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Conserved domains on  [gi|1196667353|ref|WP_086249239|]
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MULTISPECIES: exodeoxyribonuclease III [Campylobacter]

Protein Classification

exonuclease/endonuclease/phosphatase family protein( domain architecture ID 662)

exonuclease/endonuclease/phosphatase (EEP) family protein may cleave phosphodiester bonds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EEP super family cl00490
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 1-250 8.85e-124

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


The actual alignment was detected with superfamily member cd09085:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 252  Bit Score: 351.96  E-value: 8.85e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKNGFEWLRDFGVDYIGLQEIKAKDDQIPKEIYNLGFDNIVLNSAQKAGYSGVMSMAKFGYESNK 80
Cdd:cd09085     1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  81 CRFFE---DSEGRVLEHRFGNIVLFNIYFPNGQQGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNTAHREIDLKN 157
Cdd:cd09085    81 EGLGVeefDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLAR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 158 PKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKiDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFILNE 237
Cdd:cd09085   161 PKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKEP-GQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPD 239

                         250
                  ....*....|...
gi 1196667353 238 IEGSDHCPVGIDI 250
Cdd:cd09085   240 VMGSDHCPVSLEL 252
 
Name Accession Description Interval E-value
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-250 8.85e-124

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: 351.96  E-value: 8.85e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKNGFEWLRDFGVDYIGLQEIKAKDDQIPKEIYNLGFDNIVLNSAQKAGYSGVMSMAKFGYESNK 80
Cdd:cd09085     1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  81 CRFFE---DSEGRVLEHRFGNIVLFNIYFPNGQQGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNTAHREIDLKN 157
Cdd:cd09085    81 EGLGVeefDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLAR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 158 PKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKiDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFILNE 237
Cdd:cd09085   161 PKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKEP-GQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPD 239

                         250
                  ....*....|...
gi 1196667353 238 IEGSDHCPVGIDI 250
Cdd:cd09085   240 VMGSDHCPVSLEL 252
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-251 3.54e-113

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 325.11  E-value: 3.54e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKNgFEWLRDFGVDYIGLQEIKAKDDQIPKEIYN-LGFdNIVLNSaQKaGYSGVMSMAKFGYESN 79
Cdd:COG0708     1 MKIASWNVNGIRARLPKL-LDWLAEEDPDVLCLQETKAQDEQFPLEAFEaAGY-HVYFHG-QK-GYNGVAILSRLPPEDV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  80 KCRF---FEDSEGRVLEHRFGNIVLFNIYFPNGQ-QGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNTAHREIDL 155
Cdd:COG0708    77 RRGLggdEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 156 KNPKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKIDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFIL 235
Cdd:COG0708   157 KNPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGID 236

                         250       260
                  ....*....|....*....|
gi 1196667353 236 NEIEG----SDHCPVGIDID 251
Cdd:COG0708   237 REPRGderpSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-251 9.30e-97

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: 283.40  E-value: 9.30e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKNGFEWLRDFGVDYIGLQEIKAKDDQIPKEIY-NLGFDNIVlnSAQKAGYSGVMSMAKFGYESN 79
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFeELGYHVFF--HGAKKGYSGVAILSKVEPLDV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  80 KCRF---FEDSEGRVLEHRFGNIVLFNIYFPNGQ-QGDDRLEYKMAFYDKFLE-YIKELNAsGLEIIFCGDVNTAHREID 154
Cdd:TIGR00633  79 RYGFggePHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKLQFWDALFQyLEKELDA-GKPVVICGDMNVAHTEID 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 155 LKNPKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKIDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFI 234
Cdd:TIGR00633 158 LGNPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYI 237

                         250
                  ....*....|....*..
gi 1196667353 235 LNEIEGSDHCPVGIDID 251
Cdd:TIGR00633 238 DSEIRGSDHCPIVLELD 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-250 5.88e-65

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 202.62  E-value: 5.88e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKNGFEWLRDFGVDYIGLQEIKAKDDQIPKEIYNLgFDniVLNSAQKAGYSGVMSMAK------- 73
Cdd:PRK13911    1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGY-FD--FWNCAIKKGYSGVVTFTKkeplsvs 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  74 FGYESNKcrffEDSEGRVLEHRFGNIVLFNIYFPNGQQGDDRLEYKMAFYDKFLEYIKELNASGlEIIFCGDVNTAHREI 153
Cdd:PRK13911   78 YGINIEE----HDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKK-PVIVCGDLNVAHNEI 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 154 DLKNPKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKIDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAF 233
Cdd:PRK13911  153 DLENPKTNRKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDAL 232

                         250
                  ....*....|....*..
gi 1196667353 234 ILNEIEGSDHCPVGIDI 250
Cdd:PRK13911  233 IYKDILGSDHCPVGLEL 249
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-148 1.44e-09

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: 56.08  E-value: 1.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   4 ISWNVNGLRAVVNKNGF------EWLRDFGVDYIGLQEIKAKDDQIPKEIYN-LGFDNIVLNSAQKAGYSGVMSMAKFGY 76
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRkldalaALIRAYDPDVVALQETDDDDASRLLLALLaYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1196667353  77 ESNKCRFFEDSEGRVLEH---RFGNIVLFNIYFPNGQQGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNT 148
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGaiaPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-250 8.85e-124

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: 351.96  E-value: 8.85e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKNGFEWLRDFGVDYIGLQEIKAKDDQIPKEIYNLGFDNIVLNSAQKAGYSGVMSMAKFGYESNK 80
Cdd:cd09085     1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  81 CRFFE---DSEGRVLEHRFGNIVLFNIYFPNGQQGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNTAHREIDLKN 157
Cdd:cd09085    81 EGLGVeefDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLAR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 158 PKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKiDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFILNE 237
Cdd:cd09085   161 PKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKEP-GQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPD 239

                         250
                  ....*....|...
gi 1196667353 238 IEGSDHCPVGIDI 250
Cdd:cd09085   240 VMGSDHCPVSLEL 252
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-251 3.54e-113

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 325.11  E-value: 3.54e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKNgFEWLRDFGVDYIGLQEIKAKDDQIPKEIYN-LGFdNIVLNSaQKaGYSGVMSMAKFGYESN 79
Cdd:COG0708     1 MKIASWNVNGIRARLPKL-LDWLAEEDPDVLCLQETKAQDEQFPLEAFEaAGY-HVYFHG-QK-GYNGVAILSRLPPEDV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  80 KCRF---FEDSEGRVLEHRFGNIVLFNIYFPNGQ-QGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNTAHREIDL 155
Cdd:COG0708    77 RRGLggdEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 156 KNPKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKIDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFIL 235
Cdd:COG0708   157 KNPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGID 236

                         250       260
                  ....*....|....*....|
gi 1196667353 236 NEIEG----SDHCPVGIDID 251
Cdd:COG0708   237 REPRGderpSDHAPVVVELD 256
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-250 3.43e-101

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: 294.84  E-value: 3.43e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKNGFEWLRDFGVDYIGLQEIKAKDDQIPKEI-YNLGFDNIVLNSAQKAGYSGVMSMAKfgYESN 79
Cdd:cd09087     1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELkELLKGYHQYWNAAEKKGYSGTAILSK--KKPL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  80 KCRF-----FEDSEGRVLEHRFGNIVLFNIYFPNGQQGDDRLEYKMAFYDKFLEYIKELNaSGLEIIFCGDVNTAHREID 154
Cdd:cd09087    79 SVTYgigieEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLD-SKKPVIWCGDLNVAHEEID 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 155 LKNPKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKIDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFI 234
Cdd:cd09087   158 LANPKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFI 237

                         250
                  ....*....|....*.
gi 1196667353 235 LNEIEGSDHCPVGIDI 250
Cdd:cd09087   238 RSDIMGSDHCPIGLEL 253
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-248 3.88e-101

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: 294.58  E-value: 3.88e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   2 RLISWNVNGLRAVVNKNGFEWLRDFGVDYIGLQEIKAKDDQIPKEIYNLGFDNIVLNSAQKAGYSGVMSMAK-------F 74
Cdd:cd09073     1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPARKKGYSGVATLSKeepldvsY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  75 GYESNKcrffEDSEGRVLEHRFGNIVLFNIYFPNGQQGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNTAHREID 154
Cdd:cd09073    81 GIGGEE----FDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEID 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 155 LKNPKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKiDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFI 234
Cdd:cd09073   157 LARPKKNEKNAGFTPEERAWFDKLLSLGYVDTFRHFHPEP-GAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGI 235

                         250
                  ....*....|....
gi 1196667353 235 LNEIEGSDHCPVGI 248
Cdd:cd09073   236 LSKVKGSDHAPVTL 249
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-251 9.30e-97

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: 283.40  E-value: 9.30e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKNGFEWLRDFGVDYIGLQEIKAKDDQIPKEIY-NLGFDNIVlnSAQKAGYSGVMSMAKFGYESN 79
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFeELGYHVFF--HGAKKGYSGVAILSKVEPLDV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  80 KCRF---FEDSEGRVLEHRFGNIVLFNIYFPNGQ-QGDDRLEYKMAFYDKFLE-YIKELNAsGLEIIFCGDVNTAHREID 154
Cdd:TIGR00633  79 RYGFggePHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKLQFWDALFQyLEKELDA-GKPVVICGDMNVAHTEID 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 155 LKNPKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKIDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFI 234
Cdd:TIGR00633 158 LGNPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYI 237

                         250
                  ....*....|....*..
gi 1196667353 235 LNEIEGSDHCPVGIDID 251
Cdd:TIGR00633 238 DSEIRGSDHCPIVLELD 254
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-250 4.42e-94

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: 276.80  E-value: 4.42e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKNGFEWLRDFGVDYIGLQEIKAKDDQIPKEIYNLGFDNIVLNSAQKAGYSGV--MSMAKFGYES 78
Cdd:cd10281     1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDAEKKGYAGVaiYSRTQPKAVI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  79 NKCRFFE-DSEGRVLEHRFGNIVLFNIYFPNGQQGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNTAHREIDLKN 157
Cdd:cd10281    81 YGLGFEEfDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 158 PKANSKTSGFLPVERAWIDRVI-EAGFIDTFRYINADKiDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFILN 236
Cdd:cd10281   161 WKANQKNSGFLPEERAWLDQVFgELGYVDAFRELNPDE-GQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYR 239

                         250
                  ....*....|....
gi 1196667353 237 EIEGSDHCPVGIDI 250
Cdd:cd10281   240 EERFSDHAPLIVDY 253
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-250 8.56e-87

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: 258.08  E-value: 8.56e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKnGFEWLRDFGVDYIGLQEIKAKDDQIPKEIY-NLGFDniVLNSAQKaGYSGVMSMAKFGYESN 79
Cdd:TIGR00195   1 MKIISWNVNGLRARPHK-GLAWLKENQPDVLCLQETKVQDEQFPLEPFhKEGYH--VFFSGQK-GYSGVAIFSKEEPISV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  80 KCRF---FEDSEGRVLEHRFGNIVLFNIYFPNG-QQGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNTAHREIDL 155
Cdd:TIGR00195  77 RRGFgveEEDAEGRIIMAEFDSFLVINGYFPNGsRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 156 KNPKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKiDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFIL 235
Cdd:TIGR00195 157 HIPDENRNHTGFLPEEREWLDRLLEAGLVDTFRKFNPDE-GAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGID 235

                         250
                  ....*....|....*....
gi 1196667353 236 NEIEG----SDHCPVGIDI 250
Cdd:TIGR00195 236 YDIRGsekpSDHCPVVLEF 254
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-246 1.19e-68

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: 211.99  E-value: 1.19e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNkNGFEWLRDFGVDYIGLQEIKAKDDQIP-KEIYNLGFDNIVlnSAQKAgYSGVMSMAKFGYESN 79
Cdd:cd09086     1 MKIATWNVNSIRARLE-QVLDWLKEEDPDVLCLQETKVEDDQFPaDAFEALGYHVAV--HGQKA-YNGVAILSRLPLEDV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  80 KCRFF---EDSEGRVLEHRFGNIVLFNIYFPNGQ-QGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNTAHREIDL 155
Cdd:cd09086    77 RTGFPgdpDDDQARLIAARVGGVRVINLYVPNGGdIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 156 KNPKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKiDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFIL 235
Cdd:cd09086   157 WDPKQLLGKVLFTPEEREALRALLDLGFVDAFRALHPDE-KLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGID 235

                         250
                  ....*....|....*
gi 1196667353 236 NEIEG----SDHCPV 246
Cdd:cd09086   236 REPRGwekpSDHAPV 250
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-250 5.88e-65

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 202.62  E-value: 5.88e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLRAVVNKNGFEWLRDFGVDYIGLQEIKAKDDQIPKEIYNLgFDniVLNSAQKAGYSGVMSMAK------- 73
Cdd:PRK13911    1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGY-FD--FWNCAIKKGYSGVVTFTKkeplsvs 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  74 FGYESNKcrffEDSEGRVLEHRFGNIVLFNIYFPNGQQGDDRLEYKMAFYDKFLEYIKELNASGlEIIFCGDVNTAHREI 153
Cdd:PRK13911   78 YGINIEE----HDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKK-PVIVCGDLNVAHNEI 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 154 DLKNPKANSKTSGFLPVERAWIDRVIEAGFIDTFRYINADKIDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAF 233
Cdd:PRK13911  153 DLENPKTNRKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDAL 232

                         250
                  ....*....|....*..
gi 1196667353 234 ILNEIEGSDHCPVGIDI 250
Cdd:PRK13911  233 IYKDILGSDHCPVGLEL 249
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-250 2.50e-54

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: 177.12  E-value: 2.50e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   2 RLISWNVNGLRAVVN------KNGFEWLRD-FGVDYIGLQEIKAKDDQIPKEI-----YNlGFDNIvlnSAQKAGYSGVm 69
Cdd:cd09088     1 RIVTWNVNGIRTRLQyqpwnkENSLKSFLDsLDADIICLQETKLTRDELDEPSaivegYD-SFFSF---SRGRKGYSGV- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  70 smAKF----------------GYESNKCRFFE-------------------------DSEGRVLEHRFGNIVLFNIYFP- 107
Cdd:cd09088    76 --ATYcrdsaatpvaaeegltGVLSSPNQKNElsenddigcygemleftdskellelDSEGRCVLTDHGTFVLINVYCPr 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 108 NGQQGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNTAHREIDLKNPKANSKTSGFLPVE---RAWIDRVIEAG-- 182
Cdd:cd09088   154 ADPEKEERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLGDSge 233

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1196667353 183 --------FIDTFRYINADKIDAYSWWSYRFNARAKNVGWRIDYFFISKGLKDKLKDAFILNEIEGSDHCPVGIDI 250
Cdd:cd09088   234 gggspgglLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYADL 309
PRK11756 PRK11756
exonuclease III; Provisional
 1-252 2.99e-46

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 155.05  E-value: 2.99e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   1 MRLISWNVNGLR-------AVVNKngfewlrdFGVDYIGLQEIKAKDDQIP-KEIYNLGFDniVLNSAQKAGYsGVMSMA 72
Cdd:PRK11756    1 MKFVSFNINGLRarphqleAIIEK--------HQPDVIGLQETKVHDEMFPlEEVEALGYH--VFYHGQKGHY-GVALLS 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  73 K-------FGYESNkcrfFEDSEGRV----LEHRFGNIVLFNIYFPngqQGDDR-----LEYKMAFYDKFLEYIKELNAS 136
Cdd:PRK11756   70 KqtpiavrKGFPTD----DEEAQRRIimatIPTPNGNLTVINGYFP---QGESRdhptkFPAKRQFYQDLQNYLETELSP 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 137 GLEIIFCGDVNTAHREIDL----KNPK---ANSKTSgFLPVERAWIDRVIEAGFIDTFRYINADKIDAYSWWSYRFNARA 209
Cdd:PRK11756  143 DNPLLIMGDMNISPTDLDIgigeENRKrwlRTGKCS-FLPEEREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFD 221

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1196667353 210 KNVGWRIDYFFISKGLKDKLKDAFILNEIEG----SDHCPVGIDIDL 252
Cdd:PRK11756  222 DNRGLRIDLILATQPLAERCVETGIDYDIRGmekpSDHAPIWATFKL 268
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-250 1.05e-32

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: 119.12  E-value: 1.05e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   3 LISWNVNGLRAVVNKNGF-EWLRDFGVDYIGLQEIK---AKDDQIPKEIYNlGFDNIVLNSAQKAGYSGV--------MS 70
Cdd:cd08372     1 VASYNVNGLNAATRASGIaRWVRELDPDIVCLQEVKdsqYSAVALNQLLPE-GYHQYQSGPSRKEGYEGVailsktpkFK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  71 MAKFGYESNKCRFfeDSEGRVLEHRFG----NIVLFNIYFPNGqqgDDRLEYKMAFYDKFLEYIKELNA-SGLEIIFCGD 145
Cdd:cd08372    80 IVEKHQYKFGEGD--SGERRAVVVKFDvhdkELCVVNAHLQAG---GTRADVRDAQLKEVLEFLKRLRQpNSAPVVICGD 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 146 VNTAHREIDLKNPKAnsktsgflpveraWIDRVIEAGFIDTFRyinaDKIDAYSWWSYRfnaraKNVGWRIDYFFISKGL 225
Cdd:cd08372   155 FNVRPSEVDSENPSS-------------MLRLFVALNLVDSFE----TLPHAYTFDTYM-----HNVKSRLDYIFVSKSL 212

                         250       260
                  ....*....|....*....|....*....
gi 1196667353 226 KDKLKDAFILNE----IEGSDHCPVGIDI 250
Cdd:cd08372   213 LPSVKSSKILSDaaraRIPSDHYPIEVTL 241
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-246 2.08e-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: 2.08e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   3 LISWNVNGLRAVVN-KNGFEWLRDFGVDYIGLQEIKAKDDQIPKeiYNLGFDNIVLNSAQKAGYSGVMSMAKFGYESNKC 81
Cdd:cd09076     1 IGTLNVRGLRSPGKrAQLLEELKRKKLDILGLQETHWTGEGELK--KKREGGTILYSGSDSGKSRGVAILLSKTAANKLL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  82 RFFEDSEGRVL----EHRFGNIVLFNIYFPNGQQGDDRLEykmaFYDKFLEYIKELNASGLeIIFCGDVNTAHREIDLKN 157
Cdd:cd09076    79 EYTKVVSGRIImvrfKIKGKRLTIINVYAPTARDEEEKEE----FYDQLQDVLDKVPRHDT-LIIGGDFNAVLGPKDDGR 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 158 PKANSKTSGFlpvERAWIDRVIEAGFIDTFRYINADKIdAYSWWSYRFNARAknvgwRIDYFFISKGLKDKLKDAFILNE 237
Cdd:cd09076   154 KGLDKRNENG---ERALSALIEEHDLVDVWRENNPKTR-EYTWRSPDHGSRS-----RIDRILVSKRLRVKVKKTKITPG 224


                  ....*....
gi 1196667353 238 IeGSDHCPV 246
Cdd:cd09076   225 A-GSDHRLV 232
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-148 1.44e-09

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: 56.08  E-value: 1.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   4 ISWNVNGLRAVVNKNGF------EWLRDFGVDYIGLQEIKAKDDQIPKEIYN-LGFDNIVLNSAQKAGYSGVMSMAKFGY 76
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRkldalaALIRAYDPDVVALQETDDDDASRLLLALLaYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1196667353  77 ESNKCRFFEDSEGRVLEH---RFGNIVLFNIYFPNGQQGDDRLEYKMAFYDKFLEYIKELNASGLEIIFCGDVNT 148
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGaiaPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 127-250 7.99e-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: 7.99e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 127 LEYIKELNAsGLEIIFCGDVNTahreidlknpkansktsgflPVERAWIDRVIEAGFIDTFRyiNADKIDAYSWWSY-RF 205
Cdd:cd09083   151 LERIKEIAG-DLPVILTGDFNA--------------------EPDSEPYKTLTSGGLKDARD--TAATTDGGPEGTFhGF 207

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1196667353 206 NARAKnvGWRIDYFFISKGLKdkLKDAFILNEIEG----SDHCPVGIDI 250
Cdd:cd09083   208 KGPPG--GSRIDYIFVSPGVK--VLSYEILTDRYDgrypSDHFPVVADL 252
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 3-246 9.24e-04

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: 39.59  E-value: 9.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353   3 LISWNVNGLRAVVNKNGFE----WLRDFGVDYIGLQEIKAKDDQIPKEIYNL--GFDNIVLNSAQKAGYSGVMSMAKFGY 76
Cdd:cd09084     1 VMSYNVRSFNRYKWKDDPDkildFIKKQDPDILCLQEYYGSEGDKDDDLRLLlkGYPYYYVVYKSDSGGTGLAIFSKYPI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353  77 ESNKCRFFEDSEGRVL--EHRFGN--IVLFNIYFP-NGQQGDDRLEYKMAFYDK-----FLEYIKE-------------- 132
Cdd:cd09084    81 LNSGSIDFPNTNNNAIfaDIRVGGdtIRVYNVHLEsFRITPSDKELYKEEKKAKelsrnLLRKLAEafkrraaqadllaa 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196667353 133 -LNASGLEIIFCGDVNtahreidlknpkaNSKTSGFLpverawidRVIEAGFIDTFRyinadkiDAYSWWSYRFNARAKn 211
Cdd:cd09084   161 dIAASPYPVIVCGDFN-------------DTPASYVY--------RTLKKGLTDAFV-------EAGSGFGYTFNGLFF- 211

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1196667353 212 vGWRIDYFFISKGLkdKLKDAFILNEIeGSDHCPV 246
Cdd:cd09084   212 -PLRIDYILTSKGF--KVLRYRVDPGK-YSDHYPI 242
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 205-252 9.58e-04

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 38.74  E-value: 9.58e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1196667353 205 FNAraknvgwrIDYFFISKGLKdkLKDAFILNEIEG---SDHCPVGIDIDL 252
Cdd:COG3568   126 FND--------IDYILVSPGLR--VLSAEVLDSPLGraaSDHLPVVADLEL 166
 
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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