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Conserved domains on  [gi|544669530|ref|WP_021102881|]
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exodeoxyribonuclease III [Litoreibacter arenae]

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 ...
 3-260 3.15e-95

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 cd09086:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 254  Bit Score: 280.17  E-value: 3.15e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   3 FTLATWNINSVRLREELVLRLLREEAPDVLCLQECKSPVDKIPLEGLHALGYtHMVARGQKGYNGVAIISRLPLVEAAAE 82
Cdd:cd09086    1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGY-HVAVHGQKAYNGVAILSRLPLEDVRTG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  83 --DYATLGHARHVAARLeNGVVIHNHYVPAGGDVPdrevNDKFGQKLDYLTELRDAFHG--DKPSKSILVGDLNIAPRED 158
Cdd:cd09086   80 fpGDPDDDQARLIAARV-GGVRVINLYVPNGGDIG----SPKFAYKLDWLDRLIRYLQKllKPDDPLVLVGDFNIAPEDI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 159 DVWSHKQLLKVVSHTPIEVEHFNEVMDAgGWADVTRNDIPEGQLYSWWSYRAkDWDAADKGRRLDHVWATADIAAAGHSS 238
Cdd:cd09086  155 DVWDPKQLLGKVLFTPEEREALRALLDL-GFVDAFRALHPDEKLFTWWDYRA-GAFERNRGLRIDHILASPALADRLKDV 232

                        250       260
                 ....*....|....*....|..
gi 544669530 239 RVLRDVRGWEKPSDHAPVFATF 260
Cdd:cd09086  233 GIDREPRGWEKPSDHAPVVAEL 254
 
Name Accession Description Interval E-value
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 3-260 3.15e-95

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: 280.17  E-value: 3.15e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   3 FTLATWNINSVRLREELVLRLLREEAPDVLCLQECKSPVDKIPLEGLHALGYtHMVARGQKGYNGVAIISRLPLVEAAAE 82
Cdd:cd09086    1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGY-HVAVHGQKAYNGVAILSRLPLEDVRTG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  83 --DYATLGHARHVAARLeNGVVIHNHYVPAGGDVPdrevNDKFGQKLDYLTELRDAFHG--DKPSKSILVGDLNIAPRED 158
Cdd:cd09086   80 fpGDPDDDQARLIAARV-GGVRVINLYVPNGGDIG----SPKFAYKLDWLDRLIRYLQKllKPDDPLVLVGDFNIAPEDI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 159 DVWSHKQLLKVVSHTPIEVEHFNEVMDAgGWADVTRNDIPEGQLYSWWSYRAkDWDAADKGRRLDHVWATADIAAAGHSS 238
Cdd:cd09086  155 DVWDPKQLLGKVLFTPEEREALRALLDL-GFVDAFRALHPDEKLFTWWDYRA-GAFERNRGLRIDHILASPALADRLKDV 232

                        250       260
                 ....*....|....*....|..
gi 544669530 239 RVLRDVRGWEKPSDHAPVFATF 260
Cdd:cd09086  233 GIDREPRGWEKPSDHAPVVAEL 254
XthA COG0708
Exonuclease III [Replication, recombination and repair];
3-261 4.71e-88

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 261.93  E-value: 4.71e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   3 FTLATWNINSVRLREELVLRLLREEAPDVLCLQECKSPVDKIPLEGLHALGYtHMVARGQKGYNGVAIISRLPLVE---- 78
Cdd:COG0708    1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGY-HVYFHGQKGYNGVAILSRLPPEDvrrg 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  79 --AAAEDyatlGHARHVAARLEnGVVIHNHYVPAGGDVPDrevnDKFGQKLDYLTELRDAFHG--DKPSKSILVGDLNIA 154
Cdd:COG0708   80 lgGDEFD----AEGRYIEADFG-GVRVVSLYVPNGGSVGS----EKFDYKLRFLDALRAYLAEllAPGRPLILCGDFNIA 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 155 PREDDVWSHKQLLKVVSHTPIEVEHFNEVMDAgGWADVTRNDIPEGQ-LYSWWSYRAKDWDaADKGRRLDHVWATADIAA 233
Cdd:COG0708  151 PTEIDVKNPKANLKNAGFLPEERAWFDRLLEL-GLVDAFRALHPDVEgQYTWWSYRAGAFA-RNRGWRIDYILASPALAD 228

                        250       260
                 ....*....|....*....|....*...
gi 544669530 234 AGHSSRVLRDVRGWEKPSDHAPVFATFD 261
Cdd:COG0708  229 RLKDAGIDREPRGDERPSDHAPVVVELD 256
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 5-260 1.73e-47

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: 158.32  E-value: 1.73e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530    5 LATWNINSVRLREELVLRLLREEAPDVLCLQECKSPVDKIPLEGLHALGYtHMVARGQKGYNGVAIISRLPLVEA----A 80
Cdd:TIGR00195   3 IISWNVNGLRARPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGY-HVFFSGQKGYSGVAIFSKEEPISVrrgfG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   81 AEDYATLGhaRHVAARLENGVVIhNHYVPAGGDVpDREvndKFGQKLDYLTELR---DAFHgDKPSKSILVGDLNIAPRE 157
Cdd:TIGR00195  82 VEEEDAEG--RIIMAEFDSFLVI-NGYFPNGSRD-DSE---KLPYKLQWLEALQnylEKLV-DKDKPVLICGDMNIAPTE 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  158 DDVWSHKQLLKVVSHTPIEVEHFNEVMDAgGWADVTRNDIPEGQLYSWWSYRAKdwdAADKGR--RLDHVWATADIAAAG 235
Cdd:TIGR00195 154 IDLHIPDENRNHTGFLPEEREWLDRLLEA-GLVDTFRKFNPDEGAYSWWDYRTK---ARDRNRgwRIDYFLVSEPLKERC 229

                         250       260
                  ....*....|....*....|....*
gi 544669530  236 HSSRVLRDVRGWEKPSDHAPVFATF 260
Cdd:TIGR00195 230 VDCGIDYDIRGSEKPSDHCPVVLEF 254
PRK11756 PRK11756
exonuclease III; Provisional
 29-262 2.66e-29

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 111.14  E-value: 2.66e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  29 PDVLCLQECKSPVDKIPLEGLHALGYtHMVARGQKGYNGVAIISRLPLVEAA------AEDyatlGHARHVAARLE--NG 100
Cdd:PRK11756  27 PDVIGLQETKVHDEMFPLEEVEALGY-HVFYHGQKGHYGVALLSKQTPIAVRkgfptdDEE----AQRRIIMATIPtpNG 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 101 -VVIHNHYVPAGgdvPDREVNDKFGQK-------LDYLTELRDafhgdkPSKSILV-GDLNIAPREDDVW----SHKQLL 167
Cdd:PRK11756 102 nLTVINGYFPQG---ESRDHPTKFPAKrqfyqdlQNYLETELS------PDNPLLImGDMNISPTDLDIGigeeNRKRWL 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 168 KV--VSHTPIEVEHFNEVMDAGgWADVTRNDIPE-GQLYSWWSYRAKDWDAaDKGRRLDHVWATADIAAAGHSSRVLRDV 244
Cdd:PRK11756 173 RTgkCSFLPEEREWLDRLMDWG-LVDTFRQLNPDvNDRFSWFDYRSKGFDD-NRGLRIDLILATQPLAERCVETGIDYDI 250

                        250
                 ....*....|....*...
gi 544669530 245 RGWEKPSDHAPVFATFDL 262
Cdd:PRK11756 251 RGMEKPSDHAPIWATFKL 268
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 6-178 1.89e-13

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 66.86  E-value: 1.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530    6 ATWNINSVRLREELVLRLLRE-------EAPDVLCLQECKSPVDKIPLEGLHALG--YTHMVARGQKGYNGVAIISRLPL 76
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRKLDAlaaliraYDPDVVALQETDDDDASRLLLALLAYGgfLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   77 VEAAAEDYATLGHARHVAARLENGVVIHNHYVPAGGDVPDREVNDKFGQKLDYLTELRDAFHGDKPskSILVGDLNIapr 156
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEP--VILAGDFNA--- 155

                         170       180
                  ....*....|....*....|..
gi 544669530  157 eDDVWSHKQLLKVVSHTPIEVE 178
Cdd:pfam03372 156 -DYILVSGGLTVLSVGVLPDLG 176
 
Name Accession Description Interval E-value
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 3-260 3.15e-95

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: 280.17  E-value: 3.15e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   3 FTLATWNINSVRLREELVLRLLREEAPDVLCLQECKSPVDKIPLEGLHALGYtHMVARGQKGYNGVAIISRLPLVEAAAE 82
Cdd:cd09086    1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGY-HVAVHGQKAYNGVAILSRLPLEDVRTG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  83 --DYATLGHARHVAARLeNGVVIHNHYVPAGGDVPdrevNDKFGQKLDYLTELRDAFHG--DKPSKSILVGDLNIAPRED 158
Cdd:cd09086   80 fpGDPDDDQARLIAARV-GGVRVINLYVPNGGDIG----SPKFAYKLDWLDRLIRYLQKllKPDDPLVLVGDFNIAPEDI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 159 DVWSHKQLLKVVSHTPIEVEHFNEVMDAgGWADVTRNDIPEGQLYSWWSYRAkDWDAADKGRRLDHVWATADIAAAGHSS 238
Cdd:cd09086  155 DVWDPKQLLGKVLFTPEEREALRALLDL-GFVDAFRALHPDEKLFTWWDYRA-GAFERNRGLRIDHILASPALADRLKDV 232

                        250       260
                 ....*....|....*....|..
gi 544669530 239 RVLRDVRGWEKPSDHAPVFATF 260
Cdd:cd09086  233 GIDREPRGWEKPSDHAPVVAEL 254
XthA COG0708
Exonuclease III [Replication, recombination and repair];
3-261 4.71e-88

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 261.93  E-value: 4.71e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   3 FTLATWNINSVRLREELVLRLLREEAPDVLCLQECKSPVDKIPLEGLHALGYtHMVARGQKGYNGVAIISRLPLVE---- 78
Cdd:COG0708    1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGY-HVYFHGQKGYNGVAILSRLPPEDvrrg 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  79 --AAAEDyatlGHARHVAARLEnGVVIHNHYVPAGGDVPDrevnDKFGQKLDYLTELRDAFHG--DKPSKSILVGDLNIA 154
Cdd:COG0708   80 lgGDEFD----AEGRYIEADFG-GVRVVSLYVPNGGSVGS----EKFDYKLRFLDALRAYLAEllAPGRPLILCGDFNIA 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 155 PREDDVWSHKQLLKVVSHTPIEVEHFNEVMDAgGWADVTRNDIPEGQ-LYSWWSYRAKDWDaADKGRRLDHVWATADIAA 233
Cdd:COG0708  151 PTEIDVKNPKANLKNAGFLPEERAWFDRLLEL-GLVDAFRALHPDVEgQYTWWSYRAGAFA-RNRGWRIDYILASPALAD 228

                        250       260
                 ....*....|....*....|....*...
gi 544669530 234 AGHSSRVLRDVRGWEKPSDHAPVFATFD 261
Cdd:COG0708  229 RLKDAGIDREPRGDERPSDHAPVVVELD 256
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 5-260 1.73e-47

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: 158.32  E-value: 1.73e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530    5 LATWNINSVRLREELVLRLLREEAPDVLCLQECKSPVDKIPLEGLHALGYtHMVARGQKGYNGVAIISRLPLVEA----A 80
Cdd:TIGR00195   3 IISWNVNGLRARPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGY-HVFFSGQKGYSGVAIFSKEEPISVrrgfG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   81 AEDYATLGhaRHVAARLENGVVIhNHYVPAGGDVpDREvndKFGQKLDYLTELR---DAFHgDKPSKSILVGDLNIAPRE 157
Cdd:TIGR00195  82 VEEEDAEG--RIIMAEFDSFLVI-NGYFPNGSRD-DSE---KLPYKLQWLEALQnylEKLV-DKDKPVLICGDMNIAPTE 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  158 DDVWSHKQLLKVVSHTPIEVEHFNEVMDAgGWADVTRNDIPEGQLYSWWSYRAKdwdAADKGR--RLDHVWATADIAAAG 235
Cdd:TIGR00195 154 IDLHIPDENRNHTGFLPEEREWLDRLLEA-GLVDTFRKFNPDEGAYSWWDYRTK---ARDRNRgwRIDYFLVSEPLKERC 229

                         250       260
                  ....*....|....*....|....*
gi 544669530  236 HSSRVLRDVRGWEKPSDHAPVFATF 260
Cdd:TIGR00195 230 VDCGIDYDIRGSEKPSDHCPVVLEF 254
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 5-261 1.09e-42

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: 145.88  E-value: 1.09e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530    5 LATWNINS-VRLREELVLRLLREEAPDVLCLQECKSPVDKIPLEGLHALGYTHMVARGQKGYNGVAIISRLPL----VEA 79
Cdd:TIGR00633   3 IISWNVNGlRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAKKGYSGVAILSKVEPldvrYGF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   80 AAEDYATLGhaRHVAARLENGVVIhNHYVPAGGDVpDREvndKFGQKLDYLTELRDAFHGDKPSKS--ILVGDLNIAPRE 157
Cdd:TIGR00633  83 GGEPHDEEG--RVITAEFDGFTVV-NVYVPNGGSR-DLE---RLEYKLQFWDALFQYLEKELDAGKpvVICGDMNVAHTE 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  158 DDVWSHKQLLKVVSHTPIEVEHFNEVMDAgGWADVTRNDIPE-GQLYSWWSYRAKdwdAADKGR--RLDHVWATADIAAA 234
Cdd:TIGR00633 156 IDLGNPKENKGNAGFTPEEREWFDELLEA-GFVDTFRHFNPDtGDAYTWWDYRSG---ARDRNRgwRIDYFLVSEPLAER 231

                         250       260
                  ....*....|....*....|....*..
gi 544669530  235 GHSSRVLRDVRGwekpSDHAPVFATFD 261
Cdd:TIGR00633 232 VVDSYIDSEIRG----SDHCPIVLELD 254
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 5-260 1.04e-41

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: 143.20  E-value: 1.04e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   5 LATWNINS-VRLREELVLRLLREEAPDVLCLQECKSPVDKIPLEGLHALGYtHMVARGQ--KGYNGVAIISRLPLVEA-- 79
Cdd:cd09073    2 IISWNVNGlRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGY-HSYWSPArkKGYSGVATLSKEEPLDVsy 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  80 --AAEDYATLGhaRHVAARLENGVVIhNHYVPAGGDVPDR-EVNDKFGQKL-DYLTELRdafhgDKPSKSILVGDLNIAP 155
Cdd:cd09073   81 giGGEEFDSEG--RVITAEFDDFYLI-NVYFPNGGRGLERlDYKLRFYEAFlEFLEKLR-----KRGKPVVICGDFNVAH 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 156 REDDVWSHKQLLKVVSHTPIEVEHFNEVMDAgGWADVTRNDIPEGQLYSWWSYRAKdwdAADK--GRRLDHVWATADIAA 233
Cdd:cd09073  153 EEIDLARPKKNEKNAGFTPEERAWFDKLLSL-GYVDTFRHFHPEPGAYTWWSYRGN---ARERnvGWRIDYFLVSEELAE 228

                        250       260
                 ....*....|....*....|....*..
gi 544669530 234 AGHSSRVLRDVrgweKPSDHAPVFATF 260
Cdd:cd09073  229 KVKDSGILSKV----KGSDHAPVTLEL 251
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 29-256 8.03e-34

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: 122.72  E-value: 8.03e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  29 PDVLCLQECKSPVDKIPLEGLHALGY-THMVARGQKGYNGVAIISRLP----LVEAAAEDYATLGhaRHVAARLENgVVI 103
Cdd:cd10281   28 ADVVCLQEVRAQEEQLDDDFFEPEGYnAYFFDAEKKGYAGVAIYSRTQpkavIYGLGFEEFDDEG--RYIEADFDN-VSV 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 104 HNHYVPAG-GDVPDREVNDKFGQK-LDYLTELRDafhgdKPSKSILVGDLNIAPREDDVWSHKQLLKVVSHTPIEVEHFN 181
Cdd:cd10281  105 ASLYVPSGsSGDERQEAKMAFLDAfLEHLKELRR-----KRREFIVCGDFNIAHTEIDIKNWKANQKNSGFLPEERAWLD 179

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 544669530 182 EVMDAGGWADVTRNDIPEGQLYSWWSYRAKDWdAADKGRRLDHVWATADIAAAGHSSRVLRDVRGwekpSDHAPV 256
Cdd:cd10281  180 QVFGELGYVDAFRELNPDEGQYTWWSNRGQAR-ANNVGWRIDYQIATPGLASKVVSAWIYREERF----SDHAPL 249
PRK11756 PRK11756
exonuclease III; Provisional
 29-262 2.66e-29

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 111.14  E-value: 2.66e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  29 PDVLCLQECKSPVDKIPLEGLHALGYtHMVARGQKGYNGVAIISRLPLVEAA------AEDyatlGHARHVAARLE--NG 100
Cdd:PRK11756  27 PDVIGLQETKVHDEMFPLEEVEALGY-HVFYHGQKGHYGVALLSKQTPIAVRkgfptdDEE----AQRRIIMATIPtpNG 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 101 -VVIHNHYVPAGgdvPDREVNDKFGQK-------LDYLTELRDafhgdkPSKSILV-GDLNIAPREDDVW----SHKQLL 167
Cdd:PRK11756 102 nLTVINGYFPQG---ESRDHPTKFPAKrqfyqdlQNYLETELS------PDNPLLImGDMNISPTDLDIGigeeNRKRWL 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 168 KV--VSHTPIEVEHFNEVMDAGgWADVTRNDIPE-GQLYSWWSYRAKDWDAaDKGRRLDHVWATADIAAAGHSSRVLRDV 244
Cdd:PRK11756 173 RTgkCSFLPEEREWLDRLMDWG-LVDTFRQLNPDvNDRFSWFDYRSKGFDD-NRGLRIDLILATQPLAERCVETGIDYDI 250

                        250
                 ....*....|....*...
gi 544669530 245 RGWEKPSDHAPVFATFDL 262
Cdd:PRK11756 251 RGMEKPSDHAPIWATFKL 268
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 29-257 1.05e-26

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: 103.90  E-value: 1.05e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  29 PDVLCLQECKSPVDKIPLEGLHALGY-THMVARGQKGYNGVAIISRL-PL-VEAAAEDYATLGHARHVAARLENgVVIHN 105
Cdd:cd09085   28 PDILCLQETKAQPEQLPEDLRNIEGYhSYFNSAERKGYSGVALYSKIePDsVREGLGVEEFDNEGRILIADFDD-FTLFN 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 106 HYVPAGGDVPDR-----EVNDKFgqkLDYLTELRDafhgdKPSKSILVGDLNIAPREDDVWSHKQLLKVVSHTPIEVEHF 180
Cdd:cd09085  107 IYFPNGQMSEERldyklEFYDAF---LEYLNELRD-----SGKNVIICGDFNTAHKEIDLARPKENEKVSGFLPEERAWM 178

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 544669530 181 NEVMDAGgWADVTRNDIPEGQLYSWWSYRAKdwdAADK--GRRLDHVWATADIAAAGHSSRVLRDVRGwekpSDHAPVF 257
Cdd:cd09085  179 DKFIENG-YVDTFRMFNKEPGQYTWWSYRTR---ARERnvGWRIDYFFVNEEFKPKVKDAGILPDVMG----SDHCPVS 249
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 3-260 6.49e-26

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: 101.86  E-value: 6.49e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   3 FTLATWNINS-VRLREELVLRLLREEAPDVLCLQECKSPVDKIPLEGLHALGYTHMV---ARgQKGYNGVAIISRL-PL- 76
Cdd:cd09087    1 LKIISWNVNGlRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGYHQYwnaAE-KKGYSGTAILSKKkPLs 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  77 ----VEAAAEDyatlGHARHVAARLENGVVIhNHYVPAGGDVPDR-----EVNDKFgqkLDYLTELRDafhgDKPskSIL 147
Cdd:cd09087   80 vtygIGIEEHD----QEGRVITAEFENFYLV-NTYVPNSGRGLERldrrkEWDVDF---RAYLKKLDS----KKP--VIW 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 148 VGDLNIAPREDDVWSHKQLLKVVSHTPIEVEHFNEVMDAgGWADVTRNDIP--EGQlYSWWSYRAKDwDAADKGRRLDHV 225
Cdd:cd09087  146 CGDLNVAHEEIDLANPKTNKKSAGFTPEERESFTELLEA-GFVDTFRHLHPdkEGA-YTFWSYRGNA-RAKNVGWRLDYF 222

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 544669530 226 WATADIAAAGHSSRVLRDVRGwekpSDHAPVFATF 260
Cdd:cd09087  223 LVSERLKDRVVDSFIRSDIMG----SDHCPIGLEL 253
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 2-262 2.62e-16

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 76.96  E-value: 2.62e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   2 PFTLATWNINSVRLREELVLRLLREEAPDVLCLQECkSPVDKIPLEGLHAlGYTHMVARGQKGYNGVAIISRLPLVEAAA 81
Cdd:COG3021   94 DLRVLTANVLFGNADAEALAALVREEDPDVLVLQET-TPAWEEALAALEA-DYPYRVLCPLDNAYGMALLSRLPLTEAEV 171

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  82 eDYATLGHARHVAARLE---NGVVIHN-HYVPAGGDVPDREvndkfgqklDYLTELRDAFHGDKPSkSILVGDLNIAPre 157
Cdd:COG3021  172 -VYLVGDDIPSIRATVElpgGPVRLVAvHPAPPVGGSAERD---------AELAALAKAVAALDGP-VIVAGDFNATP-- 238

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 158 ddvWSHkqllkvvshtpieveHFNEVMDAGGWADVTRNdipEGQLYSWWSyrakdwDAADKGRRLDHVWATADIAAAghS 237
Cdd:COG3021  239 ---WSP---------------TLRRLLRASGLRDARAG---RGLGPTWPA------NLPFLRLPIDHVLVSRGLTVV--D 289

                        250       260
                 ....*....|....*....|....*
gi 544669530 238 SRVLRDVRgwekpSDHAPVFATFDL 262
Cdd:COG3021  290 VRVLPVIG-----SDHRPLLAELAL 309
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 5-259 8.38e-15

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: 71.74  E-value: 8.38e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   5 LATWNIN--SVRLREELVLRLLREEAPDVLCLQECKSPVDKIPLEGLHALGYTHMV---ARGQKGYNGVAIISRLPLVEA 79
Cdd:cd08372    1 VASYNVNglNAATRASGIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGYHQYqsgPSRKEGYEGVAILSKTPKFKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  80 AA----EDYATLGHARH-VAARLE---NGVVIHNHYVPAGGDVPDREVNDKFgQKLDYLTELRDafhgDKPSKSILVGDL 151
Cdd:cd08372   81 VEkhqyKFGEGDSGERRaVVVKFDvhdKELCVVNAHLQAGGTRADVRDAQLK-EVLEFLKRLRQ----PNSAPVVICGDF 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 152 NIAPREDDVWSHKQLLKVVsHTPIEVEHFNEVMDAggwadvtrndipegqlYSWWSYRakdwdaADKGRRLDHVWATADI 231
Cdd:cd08372  156 NVRPSEVDSENPSSMLRLF-VALNLVDSFETLPHA----------------YTFDTYM------HNVKSRLDYIFVSKSL 212

                        250       260
                 ....*....|....*....|....*...
gi 544669530 232 AAAGHSSRVLRDVRGWEKPSDHAPVFAT 259
Cdd:cd08372  213 LPSVKSSKILSDAARARIPSDHYPIEVT 240
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 6-178 1.89e-13

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 66.86  E-value: 1.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530    6 ATWNINSVRLREELVLRLLRE-------EAPDVLCLQECKSPVDKIPLEGLHALG--YTHMVARGQKGYNGVAIISRLPL 76
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRKLDAlaaliraYDPDVVALQETDDDDASRLLLALLAYGgfLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   77 VEAAAEDYATLGHARHVAARLENGVVIHNHYVPAGGDVPDREVNDKFGQKLDYLTELRDAFHGDKPskSILVGDLNIapr 156
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEP--VILAGDFNA--- 155

                         170       180
                  ....*....|....*....|..
gi 544669530  157 eDDVWSHKQLLKVVSHTPIEVE 178
Cdd:pfam03372 156 -DYILVSGGLTVLSVGVLPDLG 176
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 7-260 5.96e-11

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: 61.56  E-value: 5.96e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   7 TWNINSVRLREELVLRLLREEA--------PDVLCLQECKSPVDKIPLEGLHALGYT--HMVARGQKGYNGVAIISRLPL 76
Cdd:cd09088    4 TWNVNGIRTRLQYQPWNKENSLksfldsldADIICLQETKLTRDELDEPSAIVEGYDsfFSFSRGRKGYSGVATYCRDSA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  77 ---VEA---------------AAEDYATLGH--------ARHVAARLEN----------GVVIHNHYVP-AGGDVPDRev 119
Cdd:cd09088   84 atpVAAeegltgvlsspnqknELSENDDIGCygemleftDSKELLELDSegrcvltdhgTFVLINVYCPrADPEKEER-- 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 120 nDKFgqKLDYLTELRDAFHG--DKPSKSILVGDLNIAPREDDVWSHKQLLK----VVSHTPI--------EVEHFNEVMD 185
Cdd:cd09088  162 -LEF--KLDFYRLLEERVEAllKAGRRVILVGDVNVSHRPIDHCDPDDSEDfggeSFEDNPSrqwldqllGDSGEGGGSP 238

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 544669530 186 AGGWADVTRNDIPEGQ-LYSWWSYRaKDWDAADKGRRLDHVWATADIAAAGHSSRVLRDVRGwekpSDHAPVFATF 260
Cdd:cd09088  239 GGLLIDSFRYFHPTRKgAYTCWNTL-TGARPTNYGTRIDYILADRGLLPWVKAADILPEVEG----SDHCPVYADL 309
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 30-256 8.27e-09

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 54.70  E-value: 8.27e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  30 DVLCLQECKSPVDKIPLEGLHALGYTHMVARgqKGYNGVAIISRLPLVEAA----AEDYATLGhaRHVAARLENGVVIhN 105
Cdd:PRK13911  29 DVFCIQESKMQQEQNTFEFKGYFDFWNCAIK--KGYSGVVTFTKKEPLSVSyginIEEHDKEG--RVITCEFESFYLV-N 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 106 HYVPAggdvpDREVNDKFGQKLDYLTELRDAFHGDKPSKSILV-GDLNIAPREDDVWSHKQLLKVVSHTPIEVEHFNEVM 184
Cdd:PRK13911 104 VYTPN-----SQQALSRLSYRMSWEVEFKKFLKALELKKPVIVcGDLNVAHNEIDLENPKTNRKNAGFSDEERGKFSELL 178

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544669530 185 DAGgWADVTRNDIPEGQ-LYSWWSYRAKDWDaADKGRRLDHVWATADIAAAGHSSRVLRDVRGwekpSDHAPV 256
Cdd:PRK13911 179 NAG-FIDTFRYFYPNKEkAYTWWSYMQQARD-KNIGWRIDYFLCSNPLKTRLKDALIYKDILG----SDHCPV 245
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 146-260 2.33e-07

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: 50.29  E-value: 2.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 146 ILVGDLNIAPREDdvwSHKQLLKvvshtpievehfnevmdaGGWADvTRNDIPEGQLYSWWSYraKDWDAADKGRRLDHV 225
Cdd:cd09083  164 ILTGDFNAEPDSE---PYKTLTS------------------GGLKD-ARDTAATTDGGPEGTF--HGFKGPPGGSRIDYI 219

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 544669530 226 WATADIAAagHSSRVLRDVRGWEKPSDHAPVFATF 260
Cdd:cd09083  220 FVSPGVKV--LSYEILTDRYDGRYPSDHFPVVADL 252
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 29-152 5.35e-06

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


Pssm-ID: 197318 [Multi-domain]  Cd Length: 246  Bit Score: 46.52  E-value: 5.35e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  29 PDVLCLQECkSPVDKIPLEGLHALG----YTHMVARGQKGYNGVAIISRLPLVEAAAEDYatlGHARHVAARLE---NG- 100
Cdd:cd09084   30 PDILCLQEY-YGSEGDKDDDLRLLLkgypYYYVVYKSDSGGTGLAIFSKYPILNSGSIDF---PNTNNNAIFADirvGGd 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544669530 101 --VVIHNH-YVPAGGDVPDREVNDKFGQK---LDYLTELRDAFH-------------GDKPSKSILVGDLN 152
Cdd:cd09084  106 tiRVYNVHlESFRITPSDKELYKEEKKAKelsRNLLRKLAEAFKrraaqadllaadiAASPYPVIVCGDFN 176
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 5-260 1.11e-05

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: 45.42  E-value: 1.11e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   5 LATWNINSVRLREELVLRLLR--EEAPDVLCLQECKSpVDKIPLEGLHALGYTHMVARGQKGYNGVAIISRlPLVEAAAE 82
Cdd:cd09076    1 IGTLNVRGLRSPGKRAQLLEElkRKKLDILGLQETHW-TGEGELKKKREGGTILYSGSDSGKSRGVAILLS-KTAANKLL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  83 DYATLGHARHVAARLENGVVIH---NHYVPAGGDVPDREvndkfgqklDYLTELRDAFhgDKPSKS---ILVGDLN--IA 154
Cdd:cd09076   79 EYTKVVSGRIIMVRFKIKGKRLtiiNVYAPTARDEEEKE---------EFYDQLQDVL--DKVPRHdtlIIGGDFNavLG 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 155 PREDDVWSHKQLLKVVSHTPIEVEHFNEVmdaggwADVTRNDIPEGQLYSWWSYRAKDWdaadkgRRLDHVWATADiaaa 234
Cdd:cd09076  148 PKDDGRKGLDKRNENGERALSALIEEHDL------VDVWRENNPKTREYTWRSPDHGSR------SRIDRILVSKR---- 211

                        250       260
                 ....*....|....*....|....*.
gi 544669530 235 gHSSRVLRDVRGWEKPSDHAPVFATF 260
Cdd:cd09076  212 -LRVKVKKTKITPGAGSDHRLVTLKL 236
nSMase cd09078
Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological ...
 29-260 4.10e-05

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: 43.87  E-value: 4.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  29 PDVLCLQEC--KSPVDKIpLEGLHALGY--THMVARGQKGYN------GVAIISRLPLVEAA---------AEDYATLGh 89
Cdd:cd09078   37 YDVVVLQEVfdARARKRL-LNGLKKEYPyqTDVVGRSPSGWSsklvdgGVVILSRYPIVEKDqyifpngcgADCLAAKG- 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  90 ARHVAARLENGVVIH---NHYVPAGGDVPDREVndkfgqKLDYLTELRD---AFHGDKPSKSILVGDLNIAPREDDVwSH 163
Cdd:cd09078  115 VLYAKINKGGTKVYHvfgTHLQASDGSCLDRAV------RQKQLDELRAfieEKNIPDNEPVIIAGDFNVDKRSSRD-EY 187

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 164 KQLLKVVSHTpieveHFNEVMDAGGWA---DVTRNDIPEGQLYSWwsyrakdwdaadKGRRLDHVWATADIAA-AGHSSR 239
Cdd:cd09078  188 DDMLEQLHDY-----NAPEPITAGETPltwDPGTNLLAKYNYPGG------------GGERLDYILYSNDHLQpSSWSNE 250

                        250       260       270
                 ....*....|....*....|....*....|
gi 544669530 240 VLR-------DVRGWEKP--SDHAPVFATF 260
Cdd:cd09078  251 VEVpksptwsVTNGYTFAdlSDHYPVSATF 280
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-262 6.89e-05

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 42.20  E-value: 6.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530   1 MPFTLATWNINSVRLREELVLRLL-----REEAPDVLCLQEckspvdkipleglhalgythmvargqkgyngVAIISRLP 75
Cdd:COG3568    6 ATLRVMTYNIRYGLGTDGRADLERiarviRALDPDVVALQE-------------------------------NAILSRYP 54

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  76 LVEAAAEDYATLGHARHVA--ARLENG----VVIHNHYVPAGGDVPDREVndkfgqklDYLTELRDAFHGDKPskSILVG 149
Cdd:COG3568   55 IVSSGTFDLPDPGGEPRGAlwADVDVPgkplRVVNTHLDLRSAAARRRQA--------RALAELLAELPAGAP--VILAG 124

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 150 DLNIapreddvwshkqllkvvshtpievehfnevmdaggwadvtrndipegqlyswwsyrakdwdaadkgrrLDHVWATA 229
Cdd:COG3568  125 DFND--------------------------------------------------------------------IDYILVSP 136

                        250       260       270
                 ....*....|....*....|....*....|...
gi 544669530 230 DIAAagHSSRVLRDvRGWEKPSDHAPVFATFDL 262
Cdd:COG3568  137 GLRV--LSAEVLDS-PLGRAASDHLPVVADLEL 166
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
29-262 6.19e-04

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 40.39  E-value: 6.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  29 PDVLCLQECKSP-------VDKIPLEGlHALGYTHMVA----RGQKgyngVAIISR---LPLVEAA--AEDYATLGHAR- 91
Cdd:COG2374  115 ADIVGLQEVENNgsalqdlVAALNLAG-GTYAFVHPPDgpdgDGIR----VALLYRpdrVTLVGSAtiADLPDSPGNPDr 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530  92 ------HVAARLENG---VVIHNHYvPA-GGDVPDRevndkfGQKLDYL------TELRDA----FHGDKPSKSILVGDL 151
Cdd:COG2374  190 fsrpplAVTFELANGepfTVIVNHF-KSkGSDDPGD------GQGASEAkrtaqaEALRAFvdslLAADPDAPVIVLGDF 262

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544669530 152 NIAPREDdvwshkqllkvvshtPIEVehfneVMDAGGWADVTRnDIPEGQLYSWwSYRakdwdaaDKGRRLDHVWATADI 231
Cdd:COG2374  263 NDYPFED---------------PLRA-----LLGAGGLTNLAE-KLPAAERYSY-VYD-------GNSGLLDHILVSPAL 313

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 544669530 232 AAAGHSSRV------------LRDVRGWEKP----SDHAPVFATFDL 262
Cdd:COG2374  314 AARVTGADIwhinadiynddfKPDFRTYADDpgraSDHDPVVVGLRL 360
 
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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