..
gi 490389715 268 ssyDSRWSDHAP 279
Cdd:cd09088  296 ---EVEGSDHCP 304
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 5-284 1.87e-10

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: 59.67  E-value: 1.87e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   5 ITTSNLNGIR-AAKRKGFDHWAKAHTPNVWCMQETRAPQEIIADiYGELAADYVHAGKiaspeelhtlvdvcRIKGRAGV 83
Cdd:cd09076    1 IGTLNVRGLRsPGKRAQLLEELKRKKLDILGLQETHWTGEGELK-KKREGGTILYSGS--------------DSGKSRGV 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  84 GMIsdmpvLETRVGLPGLEED-VDSGRWIEADVRTeQGYVITVVCVYVHAGglvDDPKEaqKYRFLDTMTERMQQlqdea 162
Cdd:cd09076   66 AIL-----LSKTAANKLLEYTkVVSGRIIMVRFKI-KGKRLTIINVYAPTA---RDEEE--KEEFYDQLQDVLDK----- 129

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 163 ASGGRQAVVCGDFNIAHNPIDLKNPKSNENNNgyfpRERAYMDKWIDQMDYVDVMRDLAGDIQGpYTWWSQRGRAFDnds 242
Cdd:cd09076  130 VPRHDTLIIGGDFNAVLGPKDDGRKGLDKRNE----NGERALSALIEEHDLVDVWRENNPKTRE-YTWRSPDHGSRS--- 201

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 490389715 243 gwRLDYQFATPEL-AQQARGFVVDRAssydsrWSDHAPLTISY 284
Cdd:cd09076  202 --RIDRILVSKRLrVKVKKTKITPGA------GSDHRLVTLKL 236
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 7-177 1.89e-07

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: 50.30  E-value: 1.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715    7 TSNLNGIRA------AKRKGFDHWAKAHTPNVWCMQETRAPQEIIADIYGELAADYVHAgkiaspeelhtlVDVCRIKGR 80
Cdd:pfam03372   2 TWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSY------------GGPGGGGGG 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   81 AGVGMISDMPVLETRVGLPGLEEDVDSGRWIEADVRTeqgyvitVVCVYVHAGGLVDDPKEAQKYRFLDtmteRMQQLQD 160
Cdd:pfam03372  70 GGVAILSRYPLSSVILVDLGEFGDPALRGAIAPFAGV-------LVVPLVLTLAPHASPRLARDEQRAD----LLLLLLA 138

                         170
                  ....*....|....*..
gi 490389715  161 EAASGGRQAVVCGDFNI 177
Cdd:pfam03372 139 LLAPRSEPVILAGDFNA 155
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 3-280 4.22e-05

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 44.22  E-value: 4.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715   3 LTITTSNLNGiRAAKRKGFDHWAKAHTPNVWCMQE-TRAPQEIIAdiygELAADYVHAgkiaspeelhtlvDVCRIKGRA 81
Cdd:COG3021   95 LRVLTANVLF-GNADAEALAALVREEDPDVLVLQEtTPAWEEALA----ALEADYPYR-------------VLCPLDNAY 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  82 GVGMISDMPVLETRVglpgLEEDVDSGRWIEADVRTEQGyVITVVCVyvHAgglvddpkeaqkYRFLDTMTERMQQLQ-- 159
Cdd:COG3021  157 GMALLSRLPLTEAEV----VYLVGDDIPSIRATVELPGG-PVRLVAV--HP------------APPVGGSAERDAELAal 217

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 160 -DEAASGGRQAVVCGDFNIAhnpidlknPKSnennngyfprerAYMDKWIDQMDYVDvmrdlAGDIQGPYTWWSQRGRAF 238
Cdd:COG3021  218 aKAVAALDGPVIVAGDFNAT--------PWS------------PTLRRLLRASGLRD-----ARAGRGLGPTWPANLPFL 272

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 490389715 239 dndsGWRLDYQFATpelaqqaRGFVVDRASSYDSRWSDHAPL 280
Cdd:COG3021  273 ----RLPIDHVLVS-------RGLTVVDVRVLPVIGSDHRPL 303
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 18-280 5.68e-05

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: 43.44  E-value: 5.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  18 RKGFDHWAKAHTPNVWCMQETRAPQEIIADIYGELAADYvhagkiasPeelHTLVDVCRIKGRAGVGMISDMPVLETRVg 97
Cdd:cd09084   18 PDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLLLKGY--------P---YYYVVYKSDSGGTGLAIFSKYPILNSGS- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715  98 lpgLEEDVDSGRWIEADVRTeQGYVITVVCVYVH---------AGGLVDDPKEAQKYRFLDTMTERM--------QQLQD 160
Cdd:cd09084   86 ---IDFPNTNNNAIFADIRV-GGDTIRVYNVHLEsfritpsdkELYKEEKKAKELSRNLLRKLAEAFkrraaqadLLAAD 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 161 EAASGGRQaVVCGDFNiahnpidlkNPksnennngyfprerAYMdkwidqmdYVdvMRDLAGDIQ------G---PYTWw 231
Cdd:cd09084  162 IAASPYPV-IVCGDFN---------DT--------------PAS--------YV--YRTLKKGLTdafveaGsgfGYTF- 206

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 490389715 232 sqRGRAFdndsGWRLDYQFATPelaqqarGFVVDRASSYDSRWSDHAPL 280
Cdd:cd09084  207 --NGLFF----PLRIDYILTSK-------GFKVLRYRVDPGKYSDHYPI 242
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 123-283 2.51e-04

Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197311 [Multi-domain]  Cd Length: 205  Bit Score: 41.12  E-value: 2.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 123 ITVVCVYVHAGGLVDDPKEaqkyrfldtmteRMQQLQDEAASGGRQAVVCGDFNiAHNPidLKNPKSNEnnngyfPRERA 202
Cdd:cd09077   83 ITVVSCYAPPSESLEEFEE------------YLENLVRIVRGLSRPVIIGGDFN-AWSP--AWGSKRTD------RRGRL 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 203 YMDkWIDQMDYVDVMRDlagdiqGPYTWwsQRGRAFDNdsgwrLDYQFATPELAQQARGFVVDRASSYdsrwSDHAPLTI 282
Cdd:cd09077  142 LED-WIANLGLVLLNDG------NSPTF--VRPRGTSI-----IDVTFCSPSLARRISNWRVLEDETL----SDHRYIRF 203


                 .
gi 490389715 283 S 283
Cdd:cd09077  204 T 204
nSMase cd09078
Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological ...
 122-259 2.56e-04

Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine; Sphingomyelinases (SMase) are phosphodiesterases that catalyze the hydrolysis of sphingomyelin to ceramide and phosphorylcholine. Eukaryotic SMases have been classified according to their pH optima and are known as acid SMase, alkaline SMase, and neutral SMase (nSMase). Eukaryotic proteins in this family are nSMases, and are activated by a variety of stress-inducing agents such as cytokines or UV radiation. Ceramides and other metabolic derivatives, including sphingosine, are lipid "second messenger" molecules that participate in the regulation of stress-induced cellular responses, including cell death, adhesion, differentiation, and proliferation. Bacterial neutral SMases, which also belong to this domain family, are secreted proteins that act as membrane-damaging virulence factors. They promote colonization of the host tissue. 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: 197312 [Multi-domain]  Cd Length: 280  Bit Score: 41.56  E-value: 2.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 122 VITVVCVYVHAGglvDDPKEAQKYRfLDTMTERMQQLQDEAASGGRQAVVCGDFNIahnpidlknpksnenNNGYFPREr 201
Cdd:cd09078  127 VYHVFGTHLQAS---DGSCLDRAVR-QKQLDELRAFIEEKNIPDNEPVIIAGDFNV---------------DKRSSRDE- 186

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490389715 202 aYMDKWIDQMDYVDVMRDLAGDIqgPYTW----WSQRGRAFDNDSGWRLDYQFATPELAQQA 259
Cdd:cd09078  187 -YDDMLEQLHDYNAPEPITAGET--PLTWdpgtNLLAKYNYPGGGGERLDYILYSNDHLQPS 245
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
159-282 2.43e-03

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 38.85  E-value: 2.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 159 QDEAASGGRQAVVCGDFNiahnpiDlknpksnennngyFPRERAyMDKWIDQMDYVDVMRDLAGDiqGPYTWwsqrgrAF 238
Cdd:COG2374  246 SLLAADPDAPVIVLGDFN------D-------------YPFEDP-LRALLGAGGLTNLAEKLPAA--ERYSY------VY 297

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490389715 239 DNDSGwRLDYQFATPELAQQARG--------------FVVDRASSYDSRW--SDHAPLTI 282
Cdd:COG2374  298 DGNSG-LLDHILVSPALAARVTGadiwhinadiynddFKPDFRTYADDPGraSDHDPVVV 356
 
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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