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Conserved domains on  [gi|1655141539|ref|WP_137626027|]
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exodeoxyribonuclease III [Lactiplantibacillus pingfangensis]

Protein Classification

exodeoxyribonuclease III( domain architecture ID 10173395)

exodeoxyribonuclease III is a Mg-dependent 3' to 5' exonuclease acting on dsDNA, which releases 5' phosphomononucleotides as degradation products; similar to bacterial exodeoxyribonuclease III and eukaryotic DNA-(apurinic or apyrimidinic site) endonuclease

CATH:  3.60.10.10
EC:  3.1.11.2
Gene Ontology:  GO:0003677|GO:0046872|GO:0004519|GO:0004527|GO:0006281|GO:0008311
PubMed:  7885481|10838565
SCOP:  4002213

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-249 4.07e-157

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: 436.21  E-value: 4.07e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHGFVDRFNELDADAFCLQETKLQAGQIALD----LPGYHQYWNYAERKGYSGTAIFTKNEPLRV 76
Cdd:cd09087     1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKElkelLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  77 AYGIGVPEHDTEGRVITLEYADYYLITCYTPNSGGELKRLAYRQTWEDAFLAYINGLNADKPVIFCGDLNVAHENIDLKN 156
Cdd:cd09087    81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLAN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 157 WQSNHHSAGFTDEERGKFNQLLASGYTDTFRHFYPDQTGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILTD 236
Cdd:cd09087   161 PKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIRSD 240

                         250
                  ....*....|...
gi 1655141539 237 VMGSDHCPVELDI 249
Cdd:cd09087   241 IMGSDHCPIGLEL 253
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-249 4.07e-157

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: 436.21  E-value: 4.07e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHGFVDRFNELDADAFCLQETKLQAGQIALD----LPGYHQYWNYAERKGYSGTAIFTKNEPLRV 76
Cdd:cd09087     1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKElkelLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  77 AYGIGVPEHDTEGRVITLEYADYYLITCYTPNSGGELKRLAYRQTWEDAFLAYINGLNADKPVIFCGDLNVAHENIDLKN 156
Cdd:cd09087    81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLAN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 157 WQSNHHSAGFTDEERGKFNQLLASGYTDTFRHFYPDQTGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILTD 236
Cdd:cd09087   161 PKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIRSD 240

                         250
                  ....*....|...
gi 1655141539 237 VMGSDHCPVELDI 249
Cdd:cd09087   241 IMGSDHCPIGLEL 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-250 6.82e-125

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 354.77  E-value: 6.82e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHgFVDRFNELDADAFCLQETKLQAGQIALDL---PGYHQYWNYaeRKGYSGTAIFTKNEPLRVA 77
Cdd:COG0708     1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAfeaAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  78 YGIGVPEHDTEGRVITLEYADYYLITCYTPNSG-GELKRLAYRQTWEDAFLAYINGL-NADKPVIFCGDLNVAHENIDLK 155
Cdd:COG0708    78 RGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELlAPGRPLILCGDFNIAPTEIDVK 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 156 NWQSNHHSAGFTDEERGKFNQLLASGYTDTFRHFYPDQTGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILT 235
Cdd:COG0708   158 NPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDR 237

                         250
                  ....*....|....*....
gi 1655141539 236 ----DVMGSDHCPVELDIR 250
Cdd:COG0708   238 eprgDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-250 2.84e-117

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: 335.40  E-value: 2.84e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHGFVDRFNELDADAFCLQETKLQAGQI---ALDLPGYHQYWNYAERkGYSGTAIFTKNEPLRVA 77
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFpaeLFEELGYHVFFHGAKK-GYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  78 YGIGVPEHDTEGRVITLEYADYYLITCYTPNSGGE-LKRLAYRQT-WEDAFLAYINGLNADKPVIFCGDLNVAHENIDLK 155
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSRdLERLEYKLQfWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 156 NWQSNHHSAGFTDEERGKFNQLLASGYTDTFRHFYPDQTGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILT 235
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS 239

                         250
                  ....*....|....*
gi 1655141539 236 DVMGSDHCPVELDIR 250
Cdd:TIGR00633 240 EIRGSDHCPIVLELD 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-249 1.72e-106

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 308.16  E-value: 1.72e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHGFVDRFNELDADAFCLQETKLQAGQIALDLPGYHQYWNYAERKGYSGTAIFTKNEPLRVAYGI 80
Cdd:PRK13911    1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGYFDFWNCAIKKGYSGVVTFTKKEPLSVSYGI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  81 GVPEHDTEGRVITLEYADYYLITCYTPNSGGELKRLAYRQTWEDAFLAYINGLNADKPVIFCGDLNVAHENIDLKNWQSN 160
Cdd:PRK13911   81 NIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKKPVIVCGDLNVAHNEIDLENPKTN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 161 HHSAGFTDEERGKFNQLLASGYTDTFRHFYPDQTGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILTDVMGS 240
Cdd:PRK13911  161 RKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDILGS 240


                  ....*....
gi 1655141539 241 DHCPVELDI 249
Cdd:PRK13911  241 DHCPVGLEL 249
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-147 1.23e-16

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: 75.34  E-value: 1.23e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   4 ISWNVNGLRA------AVKHGFVDRFNELDADAFCLQETKLQAGQI----ALDLPGYHQYWNYAERKGYSGTAIFTKNEP 73
Cdd:pfam03372   1 LTWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASRlllaLLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1655141539  74 LRVAYGIGVPEHDTEGRVIT-LEYADYYLITCYTPNSGGELKRLAYRQTWEDAFLAYINGLNADKPVIFCGDLNV 147
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIaPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-249 4.07e-157

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: 436.21  E-value: 4.07e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHGFVDRFNELDADAFCLQETKLQAGQIALD----LPGYHQYWNYAERKGYSGTAIFTKNEPLRV 76
Cdd:cd09087     1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKElkelLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  77 AYGIGVPEHDTEGRVITLEYADYYLITCYTPNSGGELKRLAYRQTWEDAFLAYINGLNADKPVIFCGDLNVAHENIDLKN 156
Cdd:cd09087    81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLAN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 157 WQSNHHSAGFTDEERGKFNQLLASGYTDTFRHFYPDQTGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILTD 236
Cdd:cd09087   161 PKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIRSD 240

                         250
                  ....*....|...
gi 1655141539 237 VMGSDHCPVELDI 249
Cdd:cd09087   241 IMGSDHCPIGLEL 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-250 6.82e-125

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 354.77  E-value: 6.82e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHgFVDRFNELDADAFCLQETKLQAGQIALDL---PGYHQYWNYaeRKGYSGTAIFTKNEPLRVA 77
Cdd:COG0708     1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAfeaAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  78 YGIGVPEHDTEGRVITLEYADYYLITCYTPNSG-GELKRLAYRQTWEDAFLAYINGL-NADKPVIFCGDLNVAHENIDLK 155
Cdd:COG0708    78 RGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELlAPGRPLILCGDFNIAPTEIDVK 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 156 NWQSNHHSAGFTDEERGKFNQLLASGYTDTFRHFYPDQTGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILT 235
Cdd:COG0708   158 NPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDR 237

                         250
                  ....*....|....*....
gi 1655141539 236 ----DVMGSDHCPVELDIR 250
Cdd:COG0708   238 eprgDERPSDHAPVVVELD 256
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-249 1.34e-118

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: 338.87  E-value: 1.34e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHGFVDRFNELDADAFCLQETKLQAGQIALDL---PGYHQYWNYAERKGYSGTAIFTKNEPLRVA 77
Cdd:cd09085     1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLrniEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  78 YGIGVPEHDTEGRVITLEYADYYLITCYTPNSGGELKRLAYRQTWEDAFLAYINGLNAD-KPVIFCGDLNVAHENIDLKN 156
Cdd:cd09085    81 EGLGVEEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSgKNVIICGDFNTAHKEIDLAR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 157 WQSNHHSAGFTDEERGKFNQLLASGYTDTFRHFYPDQtGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILTD 236
Cdd:cd09085   161 PKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKEP-GQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPD 239

                         250
                  ....*....|...
gi 1655141539 237 VMGSDHCPVELDI 249
Cdd:cd09085   240 VMGSDHCPVSLEL 252
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-247 5.38e-118

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: 337.34  E-value: 5.38e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   2 KFISWNVNGLRAAVKHGFVDRFNELDADAFCLQETKLQAGQIALDL---PGYHQYWNYAERKGYSGTAIFTKNEPLRVAY 78
Cdd:cd09073     1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELqhvEGYHSYWSPARKKGYSGVATLSKEEPLDVSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  79 GIGVPEHDTEGRVITLEYADYYLITCYTPNSGGELKRLAYRQTWEDAFLAYINGL-NADKPVIFCGDLNVAHENIDLKNW 157
Cdd:cd09073    81 GIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLrKRGKPVVICGDFNVAHEEIDLARP 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 158 QSNHHSAGFTDEERGKFNQLLASGYTDTFRHFYPDQtGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILTDV 237
Cdd:cd09073   161 KKNEKNAGFTPEERAWFDKLLSLGYVDTFRHFHPEP-GAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILSKV 239

                         250
                  ....*....|
gi 1655141539 238 MGSDHCPVEL 247
Cdd:cd09073   240 KGSDHAPVTL 249
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-250 2.84e-117

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: 335.40  E-value: 2.84e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHGFVDRFNELDADAFCLQETKLQAGQI---ALDLPGYHQYWNYAERkGYSGTAIFTKNEPLRVA 77
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFpaeLFEELGYHVFFHGAKK-GYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  78 YGIGVPEHDTEGRVITLEYADYYLITCYTPNSGGE-LKRLAYRQT-WEDAFLAYINGLNADKPVIFCGDLNVAHENIDLK 155
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSRdLERLEYKLQfWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 156 NWQSNHHSAGFTDEERGKFNQLLASGYTDTFRHFYPDQTGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILT 235
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS 239

                         250
                  ....*....|....*
gi 1655141539 236 DVMGSDHCPVELDIR 250
Cdd:TIGR00633 240 EIRGSDHCPIVLELD 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-249 1.72e-106

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 308.16  E-value: 1.72e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHGFVDRFNELDADAFCLQETKLQAGQIALDLPGYHQYWNYAERKGYSGTAIFTKNEPLRVAYGI 80
Cdd:PRK13911    1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGYFDFWNCAIKKGYSGVVTFTKKEPLSVSYGI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  81 GVPEHDTEGRVITLEYADYYLITCYTPNSGGELKRLAYRQTWEDAFLAYINGLNADKPVIFCGDLNVAHENIDLKNWQSN 160
Cdd:PRK13911   81 NIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKKPVIVCGDLNVAHNEIDLENPKTN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 161 HHSAGFTDEERGKFNQLLASGYTDTFRHFYPDQTGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILTDVMGS 240
Cdd:PRK13911  161 RKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDILGS 240


                  ....*....
gi 1655141539 241 DHCPVELDI 249
Cdd:PRK13911  241 DHCPVGLEL 249
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-249 3.30e-105

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: 305.08  E-value: 3.30e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHGfVDRFNELDADAFCLQETKLQAGQIALDLP---GYHQYWNYAerKGYSGTAIFTKNEPLRVA 77
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKG-LAWLKENQPDVLCLQETKVQDEQFPLEPFhkeGYHVFFSGQ--KGYSGVAIFSKEEPISVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  78 YGIGVPEHDTEGRVITLEYADYYLITCYTPN-SGGELKRLAYRQTWEDAFLAYINGL-NADKPVIFCGDLNVAHENIDLK 155
Cdd:TIGR00195  78 RGFGVEEEDAEGRIIMAEFDSFLVINGYFPNgSRDDSEKLPYKLQWLEALQNYLEKLvDKDKPVLICGDMNIAPTEIDLH 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 156 NWQSNHHSAGFTDEERGKFNQLLASGYTDTFRHFYPDqTGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILT 235
Cdd:TIGR00195 158 IPDENRNHTGFLPEEREWLDRLLEAGLVDTFRKFNPD-EGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDY 236

                         250
                  ....*....|....*...
gi 1655141539 236 DVMG----SDHCPVELDI 249
Cdd:TIGR00195 237 DIRGsekpSDHCPVVLEF 254
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-249 2.00e-86

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: 257.16  E-value: 2.00e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKHGFVDRFNELDADAFCLQETKLQAGQ---IALDLPGYHQYWNYAERKGYSGTAIFTKNEPLRVA 77
Cdd:cd10281     1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQlddDFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  78 YGIGVPEHDTEGRVITLEYADYYLITCYTPNSGGELKRLAYRQTWEDAFLAYINGLNADKP-VIFCGDLNVAHENIDLKN 156
Cdd:cd10281    81 YGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRReFIVCGDFNIAHTEIDIKN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 157 WQSNHHSAGFTDEERGKFNQLLAS-GYTDTFRHFYPDQtGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILT 235
Cdd:cd10281   161 WKANQKNSGFLPEERAWLDQVFGElGYVDAFRELNPDE-GQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYR 239

                         250
                  ....*....|....
gi 1655141539 236 DVMGSDHCPVELDI 249
Cdd:cd10281   240 EERFSDHAPLIVDY 253
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-245 3.76e-67

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: 208.14  E-value: 3.76e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRA---AVKHgFVDRFnelDADAFCLQETKLQAGQI---ALDLPGYHQYWNyaERKGYSGTAIFTKNEPL 74
Cdd:cd09086     1 MKIATWNVNSIRArleQVLD-WLKEE---DPDVLCLQETKVEDDQFpadAFEALGYHVAVH--GQKAYNGVAILSRLPLE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  75 RVAYGIGVPEHDTEGRVITLEYADYYLITCYTPNsGGELK--RLAYRQTWEDAFLAYING-LNADKPVIFCGDLNVAHEN 151
Cdd:cd09086    75 DVRTGFPGDPDDDQARLIAARVGGVRVINLYVPN-GGDIGspKFAYKLDWLDRLIRYLQKlLKPDDPLVLVGDFNIAPED 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 152 IDL---KNWQsNHhsAGFTDEERGKFNQLLASGYTDTFRHFYPDQtGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRL 228
Cdd:cd09086   154 IDVwdpKQLL-GK--VLFTPEEREALRALLDLGFVDAFRALHPDE-KLFTWWDYRAGAFERNRGLRIDHILASPALADRL 229

                         250       260
                  ....*....|....*....|.
gi 1655141539 229 LNARILTDVMG----SDHCPV 245
Cdd:cd09086   230 KDVGIDREPRGwekpSDHAPV 250
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-249 2.87e-51

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: 169.42  E-value: 2.87e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   2 KFISWNVNGLRAaVKHGFVDR--------FNELDADAFCLQETKLQAGQ----IALdLPGYHQYWNY-AERKGYSGTAIF 68
Cdd:cd09088     1 RIVTWNVNGIRT-RLQYQPWNkenslksfLDSLDADIICLQETKLTRDEldepSAI-VEGYDSFFSFsRGRKGYSGVATY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  69 TK---NEPLRVAYGI-GV----------PEH---------------------DTEGRVITLEYADYYLITCYTP-NSGGE 112
Cdd:cd09088    79 CRdsaATPVAAEEGLtGVlsspnqknelSENddigcygemleftdskellelDSEGRCVLTDHGTFVLINVYCPrADPEK 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 113 LKRLAYRqtweDAFLAYI-----NGLNADKPVIFCGDLNVAHENIDLKNWQSNHHSAGFTDEE---RGKFNQLLASG--- 181
Cdd:cd09088   159 EERLEFK----LDFYRLLeerveALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLGDSgeg 234

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1655141539 182 -------YTDTFRHFYPDQTGIYSWWSYRAHARENNSGWRIDYFIASEKLNDRLLNARILTDVMGSDHCPVELDI 249
Cdd:cd09088   235 ggspgglLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYADL 309
PRK11756 PRK11756
exonuclease III; Provisional
 1-249 9.38e-42

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 143.50  E-value: 9.38e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAavkhgfvdRFNELDA-------DAFCLQETKLQAGQIALDLP---GYHQYwnYAERKGYSGTAIFTK 70
Cdd:PRK11756    1 MKFVSFNINGLRA--------RPHQLEAiiekhqpDVIGLQETKVHDEMFPLEEVealGYHVF--YHGQKGHYGVALLSK 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  71 NEPLRVAYGIGVPEHDTEGRVITLEYAD----YYLITCYTP---NSGGELKRLAYRQTWEDaFLAYING-LNADKPVIFC 142
Cdd:PRK11756   71 QTPIAVRKGFPTDDEEAQRRIIMATIPTpngnLTVINGYFPqgeSRDHPTKFPAKRQFYQD-LQNYLETeLSPDNPLLIM 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 143 GDLNVAHENIDL-------KNWQSNhhsaG---FTDEERGKFNQLLASGYTDTFRHFYPDQTGIYSWWSYRAHARENNSG 212
Cdd:PRK11756  150 GDMNISPTDLDIgigeenrKRWLRT----GkcsFLPEEREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFDDNRG 225

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1655141539 213 WRIDYFIASEKLNDRLLNARILTDVMG----SDHCPV--ELDI 249
Cdd:PRK11756  226 LRIDLILATQPLAERCVETGIDYDIRGmekpSDHAPIwaTFKL 268
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 4-249 4.79e-36

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: 127.98  E-value: 4.79e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   4 ISWNVNGLRAAVK-HGFVDRFNELDADAFCLQETKL----QAGQIALDLPGYHQYWNYAER-KGYSGTAIFTKN---EPL 74
Cdd:cd08372     2 ASYNVNGLNAATRaSGIARWVRELDPDIVCLQEVKDsqysAVALNQLLPEGYHQYQSGPSRkEGYEGVAILSKTpkfKIV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  75 RVAYGIGVPEHDTEGRV----ITLEYADYYLITCYTPNSGGelkRLAYRQTWEDAFLAYINGLNADK--PVIFCGDLNVA 148
Cdd:cd08372    82 EKHQYKFGEGDSGERRAvvvkFDVHDKELCVVNAHLQAGGT---RADVRDAQLKEVLEFLKRLRQPNsaPVVICGDFNVR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 149 HENIDLKNWQSnhhsagftDEERGKFNQLLASgytdtfrhfYPDQTGIYSWWSYRAharenNSGWRIDYFIASEKLNDRL 228
Cdd:cd08372   159 PSEVDSENPSS--------MLRLFVALNLVDS---------FETLPHAYTFDTYMH-----NVKSRLDYIFVSKSLLPSV 216

                         250       260
                  ....*....|....*....|....*
gi 1655141539 229 LNARILTDV----MGSDHCPVELDI 249
Cdd:cd08372   217 KSSKILSDAararIPSDHYPIEVTL 241
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-249 2.28e-20

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: 86.64  E-value: 2.28e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   3 FISWNVNGLRAAVK-HGFVDRFNELDADAFCLQETKL-QAGQIALDLPGYHQYWNYAERKGYSGTAIFTKNEPLRVAygI 80
Cdd:cd09076     1 IGTLNVRGLRSPGKrAQLLEELKRKKLDILGLQETHWtGEGELKKKREGGTILYSGSDSGKSRGVAILLSKTAANKL--L 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  81 GVpEHDTEGRVITL----EYADYYLITCYTPNSGGELKRLAYRQTWEDaflaYINGLNADKPVIFCGDLNvAHENIDLKN 156
Cdd:cd09076    79 EY-TKVVSGRIIMVrfkiKGKRLTIINVYAPTARDEEEKEEFYDQLQD----VLDKVPRHDTLIIGGDFN-AVLGPKDDG 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 157 WQSNHHSAGftDEERGKFNQLLASGYTDTFRHFYPDQTgiysWWSYRAHARENNSgwRIDYFIASEKLNDRLLNARIlTD 236
Cdd:cd09076   153 RKGLDKRNE--NGERALSALIEEHDLVDVWRENNPKTR----EYTWRSPDHGSRS--RIDRILVSKRLRVKVKKTKI-TP 223

                         250
                  ....*....|...
gi 1655141539 237 VMGSDHCPVELDI 249
Cdd:cd09076   224 GAGSDHRLVTLKL 236
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-147 1.23e-16

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: 75.34  E-value: 1.23e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   4 ISWNVNGLRA------AVKHGFVDRFNELDADAFCLQETKLQAGQI----ALDLPGYHQYWNYAERKGYSGTAIFTKNEP 73
Cdd:pfam03372   1 LTWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASRlllaLLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1655141539  74 LRVAYGIGVPEHDTEGRVIT-LEYADYYLITCYTPNSGGELKRLAYRQTWEDAFLAYINGLNADKPVIFCGDLNV 147
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIaPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 4-249 1.21e-10

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: 59.62  E-value: 1.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   4 ISWNVNGLRAAVKHGFVDRF----NELDADAFCLQETKLQAGQ----IALDLPGY-HQYWNYAERKGYSGTAIFTKnepl 74
Cdd:cd09084     2 MSYNVRSFNRYKWKDDPDKIldfiKKQDPDILCLQEYYGSEGDkdddLRLLLKGYpYYYVVYKSDSGGTGLAIFSK---- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  75 rvaYGIG----VPEHDTE-----------GRVITL-------------EYADYYLITCYTPNSGGELKRLAYRQTWE--- 123
Cdd:cd09084    78 ---YPILnsgsIDFPNTNnnaifadirvgGDTIRVynvhlesfritpsDKELYKEEKKAKELSRNLLRKLAEAFKRRaaq 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 124 -DAFLAYINglNADKPVIFCGDLN-----VAHENIdlknwqsnhhSAGFTD--EERGkfnqllaSGYTDTFRHFYPdqtg 195
Cdd:cd09084   155 aDLLAADIA--ASPYPVIVCGDFNdtpasYVYRTL----------KKGLTDafVEAG-------SGFGYTFNGLFF---- 211

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1655141539 196 iyswwsyraharennsGWRIDYFIASEKLndRLLNARILTDVMgSDHCPVELDI 249
Cdd:cd09084   212 ----------------PLRIDYILTSKGF--KVLRYRVDPGKY-SDHYPIVATL 246
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-251 1.57e-07

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 49.91  E-value: 1.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNV-NGL---RAAVKHGFVDRFNELDADAFCLQETklqagqialdlpgyhqywnyaerkgysgtAIFTKnEPLRV 76
Cdd:COG3568     8 LRVMTYNIrYGLgtdGRADLERIARVIRALDPDVVALQEN-----------------------------AILSR-YPIVS 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  77 AYGIGVPEHDTEGR-----VITLEYADYYLITCYTpNSGGELKRLayRQTweDAFLAYINGLNADKPVIFCGDLNVahen 151
Cdd:COG3568    58 SGTFDLPDPGGEPRgalwaDVDVPGKPLRVVNTHL-DLRSAAARR--RQA--RALAELLAELPAGAPVILAGDFND---- 128

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 152 idlknwqsnhhsagftdeergkfnqllasgytdtfrhfypdqtgiyswwsyraharennsgwrIDYFIASEKLndRLLNA 231
Cdd:COG3568   129 ---------------------------------------------------------------IDYILVSPGL--RVLSA 143

                         250       260
                  ....*....|....*....|...
gi 1655141539 232 RILTDVMG---SDHCPVELDIRV 251
Cdd:COG3568   144 EVLDSPLGraaSDHLPVVADLEL 166
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-251 8.66e-07

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 48.84  E-value: 8.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539   1 MKFISWNVNGLRAAVKhGFVDRFNELDADAFCLQETKLQAGQIALDLPGYHQYWNYAERKGYSGTAIFTKnEPL---RVA 77
Cdd:COG3021    95 LRVLTANVLFGNADAE-ALAALVREEDPDVLVLQETTPAWEEALAALEADYPYRVLCPLDNAYGMALLSR-LPLteaEVV 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539  78 YGIGVP------EHDTEGRVITLeyadyYLITCYTPNSG-----GELKRLAyrqtwedaflAYINGLnaDKPVIFCGDLN 146
Cdd:COG3021   173 YLVGDDipsiraTVELPGGPVRL-----VAVHPAPPVGGsaerdAELAALA----------KAVAAL--DGPVIVAGDFN 235

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 147 -VAhenidlknWQsnHHSAGFTDeergkfnqllASGYTD--TFRHFYPdqtgiySWwsyraHARENNSGWRIDYFIASEK 223
Cdd:COG3021   236 aTP--------WS--PTLRRLLR----------ASGLRDarAGRGLGP------TW-----PANLPFLRLPIDHVLVSRG 284

                         250       260
                  ....*....|....*....|....*...
gi 1655141539 224 LndRLLNARILtDVMGSDHCPVELDIRV 251
Cdd:COG3021   285 L--TVVDVRVL-PVIGSDHRPLLAELAL 309
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 127-249 1.61e-04

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


Pssm-ID: 197317 [Multi-domain]  Cd Length: 252  Bit Score: 41.82  E-value: 1.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 127 LAYINGLNADKPVIFCGDLNvahenidlknwqSNHHSAGftdeergkFNQLLASGYTDTFRH-FYPDQTGIYSWWSYRAh 205
Cdd:cd09083   151 LERIKEIAGDLPVILTGDFN------------AEPDSEP--------YKTLTSGGLKDARDTaATTDGGPEGTFHGFKG- 209

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1655141539 206 areNNSGWRIDYFIASEKLndRLLNARILTDVMG----SDHCPVELDI 249
Cdd:cd09083   210 ---PPGGSRIDYIFVSPGV--KVLSYEILTDRYDgrypSDHFPVVADL 252
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
125-250 3.90e-03

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 38.08  E-value: 3.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 125 AFLAYINGLNADKPVIFCGDLNvahenidlknwqSNHHSAGFTDEERgkfnqllASGYTDTFRHFYPDQTGIYSWwsyra 204
Cdd:COG2374   242 AFVDSLLAADPDAPVIVLGDFN------------DYPFEDPLRALLG-------AGGLTNLAEKLPAAERYSYVY----- 297

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1655141539 205 harENNSGwRIDYFIASEKLNDRL-------LNARILTDVMG-------------SDHCPVELDIR 250
Cdd:COG2374   298 ---DGNSG-LLDHILVSPALAARVtgadiwhINADIYNDDFKpdfrtyaddpgraSDHDPVVVGLR 359
nSMase cd09078
Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological ...
 131-249 9.46e-03

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: 36.55  E-value: 9.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655141539 131 NGLNADKPVIFCGDLNVahenidlknwqsNHHSagFTDEERGKFNQLlaSGYTDTFRHF-----YPDQTGIYSWWSYRAh 205
Cdd:cd09078   162 KNIPDNEPVIIAGDFNV------------DKRS--SRDEYDDMLEQL--HDYNAPEPITagetpLTWDPGTNLLAKYNY- 224

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1655141539 206 arENNSGWRIDYFIASeklNDRLLNARILTDVMG-----------------SDHCPVELDI 249
Cdd:cd09078   225 --PGGGGERLDYILYS---NDHLQPSSWSNEVEVpksptwsvtngytfadlSDHYPVSATF 280
 
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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