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Conserved domains on  [gi|644636476|ref|WP_025345266|]
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exodeoxyribonuclease III [Sulfurospirillum multivorans]

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 ...
 1-252 2.26e-132

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: 373.92  E-value: 2.26e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   1 MKLISWNVNGIRAVANKNAFAWVDEFAPNVLCLQEIKAEAEQIPEPLFSHTFTCKHVNSASKKGYSGTMSFSTLPFEKTD 80
Cdd:cd09085    1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  81 TAWHI-DHTHEGRILEHHFGDVALFNVYFPNGQQSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHRAIDLKN 159
Cdd:cd09085   81 EGLGVeEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLAR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 160 PKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDiTDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDAFILSH 239
Cdd:cd09085  161 PKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKE-PGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPD 239

                        250
                 ....*....|...
gi 644636476 240 IGGSDHCPVGIEI 252
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 ...
 1-252 2.26e-132

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: 373.92  E-value: 2.26e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   1 MKLISWNVNGIRAVANKNAFAWVDEFAPNVLCLQEIKAEAEQIPEPLFSHTFTCKHVNSASKKGYSGTMSFSTLPFEKTD 80
Cdd:cd09085    1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  81 TAWHI-DHTHEGRILEHHFGDVALFNVYFPNGQQSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHRAIDLKN 159
Cdd:cd09085   81 EGLGVeEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLAR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 160 PKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDiTDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDAFILSH 239
Cdd:cd09085  161 PKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKE-PGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPD 239

                        250
                 ....*....|...
gi 644636476 240 IGGSDHCPVGIEI 252
Cdd:cd09085  240 VMGSDHCPVSLEL 252
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-253 7.35e-117

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 334.74  E-value: 7.35e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   1 MKLISWNVNGIRAVANKnAFAWVDEFAPNVLCLQEIKAEAEQIPEPLFS----HTFTckhvnsASKKGYSGTMSFSTLPF 76
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAFEaagyHVYF------HGQKGYNGVAILSRLPP 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  77 EKTDTAW-HIDHTHEGRILEHHFGDVALFNVYFPNGQ-QSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHRA 154
Cdd:COG0708   74 EDVRRGLgGDEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 155 IDLKNPKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDITDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDA 234
Cdd:COG0708  154 IDVKNPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDA 233

                        250       260
                 ....*....|....*....|...
gi 644636476 235 FILSH----IGGSDHCPVGIEID 253
Cdd:COG0708  234 GIDREprgdERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-253 1.89e-99

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: 290.33  E-value: 1.89e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476    1 MKLISWNVNGIRAVANKNAFAWVDEFAPNVLCLQEIKAEAEQIPEPLFSHTfTCKHVNSASKKGYSGTMSFSTLP----F 76
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEEL-GYHVFFHGAKKGYSGVAILSKVEpldvR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   77 EKTDTAwhiDHTHEGRILEHHFGDVALFNVYFPNGQ-QSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHRAI 155
Cdd:TIGR00633  80 YGFGGE---PHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEI 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  156 DLKNPKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDITDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDAF 235
Cdd:TIGR00633 157 DLGNPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSY 236

                         250
                  ....*....|....*...
gi 644636476  236 ILSHIGGSDHCPVGIEID 253
Cdd:TIGR00633 237 IDSEIRGSDHCPIVLELD 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-252 1.44e-66

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 206.85  E-value: 1.44e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   1 MKLISWNVNGIRAVANKNAFAWVDEFAPNVLCLQEIKAEAEQipeplfsHTFTCKHV----NSASKKGYSGTMSFSTLpf 76
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQ-------NTFEFKGYfdfwNCAIKKGYSGVVTFTKK-- 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  77 EKTDTAWHI---DHTHEGRILEHHFGDVALFNVYFPNGQQSEERLAHKLKFYSDFLAHTEALRKEgKGIIICGDVNTAHR 153
Cdd:PRK13911  72 EPLSVSYGInieEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELK-KPVIVCGDLNVAHN 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 154 AIDLKNPKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDITDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRD 233
Cdd:PRK13911 151 EIDLENPKTNRKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKD 230

                        250
                 ....*....|....*....
gi 644636476 234 AFILSHIGGSDHCPVGIEI 252
Cdd:PRK13911 231 ALIYKDILGSDHCPVGLEL 249
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-150 1.32e-12

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: 64.55  E-value: 1.32e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476    4 ISWNVNGIRAVANKNAF------AWVDEFAPNVLCLQEIKAEAEQ-IPEPLFSHTFTCKHVNSASKKGYSGTMSFSTLP- 75
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRkldalaALIRAYDPDVVALQETDDDDASrLLLALLAYGGFLSYGGPGGGGGGGGVAILSRYPl 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 644636476   76 FEKTDTAWHIDHTHEGRILEHHFGDVALFNVYFPNGQQSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNT 150
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 ...
 1-252 2.26e-132

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: 373.92  E-value: 2.26e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   1 MKLISWNVNGIRAVANKNAFAWVDEFAPNVLCLQEIKAEAEQIPEPLFSHTFTCKHVNSASKKGYSGTMSFSTLPFEKTD 80
Cdd:cd09085    1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  81 TAWHI-DHTHEGRILEHHFGDVALFNVYFPNGQQSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHRAIDLKN 159
Cdd:cd09085   81 EGLGVeEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLAR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 160 PKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDiTDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDAFILSH 239
Cdd:cd09085  161 PKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKE-PGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPD 239

                        250
                 ....*....|...
gi 644636476 240 IGGSDHCPVGIEI 252
Cdd:cd09085  240 VMGSDHCPVSLEL 252
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-253 7.35e-117

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 334.74  E-value: 7.35e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   1 MKLISWNVNGIRAVANKnAFAWVDEFAPNVLCLQEIKAEAEQIPEPLFS----HTFTckhvnsASKKGYSGTMSFSTLPF 76
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAFEaagyHVYF------HGQKGYNGVAILSRLPP 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  77 EKTDTAW-HIDHTHEGRILEHHFGDVALFNVYFPNGQ-QSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHRA 154
Cdd:COG0708   74 EDVRRGLgGDEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 155 IDLKNPKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDITDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDA 234
Cdd:COG0708  154 IDVKNPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDA 233

                        250       260
                 ....*....|....*....|...
gi 644636476 235 FILSH----IGGSDHCPVGIEID 253
Cdd:COG0708  234 GIDREprgdERPSDHAPVVVELD 256
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-252 1.05e-103

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: 301.13  E-value: 1.05e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   2 KLISWNVNGIRAVANKNAFAWVDEFAPNVLCLQEIKAEAEQIPEPLFSHTFTCKHVNSASKKGYSGTMSFSTLPFEKTDT 81
Cdd:cd09073    1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPARKKGYSGVATLSKEEPLDVSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  82 AWHID-HTHEGRILEHHFGDVALFNVYFPNGQQSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHRAIDLKNP 160
Cdd:cd09073   81 GIGGEeFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEIDLARP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 161 KANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDiTDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDAFILSHI 240
Cdd:cd09073  161 KKNEKNAGFTPEERAWFDKLLSLGYVDTFRHFHPE-PGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILSKV 239

                        250
                 ....*....|..
gi 644636476 241 GGSDHCPVGIEI 252
Cdd:cd09073  240 KGSDHAPVTLEL 251
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-252 1.66e-102

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: 297.93  E-value: 1.66e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   1 MKLISWNVNGIRAVANKNAFAWVDEFAPNVLCLQEIKAEAEQIPE---PLFSHTFTckHVNSASKKGYSGTMSFStlPFE 77
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKelkELLKGYHQ--YWNAAEKKGYSGTAILS--KKK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  78 KTDTAWHID---HTHEGRILEHHFGDVALFNVYFPNGQQSEERLAHKLKFYSDFLAHTEALRKeGKGIIICGDVNTAHRA 154
Cdd:cd09087   77 PLSVTYGIGieeHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDS-KKPVIWCGDLNVAHEE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 155 IDLKNPKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDITDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDA 234
Cdd:cd09087  156 IDLANPKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDS 235

                        250
                 ....*....|....*...
gi 644636476 235 FILSHIGGSDHCPVGIEI 252
Cdd:cd09087  236 FIRSDIMGSDHCPIGLEL 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-253 1.89e-99

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: 290.33  E-value: 1.89e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476    1 MKLISWNVNGIRAVANKNAFAWVDEFAPNVLCLQEIKAEAEQIPEPLFSHTfTCKHVNSASKKGYSGTMSFSTLP----F 76
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEEL-GYHVFFHGAKKGYSGVAILSKVEpldvR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   77 EKTDTAwhiDHTHEGRILEHHFGDVALFNVYFPNGQ-QSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHRAI 155
Cdd:TIGR00633  80 YGFGGE---PHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEI 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  156 DLKNPKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDITDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDAF 235
Cdd:TIGR00633 157 DLGNPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSY 236

                         250
                  ....*....|....*...
gi 644636476  236 ILSHIGGSDHCPVGIEID 253
Cdd:TIGR00633 237 IDSEIRGSDHCPIVLELD 254
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-252 1.07e-92

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: 273.49  E-value: 1.07e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476    1 MKLISWNVNGIRAVANKnAFAWVDEFAPNVLCLQEIKAEAEQIPEPLFSHTftCKHVNSASKKGYSGTMSFSTLPFEKTD 80
Cdd:TIGR00195   1 MKIISWNVNGLRARPHK-GLAWLKENQPDVLCLQETKVQDEQFPLEPFHKE--GYHVFFSGQKGYSGVAIFSKEEPISVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   81 TAWHID-HTHEGRILEHHFGDVALFNVYFPNG-QQSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHRAIDLK 158
Cdd:TIGR00195  78 RGFGVEeEDAEGRIIMAEFDSFLVINGYFPNGsRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDLH 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  159 NPKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDiTDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDAFILS 238
Cdd:TIGR00195 158 IPDENRNHTGFLPEEREWLDRLLEAGLVDTFRKFNPD-EGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDY 236

                         250
                  ....*....|....*...
gi 644636476  239 HIGG----SDHCPVGIEI 252
Cdd:TIGR00195 237 DIRGsekpSDHCPVVLEF 254
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-252 4.28e-85

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: 254.07  E-value: 4.28e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   1 MKLISWNVNGIRAVANKNAFAWVDEFAPNVLCLQEIKAEAEQIPEPLFSHTFTCKHVNSASKKGYSGTMSFST------- 73
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDAEKKGYAGVAIYSRtqpkavi 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  74 --LPFEKTDTawhidhthEGRILEHHFGDVALFNVYFPNGQQSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTA 151
Cdd:cd10281   81 ygLGFEEFDD--------EGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 152 HRAIDLKNPKANEDTSGFLPIERAWIDRLL-EKGYIDTFRHIHGDiTDAYSWWSYRFGARERNVGWRIDYFFISKELEPR 230
Cdd:cd10281  153 HTEIDIKNWKANQKNSGFLPEERAWLDQVFgELGYVDAFRELNPD-EGQYTWWSNRGQARANNVGWRIDYQIATPGLASK 231

                        250       260
                 ....*....|....*....|..
gi 644636476 231 LRDAFILSHIGGSDHCPVGIEI 252
Cdd:cd10281  232 VVSAWIYREERFSDHAPLIVDY 253
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-252 2.72e-73

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: 223.93  E-value: 2.72e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   1 MKLISWNVNGIRAVANkNAFAWVDEFAPNVLCLQEIKAEAEQIP-EPLFSHTFtckHVNSASKKGYSGTMSFSTLPFEKT 79
Cdd:cd09086    1 MKIATWNVNSIRARLE-QVLDWLKEEDPDVLCLQETKVEDDQFPaDAFEALGY---HVAVHGQKAYNGVAILSRLPLEDV 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  80 DTA-WHIDHTHEGRILEHHFGDVALFNVYFPNGQ-QSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHRAIDL 157
Cdd:cd09086   77 RTGfPGDPDDDQARLIAARVGGVRVINLYVPNGGdIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 158 KNPKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDiTDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDAFIL 237
Cdd:cd09086  157 WDPKQLLGKVLFTPEEREALRALLDLGFVDAFRALHPD-EKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGID 235

                        250
                 ....*....|....*....
gi 644636476 238 SHIGG----SDHCPVGIEI 252
Cdd:cd09086  236 REPRGwekpSDHAPVVAEL 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-252 1.44e-66

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 206.85  E-value: 1.44e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   1 MKLISWNVNGIRAVANKNAFAWVDEFAPNVLCLQEIKAEAEQipeplfsHTFTCKHV----NSASKKGYSGTMSFSTLpf 76
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQ-------NTFEFKGYfdfwNCAIKKGYSGVVTFTKK-- 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  77 EKTDTAWHI---DHTHEGRILEHHFGDVALFNVYFPNGQQSEERLAHKLKFYSDFLAHTEALRKEgKGIIICGDVNTAHR 153
Cdd:PRK13911  72 EPLSVSYGInieEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELK-KPVIVCGDLNVAHN 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 154 AIDLKNPKANEDTSGFLPIERAWIDRLLEKGYIDTFRHIHGDITDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRD 233
Cdd:PRK13911 151 EIDLENPKTNRKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKD 230

                        250
                 ....*....|....*....
gi 644636476 234 AFILSHIGGSDHCPVGIEI 252
Cdd:PRK13911 231 ALIYKDILGSDHCPVGLEL 249
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-252 3.67e-58

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: 187.14  E-value: 3.67e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   2 KLISWNVNGIRAVanKNAFAW---------VDEFAPNVLCLQEIKAEAEQIPEPL-----FSHTFTCkhvnSASKKGYSG 67
Cdd:cd09088    1 RIVTWNVNGIRTR--LQYQPWnkenslksfLDSLDADIICLQETKLTRDELDEPSaivegYDSFFSF----SRGRKGYSG 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  68 TMSF--------------------------------------STLPFEKTDTAWHIDHthEGR--ILEHhfGDVALFNVY 107
Cdd:cd09088   75 VATYcrdsaatpvaaeegltgvlsspnqknelsenddigcygEMLEFTDSKELLELDS--EGRcvLTDH--GTFVLINVY 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 108 FP-NGQQSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHRAIDLKNPKANEDTSGFLPIE---RAWIDRLLEK 183
Cdd:cd09088  151 CPrADPEKEERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLGD 230

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 644636476 184 G----------YIDTFRHIHGDITDAYSWWSYRFGARERNVGWRIDYFFISKELEPRLRDAFILSHIGGSDHCPVGIEI 252
Cdd:cd09088  231 SgegggspgglLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYADL 309
PRK11756 PRK11756
exonuclease III; Provisional
 1-254 1.25e-45

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 153.51  E-value: 1.25e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   1 MKLISWNVNGIRAVANKNAfAWVDEFAPNVLCLQEIKAEAEQIPEPLFSHTftCKHVNSASKKGYSGTMSFSTLPFEKTD 80
Cdd:PRK11756   1 MKFVSFNINGLRARPHQLE-AIIEKHQPDVIGLQETKVHDEMFPLEEVEAL--GYHVFYHGQKGHYGVALLSKQTPIAVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  81 TAWHIDH-THEGRI----LEHHFGDVALFNVYFPNGQ--QSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNTAHR 153
Cdd:PRK11756  78 KGFPTDDeEAQRRIimatIPTPNGNLTVINGYFPQGEsrDHPTKFPAKRQFYQDLQNYLETELSPDNPLLIMGDMNISPT 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 154 AID-----------LKNPKanedTSgFLPIERAWIDRLLEKGYIDTFRHIHGDITDAYSWWSYRFGARERNVGWRIDYFF 222
Cdd:PRK11756 158 DLDigigeenrkrwLRTGK----CS-FLPEEREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLIL 232

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 644636476 223 ISKELEPRLRDAFILSHIGG----SDHCPVGIEIDL 254
Cdd:PRK11756 233 ATQPLAERCVETGIDYDIRGmekpSDHAPIWATFKL 268
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-252 3.69e-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: 117.97  E-value: 3.69e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   3 LISWNVNGIRAVANKNAFA-WVDEFAPNVLCLQEIKAEAEQIPEPLFSHTFTCKHVNSA--SKKGYSGTMSFS----TLP 75
Cdd:cd08372    1 VASYNVNGLNAATRASGIArWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGYHQYQSGpsRKEGYEGVAILSktpkFKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  76 FEKTDTAWHIDHTHEGRILEHHFG----DVALFNVYFPN-GQQSEERLAHKLKFYSDFLahtEALRKEGKGIIICGDVNT 150
Cdd:cd08372   81 VEKHQYKFGEGDSGERRAVVVKFDvhdkELCVVNAHLQAgGTRADVRDAQLKEVLEFLK---RLRQPNSAPVVICGDFNV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 151 AHRAIDLKNPKAnedtsgflpieraWIDRLLEKGYIDTFRHIHgditDAYSWWSYRfgareRNVGWRIDYFFISKELEPR 230
Cdd:cd08372  158 RPSEVDSENPSS-------------MLRLFVALNLVDSFETLP----HAYTFDTYM-----HNVKSRLDYIFVSKSLLPS 215

                        250       260
                 ....*....|....*....|....*.
gi 644636476 231 LRDAFILS----HIGGSDHCPVGIEI 252
Cdd:cd08372  216 VKSSKILSdaarARIPSDHYPIEVTL 241
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-248 1.17e-17

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: 79.32  E-value: 1.17e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   3 LISWNVNGIRAVAN-KNAFAWVDEFAPNVLCLQEIKaeaeqipeplfshtftCKHVNSASKKGYSGTMSFSTLP------ 75
Cdd:cd09076    1 IGTLNVRGLRSPGKrAQLLEELKRKKLDILGLQETH----------------WTGEGELKKKREGGTILYSGSDsgksrg 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  76 ----FEKTDTAWHIDHTHE--GRIL----EHHFGDVALFNVYFPNGQQSEERLahklKFYSDFLAHTEALRKEGKgIIIC 145
Cdd:cd09076   65 vailLSKTAANKLLEYTKVvsGRIImvrfKIKGKRLTIINVYAPTARDEEEKE----EFYDQLQDVLDKVPRHDT-LIIG 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 146 GDVNT---AHRAIDLKNPKANEDTsgflpiERAWIDRLLEKGYIDTFRHIHGDITdAYSWWSYRFGARERnvgwrIDYFF 222
Cdd:cd09076  140 GDFNAvlgPKDDGRKGLDKRNENG------ERALSALIEEHDLVDVWRENNPKTR-EYTWRSPDHGSRSR-----IDRIL 207

                        250       260
                 ....*....|....*....|....*.
gi 644636476 223 ISKELEPRLRDAFIlSHIGGSDHCPV 248
Cdd:cd09076  208 VSKRLRVKVKKTKI-TPGAGSDHRLV 232
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-150 1.32e-12

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: 64.55  E-value: 1.32e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476    4 ISWNVNGIRAVANKNAF------AWVDEFAPNVLCLQEIKAEAEQ-IPEPLFSHTFTCKHVNSASKKGYSGTMSFSTLP- 75
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRkldalaALIRAYDPDVVALQETDDDDASrLLLALLAYGGFLSYGGPGGGGGGGGVAILSRYPl 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 644636476   76 FEKTDTAWHIDHTHEGRILEHHFGDVALFNVYFPNGQQSEERLAHKLKFYSDFLAHTEALRKEGKGIIICGDVNT 150
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 3-248 7.23e-07

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: 48.83  E-value: 7.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476   3 LISWNVNGIRAVANKN----AFAWVDEFAPNVLCLQE--IKAEAEQIPEPLFSHTFTCKHVNSASKKGYSGTMSFSTLPF 76
Cdd:cd09084    1 VMSYNVRSFNRYKWKDdpdkILDFIKKQDPDILCLQEyyGSEGDKDDDLRLLLKGYPYYYVVYKSDSGGTGLAIFSKYPI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476  77 EKTDTawhID--HTHEGRIlehhFGD-------VALFNVYFP----------NGQQSEERLAHKLKFYsDFLAHT----- 132
Cdd:cd09084   81 LNSGS---IDfpNTNNNAI----FADirvggdtIRVYNVHLEsfritpsdkeLYKEEKKAKELSRNLL-RKLAEAfkrra 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644636476 133 -------EALRKEGKGIIICGDVNtahraidlknpkaneDTsgflPIERAWidRLLEKGYIDTFR---HIHGditdaysw 202
Cdd:cd09084  153 aqadllaADIAASPYPVIVCGDFN---------------DT----PASYVY--RTLKKGLTDAFVeagSGFG-------- 203

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 644636476 203 WSYRFGARernvGWRIDYFFISKELEPrlRDAFILSHIgGSDHCPV 248
Cdd:cd09084  204 YTFNGLFF----PLRIDYILTSKGFKV--LRYRVDPGK-YSDHYPI 242
 
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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