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Conserved domains on  [gi|949496737|ref|WP_056939283|]
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exodeoxyribonuclease III [Lentilactobacillus buchneri]

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 ...
 1-248 4.31e-161

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: 446.61  E-value: 4.31e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAVKHDFAETFQQLDADFFCIQETKMQEGQLELD----LPGYQQYFNYAERKGYSGTAIFTKHAPMHV 76
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKElkelLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  77 TYGINGDEFDHEGRAITLEYPDFYLVTSYVPNSGAGLKRLDFRMGWNKAFYQYLTELDAKKPVILCGDLNVAHKEIDLKN 156
Cdd:cd09087   81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLAN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 157 PQSNHHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQTDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILTD 236
Cdd:cd09087  161 PKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIRSD 240

                        250
                 ....*....|..
gi 949496737 237 VFGSDHCPVELD 248
Cdd:cd09087  241 IMGSDHCPIGLE 252
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-248 4.31e-161

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: 446.61  E-value: 4.31e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAVKHDFAETFQQLDADFFCIQETKMQEGQLELD----LPGYQQYFNYAERKGYSGTAIFTKHAPMHV 76
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKElkelLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  77 TYGINGDEFDHEGRAITLEYPDFYLVTSYVPNSGAGLKRLDFRMGWNKAFYQYLTELDAKKPVILCGDLNVAHKEIDLKN 156
Cdd:cd09087   81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLAN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 157 PQSNHHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQTDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILTD 236
Cdd:cd09087  161 PKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIRSD 240

                        250
                 ....*....|..
gi 949496737 237 VFGSDHCPVELD 248
Cdd:cd09087  241 IMGSDHCPIGLE 252
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-248 9.24e-125

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 354.77  E-value: 9.24e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAVKHdFAETFQQLDADFFCIQETKMQEGQLELDL---PGYQQYFNYaeRKGYSGTAIFTKHAPMHVT 77
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAfeaAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  78 YGINGDEFDHEGRAITLEYPDFYLVTSYVPNSGA-GLKRLDFRMGWNKAFYQYLTELDAK-KPVILCGDLNVAHKEIDLK 155
Cdd:COG0708   78 RGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLAPgRPLILCGDFNIAPTEIDVK 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 156 NPQSNHHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQTDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILT 235
Cdd:COG0708  158 NPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDR 237

                        250
                 ....*....|....*..
gi 949496737 236 ----DVFGSDHCPVELD 248
Cdd:COG0708  238 eprgDERPSDHAPVVVE 254
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-248 3.05e-122

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: 348.11  E-value: 3.05e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737    1 MKFISWNVNGLRAAVKHDFAETFQQLDADFFCIQETKMQEGQLELDL---PGYQQYFNYAERkGYSGTAIFTKHAPMHVT 77
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELfeeLGYHVFFHGAKK-GYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   78 YGINGDEFDHEGRAITLEYPDFYLVTSYVPNSGA-GLKRLDFRMGWNKAFYQ-YLTELDAKKPVILCGDLNVAHKEIDLK 155
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSrDLERLEYKLQFWDALFQyLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  156 NPQSNHHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQTDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILT 235
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS 239

                         250
                  ....*....|...
gi 949496737  236 DVFGSDHCPVELD 248
Cdd:TIGR00633 240 EIRGSDHCPIVLE 252
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-248 2.26e-105

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 305.46  E-value: 2.26e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAVKHDFAETFQQLDADFFCIQETKMQEGQLELDLPGYQQYFNYAERKGYSGTAIFTKHAPMHVTYGI 80
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGYFDFWNCAIKKGYSGVVTFTKKEPLSVSYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  81 NGDEFDHEGRAITLEYPDFYLVTSYVPNSGAGLKRLDFRMGWNKAFYQYLTELDAKKPVILCGDLNVAHKEIDLKNPQSN 160
Cdd:PRK13911  81 NIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKKPVIVCGDLNVAHNEIDLENPKTN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 161 HHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQTDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILTDVFGS 240
Cdd:PRK13911 161 RKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDILGS 240


                 ....*...
gi 949496737 241 DHCPVELD 248
Cdd:PRK13911 241 DHCPVGLE 248
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-147 7.83e-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: 73.41  E-value: 7.83e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737    4 ISWNVNGLRA------AVKHDFAETFQQLDADFFCIQETKMQEGQ----LELDLPGYQQYFNYAERKGYSGTAIFTKHAP 73
Cdd:pfam03372   1 LTWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASrlllALLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 949496737   74 MHVTYGINGDEFDHEGR-AITLEYPDFYLVTSYVPNSGAGLKRLDFRMGWNKAFYQYLTELDAKKPVILCGDLNV 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 ...
 1-248 4.31e-161

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: 446.61  E-value: 4.31e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAVKHDFAETFQQLDADFFCIQETKMQEGQLELD----LPGYQQYFNYAERKGYSGTAIFTKHAPMHV 76
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKElkelLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  77 TYGINGDEFDHEGRAITLEYPDFYLVTSYVPNSGAGLKRLDFRMGWNKAFYQYLTELDAKKPVILCGDLNVAHKEIDLKN 156
Cdd:cd09087   81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLAN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 157 PQSNHHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQTDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILTD 236
Cdd:cd09087  161 PKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIRSD 240

                        250
                 ....*....|..
gi 949496737 237 VFGSDHCPVELD 248
Cdd:cd09087  241 IMGSDHCPIGLE 252
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-248 9.24e-125

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 354.77  E-value: 9.24e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAVKHdFAETFQQLDADFFCIQETKMQEGQLELDL---PGYQQYFNYaeRKGYSGTAIFTKHAPMHVT 77
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAfeaAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  78 YGINGDEFDHEGRAITLEYPDFYLVTSYVPNSGA-GLKRLDFRMGWNKAFYQYLTELDAK-KPVILCGDLNVAHKEIDLK 155
Cdd:COG0708   78 RGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLAPgRPLILCGDFNIAPTEIDVK 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 156 NPQSNHHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQTDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILT 235
Cdd:COG0708  158 NPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDR 237

                        250
                 ....*....|....*..
gi 949496737 236 ----DVFGSDHCPVELD 248
Cdd:COG0708  238 eprgDERPSDHAPVVVE 254
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-248 3.05e-122

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: 348.11  E-value: 3.05e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737    1 MKFISWNVNGLRAAVKHDFAETFQQLDADFFCIQETKMQEGQLELDL---PGYQQYFNYAERkGYSGTAIFTKHAPMHVT 77
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELfeeLGYHVFFHGAKK-GYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   78 YGINGDEFDHEGRAITLEYPDFYLVTSYVPNSGA-GLKRLDFRMGWNKAFYQ-YLTELDAKKPVILCGDLNVAHKEIDLK 155
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSrDLERLEYKLQFWDALFQyLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  156 NPQSNHHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQTDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILT 235
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS 239

                         250
                  ....*....|...
gi 949496737  236 DVFGSDHCPVELD 248
Cdd:TIGR00633 240 EIRGSDHCPIVLE 252
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-247 2.81e-121

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: 345.81  E-value: 2.81e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   2 KFISWNVNGLRAAVKHDFAETFQQLDADFFCIQETKMQEGQLELDL---PGYQQYFNYAERKGYSGTAIFTKHAPMHVTY 78
Cdd:cd09073    1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELqhvEGYHSYWSPARKKGYSGVATLSKEEPLDVSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  79 GINGDEFDHEGRAITLEYPDFYLVTSYVPNSGAGLKRLDFRMGWNKAFYQYL-TELDAKKPVILCGDLNVAHKEIDLKNP 157
Cdd:cd09073   81 GIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLeKLRKRGKPVVICGDFNVAHEEIDLARP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 158 QSNHHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQtDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILTDV 237
Cdd:cd09073  161 KKNEKNAGFTPEERAWFDKLLSLGYVDTFRHFHPEP-GAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILSKV 239

                        250
                 ....*....|
gi 949496737 238 FGSDHCPVEL 247
Cdd:cd09073  240 KGSDHAPVTL 249
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-248 1.61e-116

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: 333.86  E-value: 1.61e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAVKHDFAETFQQLDADFFCIQETKMQEGQLELDL---PGYQQYFNYAERKGYSGTAIFTKHAPMHVT 77
Cdd:cd09085    1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLrniEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  78 YGINGDEFDHEGRAITLEYPDFYLVTSYVPNSGAGLKRLDFRMGWNKAFYQYLTELDAK-KPVILCGDLNVAHKEIDLKN 156
Cdd:cd09085   81 EGLGVEEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSgKNVIICGDFNTAHKEIDLAR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 157 PQSNHHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQtDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILTD 236
Cdd:cd09085  161 PKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKEP-GQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPD 239

                        250
                 ....*....|..
gi 949496737 237 VFGSDHCPVELD 248
Cdd:cd09085  240 VMGSDHCPVSLE 251
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-247 5.96e-106

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: 307.00  E-value: 5.96e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737    1 MKFISWNVNGLRAaVKHDFAETFQQLDADFFCIQETKMQEGQLELDLP---GYQQYFNYAerKGYSGTAIFTKHAPMHVT 77
Cdd:TIGR00195   1 MKIISWNVNGLRA-RPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFhkeGYHVFFSGQ--KGYSGVAIFSKEEPISVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   78 YGINGDEFDHEGRAITLEYPDFYLVTSYVPN-SGAGLKRLDFRMGWNKAFYQYL-TELDAKKPVILCGDLNVAHKEIDLK 155
Cdd:TIGR00195  78 RGFGVEEEDAEGRIIMAEFDSFLVINGYFPNgSRDDSEKLPYKLQWLEALQNYLeKLVDKDKPVLICGDMNIAPTEIDLH 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  156 NPQSNHHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDqTDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILT 235
Cdd:TIGR00195 158 IPDENRNHTGFLPEEREWLDRLLEAGLVDTFRKFNPD-EGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDY 236

                         250
                  ....*....|....*.
gi 949496737  236 DVFG----SDHCPVEL 247
Cdd:TIGR00195 237 DIRGsekpSDHCPVVL 252
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-248 2.26e-105

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 305.46  E-value: 2.26e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAVKHDFAETFQQLDADFFCIQETKMQEGQLELDLPGYQQYFNYAERKGYSGTAIFTKHAPMHVTYGI 80
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGYFDFWNCAIKKGYSGVVTFTKKEPLSVSYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  81 NGDEFDHEGRAITLEYPDFYLVTSYVPNSGAGLKRLDFRMGWNKAFYQYLTELDAKKPVILCGDLNVAHKEIDLKNPQSN 160
Cdd:PRK13911  81 NIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKKPVIVCGDLNVAHNEIDLENPKTN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 161 HHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQTDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILTDVFGS 240
Cdd:PRK13911 161 RKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDILGS 240


                 ....*...
gi 949496737 241 DHCPVELD 248
Cdd:PRK13911 241 DHCPVGLE 248
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-248 7.05e-93

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: 273.72  E-value: 7.05e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAVKHDFAETFQQLDADFFCIQETKMQEGQLELDL---PGYQQYFNYAERKGYSGTAIFTKHAPMHVT 77
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFfepEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  78 YGINGDEFDHEGRAITLEYPDFYLVTSYVPNSGAGLKRLDFRMGWNKAFYQYLTELDAKKP-VILCGDLNVAHKEIDLKN 156
Cdd:cd10281   81 YGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRReFIVCGDFNIAHTEIDIKN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 157 PQSNHHNAGFTDEERQDFTKLL-KAGFMDTFRHFYPDQtDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILT 235
Cdd:cd10281  161 WKANQKNSGFLPEERAWLDQVFgELGYVDAFRELNPDE-GQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYR 239

                        250
                 ....*....|...
gi 949496737 236 DVFGSDHCPVELD 248
Cdd:cd10281  240 EERFSDHAPLIVD 252
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-245 2.05e-66

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: 206.60  E-value: 2.05e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAVKH--DFAETFQqldADFFCIQETKMQEGQL---ELDLPGYQQYFNyaERKGYSGTAIFTKHAPMH 75
Cdd:cd09086    1 MKIATWNVNSIRARLEQvlDWLKEED---PDVLCLQETKVEDDQFpadAFEALGYHVAVH--GQKAYNGVAILSRLPLED 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  76 VTYGINGDEFDHEGRAITLEYPDFYLVTSYVPNSGA-GLKRLDFRMGWNKAFYQYL-TELDAKKPVILCGDLNVAHKEID 153
Cdd:cd09086   76 VRTGFPGDPDDDQARLIAARVGGVRVINLYVPNGGDiGSPKFAYKLDWLDRLIRYLqKLLKPDDPLVLVGDFNIAPEDID 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 154 LKNPQSNHHNAGFTDEERQDFTKLLKAGFMDTFRHFYPDQtDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKI 233
Cdd:cd09086  156 VWDPKQLLGKVLFTPEEREALRALLDLGFVDAFRALHPDE-KLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGI 234

                        250
                 ....*....|....*.
gi 949496737 234 LTDVFG----SDHCPV 245
Cdd:cd09086  235 DREPRGwekpSDHAPV 250
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-248 4.92e-61

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: 194.46  E-value: 4.92e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   2 KFISWNVNGLRA-------AVKHDFAETFQQLDADFFCIQETKMQEGQLELD---LPGYQQYFNY-AERKGYSGTAIFTK 70
Cdd:cd09088    1 RIVTWNVNGIRTrlqyqpwNKENSLKSFLDSLDADIICLQETKLTRDELDEPsaiVEGYDSFFSFsRGRKGYSGVATYCR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  71 HA---PMHVTYGING-----------------------DEF---------DHEGRAITLEYPDFYLVTSYVP-NSGAGLK 114
Cdd:cd09088   81 DSaatPVAAEEGLTGvlsspnqknelsenddigcygemLEFtdskellelDSEGRCVLTDHGTFVLINVYCPrADPEKEE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 115 RLDFRMgwnkAFYQYLTE-----LDAKKPVILCGDLNVAHKEIDLKNPQSNHHNAGFTDEE---RQDFTKLLKAG----- 181
Cdd:cd09088  161 RLEFKL----DFYRLLEErvealLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLGDSgeggg 236

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 949496737 182 -----FMDTFRHFYPDQTDIYSWWSYRFHSRDRNAGWRIDYFVASNRLADQIEDSKILTDVFGSDHCPVELD 248
Cdd:cd09088  237 spgglLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYAD 308
PRK11756 PRK11756
exonuclease III; Provisional
 1-251 1.02e-41

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 143.50  E-value: 1.02e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAVkHDFAETFQQLDADFFCIQETKMQEGQLELDLP---GYQQYfnYAERKGYSGTAIFTKHAPMHVT 77
Cdd:PRK11756   1 MKFVSFNINGLRARP-HQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVealGYHVF--YHGQKGHYGVALLSKQTPIAVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  78 YGINGDEFDHEGRAITLEYPD----FYLVTSYVPNsgaGLKR---LDFRMgwNKAFYQ----YL-TELDAKKPVILCGDL 145
Cdd:PRK11756  78 KGFPTDDEEAQRRIIMATIPTpngnLTVINGYFPQ---GESRdhpTKFPA--KRQFYQdlqnYLeTELSPDNPLLIMGDM 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 146 NVAHKEIDLKNPQSNHH------NAGFTDEERQDFTKLLKAGFMDTFRHFYPDQTDIYSWWSYRFHSRDRNAGWRIDYFV 219
Cdd:PRK11756 153 NISPTDLDIGIGEENRKrwlrtgKCSFLPEEREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLIL 232

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 949496737 220 ASNRLADQIEDSKILTDVFG----SDHCPVELDTKL 251
Cdd:PRK11756 233 ATQPLAERCVETGIDYDIRGmekpSDHAPIWATFKL 268
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 4-247 4.74e-37

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: 130.68  E-value: 4.74e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   4 ISWNVNGLRAAVK-HDFAETFQQLDADFFCIQETK-MQEGQLELDLPGYQQYFNYA----ERKGYSGTAIFTK---HAPM 74
Cdd:cd08372    2 ASYNVNGLNAATRaSGIARWVRELDPDIVCLQEVKdSQYSAVALNQLLPEGYHQYQsgpsRKEGYEGVAILSKtpkFKIV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  75 HVTYGINGDEFDHEGRA----ITLEYPDFYLVTSYVPNSGaglKRLDFRMGWNKAFYQYLTEL--DAKKPVILCGDLNVA 148
Cdd:cd08372   82 EKHQYKFGEGDSGERRAvvvkFDVHDKELCVVNAHLQAGG---TRADVRDAQLKEVLEFLKRLrqPNSAPVVICGDFNVR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 149 HKEIDLKNPQSnhhnagftdeerqDFTKLLKAGFMDTFRHFypdqTDIYSWWSYrfhsrDRNAGWRIDYFVASNRLADQI 228
Cdd:cd08372  159 PSEVDSENPSS-------------MLRLFVALNLVDSFETL----PHAYTFDTY-----MHNVKSRLDYIFVSKSLLPSV 216

                        250       260
                 ....*....|....*....|...
gi 949496737 229 EDSKILTDV----FGSDHCPVEL 247
Cdd:cd08372  217 KSSKILSDAararIPSDHYPIEV 239
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-248 4.24e-22

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: 91.26  E-value: 4.24e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   3 FISWNVNGLRAAVK-HDFAETFQQLDADFFCIQETK-MQEGQLELDLPGYQQYFNYAERKGYSGTAIFTKH--APMHVTY 78
Cdd:cd09076    1 IGTLNVRGLRSPGKrAQLLEELKRKKLDILGLQETHwTGEGELKKKREGGTILYSGSDSGKSRGVAILLSKtaANKLLEY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  79 gingdEFDHEGRAITL----EYPDFYLVTSYVPNSGAGLKRLDfrmgwnkaFYQ----YLTELDAKKPVILCGDLN--VA 148
Cdd:cd09076   81 -----TKVVSGRIIMVrfkiKGKRLTIINVYAPTARDEEEKEE--------FYDqlqdVLDKVPRHDTLIIGGDFNavLG 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 149 HKEIDLKNPQSNHHNagftdEERQDFTKLLKAGFMDTFRHFYPDQTDiyswwsYRFHSRDRNAGWRIDYFVASNRLADQI 228
Cdd:cd09076  148 PKDDGRKGLDKRNEN-----GERALSALIEEHDLVDVWRENNPKTRE------YTWRSPDHGSRSRIDRILVSKRLRVKV 216

                        250       260
                 ....*....|....*....|
gi 949496737 229 EDSKIlTDVFGSDHCPVELD 248
Cdd:cd09076  217 KKTKI-TPGAGSDHRLVTLK 235
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-147 7.83e-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: 73.41  E-value: 7.83e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737    4 ISWNVNGLRA------AVKHDFAETFQQLDADFFCIQETKMQEGQ----LELDLPGYQQYFNYAERKGYSGTAIFTKHAP 73
Cdd:pfam03372   1 LTWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASrlllALLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 949496737   74 MHVTYGINGDEFDHEGR-AITLEYPDFYLVTSYVPNSGAGLKRLDFRMGWNKAFYQYLTELDAKKPVILCGDLNV 147
Cdd:pfam03372  81 SSVILVDLGEFGDPALRgAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 4-245 1.64e-05

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


Pssm-ID: 197318 [Multi-domain]  Cd Length: 246  Bit Score: 44.98  E-value: 1.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   4 ISWNVNGLR----AAVKHDFAETFQQLDADFFCIQETKMQEGQ----LELDLPGYQ-QYFNYAERKGYSGTAIFTKH--- 71
Cdd:cd09084    2 MSYNVRSFNrykwKDDPDKILDFIKKQDPDILCLQEYYGSEGDkdddLRLLLKGYPyYYVVYKSDSGGTGLAIFSKYpil 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  72 --APMHVTYGINGD---EFDHEGRAITL---------EYPDFYLVTSYVPNSGAGLKRLDFRMGWN--------KAFYQY 129
Cdd:cd09084   82 nsGSIDFPNTNNNAifaDIRVGGDTIRVynvhlesfrITPSDKELYKEEKKAKELSRNLLRKLAEAfkrraaqaDLLAAD 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 130 LTEldAKKPVILCGDLN-----VAHKEIdlknpqSNHHNAGFTDEERqdftkllkaGFMDTFRHFYPdqtdiyswwsyrf 204
Cdd:cd09084  162 IAA--SPYPVIVCGDFNdtpasYVYRTL------KKGLTDAFVEAGS---------GFGYTFNGLFF------------- 211

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 949496737 205 hsrdrnaGWRIDYFVASNRLadQIEDSKILTDVfGSDHCPV 245
Cdd:cd09084  212 -------PLRIDYILTSKGF--KVLRYRVDPGK-YSDHYPI 242
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 128-245 9.30e-05

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: 42.59  E-value: 9.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 128 QYLTELDAKKPVILCGDLNVahkeidlkNPQSNHHNAgftdeerqdftkLLKAGFMDTFRHfyPDQTDIYSWWSyrFHS- 206
Cdd:cd09083  152 ERIKEIAGDLPVILTGDFNA--------EPDSEPYKT------------LTSGGLKDARDT--AATTDGGPEGT--FHGf 207

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 949496737 207 RDRNAGWRIDYFVASNRLadQIEDSKILTDVFG----SDHCPV 245
Cdd:cd09083  208 KGPPGGSRIDYIFVSPGV--KVLSYEILTDRYDgrypSDHFPV 248
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
122-252 3.34e-04

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 41.16  E-value: 3.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 122 WNKAFYQYLTELDAKKPVILCGDLNvahkeidlknpqsnhhnagftDEERQD-FTKLLKA-GFMDTFRHFYPDQTdiysw 199
Cdd:COG2374  239 ALRAFVDSLLAADPDAPVIVLGDFN---------------------DYPFEDpLRALLGAgGLTNLAEKLPAAER----- 292

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 949496737 200 WSYRFhsrDRNAGwRIDYFVASNRLADQIED-------SKILTDVFG-------------SDHCPVELDTKLP 252
Cdd:COG2374  293 YSYVY---DGNSG-LLDHILVSPALAARVTGadiwhinADIYNDDFKpdfrtyaddpgraSDHDPVVVGLRLP 361
nSMase cd09078
Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological ...
 138-249 1.50e-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: 39.25  E-value: 1.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 138 PVILCGDLNVahkeidlknpqsnhhNAGFTDEERQDFTKLLKAGFMDTFRHF----YPDQTDIYSWWSYRFhsrDRNAGW 213
Cdd:cd09078  169 PVIIAGDFNV---------------DKRSSRDEYDDMLEQLHDYNAPEPITAgetpLTWDPGTNLLAKYNY---PGGGGE 230

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 949496737 214 RIDYFVASNRLA------DQIEDSKILTDVFG--------SDHCPVELDT 249
Cdd:cd09078  231 RLDYILYSNDHLqpsswsNEVEVPKSPTWSVTngytfadlSDHYPVSATF 280
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 1-242 2.18e-03

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


Pssm-ID: 197311 [Multi-domain]  Cd Length: 205  Bit Score: 38.04  E-value: 2.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737   1 MKFISWNVNGLRAAvkHDFAETFQ-QLDADFFCIQETkmqegqleldlpgyqqYFNYAERKGY----SGTA---IFTKHA 72
Cdd:cd09077    1 LRILQINLNRCKAA--QDLLLQTArEEGADIALIQEP----------------YLVPVNNPNWvtdeSGRAaivVSDRLP 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737  73 PMHVTYGINGDEFdhegRAITLEypDFYLVTSYVPNSGAGLKrldfrmgwnkaFYQYLTELDAK-----KPVILCGDLNV 147
Cdd:cd09077   63 RKPIQRLSLGLGI----VAARVG--GITVVSCYAPPSESLEE-----------FEEYLENLVRIvrglsRPVIIGGDFNA 125

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949496737 148 AHKEIDlknpqSNHHNA------GFTDEErqDFTkLLKAGFMDTFRHfypdqtdiyswwsyrfhsrdRNAGWRIDYFVAS 221
Cdd:cd09077  126 WSPAWG-----SKRTDRrgrlleDWIANL--GLV-LLNDGNSPTFVR--------------------PRGTSIIDVTFCS 177

                        250       260
                 ....*....|....*....|.
gi 949496737 222 NRLADQIEDSKILTDVFGSDH 242
Cdd:cd09077  178 PSLARRISNWRVLEDETLSDH 198
 
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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