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Conserved domains on  [gi|491998074|ref|WP_005713693|]
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exodeoxyribonuclease III [Lacticaseibacillus rhamnosus]

Protein Classification

exodeoxyribonuclease III( domain architecture ID 10173395)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-247 2.98e-159

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: 441.61  E-value: 2.98e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLKKDFMTIFNELDADWFCLQETKMQAGQVELD----LPGYYQYFNYAERKGYSGTAIFTKHKPLNV 76
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKElkelLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  77 TYGMGIPEHDTEGRIITLEYPKFYLMTVYTPNSGGELKRLDYRQQWDRDFLAYTNELAAKKPLVYCGDLNVAHEPIDLKN 156
Cdd:cd09087   81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLAN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 157 DKTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPD-TVTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILTQ 235
Cdd:cd09087  161 PKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDkEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIRSD 240

                        250
                 ....*....|..
gi 491998074 236 IMGSDHCPVELV 247
Cdd:cd09087  241 IMGSDHCPIGLE 252
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-247 2.98e-159

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: 441.61  E-value: 2.98e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLKKDFMTIFNELDADWFCLQETKMQAGQVELD----LPGYYQYFNYAERKGYSGTAIFTKHKPLNV 76
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKElkelLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  77 TYGMGIPEHDTEGRIITLEYPKFYLMTVYTPNSGGELKRLDYRQQWDRDFLAYTNELAAKKPLVYCGDLNVAHEPIDLKN 156
Cdd:cd09087   81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLAN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 157 DKTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPD-TVTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILTQ 235
Cdd:cd09087  161 PKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDkEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIRSD 240

                        250
                 ....*....|..
gi 491998074 236 IMGSDHCPVELV 247
Cdd:cd09087  241 IMGSDHCPIGLE 252
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-246 4.96e-120

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 342.44  E-value: 4.96e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLKKdFMTIFNELDADWFCLQETKMQAGQVELDL---PGYYQYFNYaeRKGYSGTAIFTKHKPLNVT 77
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAfeaAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  78 YGMGIPEHDTEGRIITLEYPKFYLMTVYTPNSG-GELKRLDYRQQWDRDFLAYTNEL-AAKKPLVYCGDLNVAHEPIDLK 155
Cdd:COG0708   78 RGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELlAPGRPLILCGDFNIAPTEIDVK 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 156 NDKTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPD-TVTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILT 234
Cdd:COG0708  158 NPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDvEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDR 237

                        250
                 ....*....|....*.
gi 491998074 235 ----QIMGSDHCPVEL 246
Cdd:COG0708  238 eprgDERPSDHAPVVV 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-247 6.57e-117

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 334.63  E-value: 6.57e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074    1 MKMISWNVNGLRAVLKKDFMTIFNELDADWFCLQETKMQAGQVELDL---PGYYQYFNYAERkGYSGTAIFTKHKPLNVT 77
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELfeeLGYHVFFHGAKK-GYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   78 YGMGIPEHDTEGRIITLEYPKFYLMTVYTPNSGGE-LKRLDYRQQ-WDRDFLAYTNELAAKKPLVYCGDLNVAHEPIDLK 155
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSRdLERLEYKLQfWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  156 NDKTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPDTVT-YSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILT 234
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS 239

                         250
                  ....*....|...
gi 491998074  235 QIMGSDHCPVELV 247
Cdd:TIGR00633 240 EIRGSDHCPIVLE 252
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-246 5.44e-102

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 296.61  E-value: 5.44e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLKKDFMTIFNELDADWFCLQETKMQAGQVELDLPGYYQYFNYAERKGYSGTAIFTKHKPLNVTYGM 80
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGYFDFWNCAIKKGYSGVVTFTKKEPLSVSYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  81 GIPEHDTEGRIITLEYPKFYLMTVYTPNSGGELKRLDYRQQWDRDFLAYTNELAAKKPLVYCGDLNVAHEPIDLKNDKTN 160
Cdd:PRK13911  81 NIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKKPVIVCGDLNVAHNEIDLENPKTN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 161 HHNAGFTDEERADFTKQLNSGFIDTFRHFYPDT-VTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILTQIMGS 239
Cdd:PRK13911 161 RKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKeKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDILGS 240


                 ....*..
gi 491998074 240 DHCPVEL 246
Cdd:PRK13911 241 DHCPVGL 247
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-147 1.37e-15

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: 72.64  E-value: 1.37e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074    4 ISWNVNGLRA------VLKKDFMTIFNELDADWFCLQETKMQAGQV----ELDLPGYYQYFNYAERKGYSGTAIFTKHKP 73
Cdd:pfam03372   1 LTWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASRlllaLLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491998074   74 LNVTYGMGIPEHDTEGRIIT-LEYPKFYLMTVYTPNSGGELKRLDYRQQWDRDFLAYTNELAAKKPLVYCGDLNV 147
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIaPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-247 2.98e-159

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: 441.61  E-value: 2.98e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLKKDFMTIFNELDADWFCLQETKMQAGQVELD----LPGYYQYFNYAERKGYSGTAIFTKHKPLNV 76
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKElkelLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  77 TYGMGIPEHDTEGRIITLEYPKFYLMTVYTPNSGGELKRLDYRQQWDRDFLAYTNELAAKKPLVYCGDLNVAHEPIDLKN 156
Cdd:cd09087   81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEEIDLAN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 157 DKTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPD-TVTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILTQ 235
Cdd:cd09087  161 PKTNKKSAGFTPEERESFTELLEAGFVDTFRHLHPDkEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIRSD 240

                        250
                 ....*....|..
gi 491998074 236 IMGSDHCPVELV 247
Cdd:cd09087  241 IMGSDHCPIGLE 252
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-246 1.43e-120

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: 343.88  E-value: 1.43e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLKKDFMTIFNELDADWFCLQETKMQAGQVELDL---PGYYQYFNYAERKGYSGTAIFTKHKPLNVT 77
Cdd:cd09085    1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLrniEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  78 YGMGIPEHDTEGRIITLEYPKFYLMTVYTPNSGGELKRLDYRQQWDRDFLAYTNEL-AAKKPLVYCGDLNVAHEPIDLKN 156
Cdd:cd09085   81 EGLGVEEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELrDSGKNVIICGDFNTAHKEIDLAR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 157 DKTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPDTVTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILTQI 236
Cdd:cd09085  161 PKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKEPGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPDV 240

                        250
                 ....*....|
gi 491998074 237 MGSDHCPVEL 246
Cdd:cd09085  241 MGSDHCPVSL 250
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-246 4.96e-120

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 342.44  E-value: 4.96e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLKKdFMTIFNELDADWFCLQETKMQAGQVELDL---PGYYQYFNYaeRKGYSGTAIFTKHKPLNVT 77
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAfeaAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  78 YGMGIPEHDTEGRIITLEYPKFYLMTVYTPNSG-GELKRLDYRQQWDRDFLAYTNEL-AAKKPLVYCGDLNVAHEPIDLK 155
Cdd:COG0708   78 RGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGsVGSEKFDYKLRFLDALRAYLAELlAPGRPLILCGDFNIAPTEIDVK 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 156 NDKTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPD-TVTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILT 234
Cdd:COG0708  158 NPKANLKNAGFLPEERAWFDRLLELGLVDAFRALHPDvEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDR 237

                        250
                 ....*....|....*.
gi 491998074 235 ----QIMGSDHCPVEL 246
Cdd:COG0708  238 eprgDERPSDHAPVVV 253
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-247 3.50e-118

Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197307 [Multi-domain]  Cd Length: 251  Bit Score: 337.72  E-value: 3.50e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   2 KMISWNVNGLRAVLKKDFMTIFNELDADWFCLQETKMQAGQVELDL---PGYYQYFNYAERKGYSGTAIFTKHKPLNVTY 78
Cdd:cd09073    1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELqhvEGYHSYWSPARKKGYSGVATLSKEEPLDVSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  79 GMGIPEHDTEGRIITLEYPKFYLMTVYTPNSGGELKRLDYRQQWDRDFLAYTNELAAK-KPLVYCGDLNVAHEPIDLKND 157
Cdd:cd09073   81 GIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRgKPVVICGDFNVAHEEIDLARP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 158 KTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPDTVTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILTQIM 237
Cdd:cd09073  161 KKNEKNAGFTPEERAWFDKLLSLGYVDTFRHFHPEPGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILSKVK 240

                        250
                 ....*....|
gi 491998074 238 GSDHCPVELV 247
Cdd:cd09073  241 GSDHAPVTLE 250
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-247 6.57e-117

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 334.63  E-value: 6.57e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074    1 MKMISWNVNGLRAVLKKDFMTIFNELDADWFCLQETKMQAGQVELDL---PGYYQYFNYAERkGYSGTAIFTKHKPLNVT 77
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELfeeLGYHVFFHGAKK-GYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   78 YGMGIPEHDTEGRIITLEYPKFYLMTVYTPNSGGE-LKRLDYRQQ-WDRDFLAYTNELAAKKPLVYCGDLNVAHEPIDLK 155
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSRdLERLEYKLQfWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  156 NDKTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPDTVT-YSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILT 234
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS 239

                         250
                  ....*....|...
gi 491998074  235 QIMGSDHCPVELV 247
Cdd:TIGR00633 240 EIRGSDHCPIVLE 252
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-247 5.66e-103

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: 299.30  E-value: 5.66e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074    1 MKMISWNVNGLRAVLKKdFMTIFNELDADWFCLQETKMQAGQVELDLP---GYYQYFNYAerKGYSGTAIFTKHKPLNVT 77
Cdd:TIGR00195   1 MKIISWNVNGLRARPHK-GLAWLKENQPDVLCLQETKVQDEQFPLEPFhkeGYHVFFSGQ--KGYSGVAIFSKEEPISVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   78 YGMGIPEHDTEGRIITLEYPKFYLMTVYTPN-SGGELKRLDYRQQWDRDFLAYTNELAAK-KPLVYCGDLNVAHEPIDLK 155
Cdd:TIGR00195  78 RGFGVEEEDAEGRIIMAEFDSFLVINGYFPNgSRDDSEKLPYKLQWLEALQNYLEKLVDKdKPVLICGDMNIAPTEIDLH 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  156 NDKTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPDTVTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILTQ 235
Cdd:TIGR00195 158 IPDENRNHTGFLPEEREWLDRLLEAGLVDTFRKFNPDEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDYD 237

                         250
                  ....*....|....*.
gi 491998074  236 IMG----SDHCPVELV 247
Cdd:TIGR00195 238 IRGsekpSDHCPVVLE 253
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-246 5.44e-102

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 296.61  E-value: 5.44e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLKKDFMTIFNELDADWFCLQETKMQAGQVELDLPGYYQYFNYAERKGYSGTAIFTKHKPLNVTYGM 80
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGYFDFWNCAIKKGYSGVVTFTKKEPLSVSYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  81 GIPEHDTEGRIITLEYPKFYLMTVYTPNSGGELKRLDYRQQWDRDFLAYTNELAAKKPLVYCGDLNVAHEPIDLKNDKTN 160
Cdd:PRK13911  81 NIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKKPVIVCGDLNVAHNEIDLENPKTN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 161 HHNAGFTDEERADFTKQLNSGFIDTFRHFYPDT-VTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILTQIMGS 239
Cdd:PRK13911 161 RKNAGFSDEERGKFSELLNAGFIDTFRYFYPNKeKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDILGS 240


                 ....*..
gi 491998074 240 DHCPVEL 246
Cdd:PRK13911 241 DHCPVGL 247
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-244 2.05e-89

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: 264.86  E-value: 2.05e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLKKDFMTIFNELDADWFCLQETKMQAGQVELDL---PGYYQYFNYAERKGYSGTAIFTKHKPLNVT 77
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFfepEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  78 YGMGIPEHDTEGRIITLEYPKFYLMTVYTPNSGGELKRLDYRQQWDRDFLAYTNELAAKKP-LVYCGDLNVAHEPIDLKN 156
Cdd:cd10281   81 YGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRReFIVCGDFNIAHTEIDIKN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 157 DKTNHHNAGFTDEERADFTKQL-NSGFIDTFRHFYPDTVTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILTQ 235
Cdd:cd10281  161 WKANQKNSGFLPEERAWLDQVFgELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYRE 240


                 ....*....
gi 491998074 236 IMGSDHCPV 244
Cdd:cd10281  241 ERFSDHAPL 249
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-244 5.78e-61

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: 192.34  E-value: 5.78e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLK--KDFMTifnELDADWFCLQETKMQAGQ---VELDLPGYYQYFNyaERKGYSGTAIFTKHKPLN 75
Cdd:cd09086    1 MKIATWNVNSIRARLEqvLDWLK---EEDPDVLCLQETKVEDDQfpaDAFEALGYHVAVH--GQKAYNGVAILSRLPLED 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  76 VTYGMGIPEHDTEGRIITLEYPKFYLMTVYTPNsGGELK--RLDYRQQWDRDFLAY-TNELAAKKPLVYCGDLNVAHEPI 152
Cdd:cd09086   76 VRTGFPGDPDDDQARLIAARVGGVRVINLYVPN-GGDIGspKFAYKLDWLDRLIRYlQKLLKPDDPLVLVGDFNIAPEDI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 153 DLKNDKTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPDTVTYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKI 232
Cdd:cd09086  155 DVWDPKQLLGKVLFTPEEREALRALLDLGFVDAFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGI 234

                        250
                 ....*....|....*.
gi 491998074 233 LTQIMG----SDHCPV 244
Cdd:cd09086  235 DREPRGwekpSDHAPV 250
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-247 1.72e-52

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: 172.50  E-value: 1.72e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   2 KMISWNVNGLRAVL-------KKDFMTIFNELDADWFCLQETKMQAGQVELD---LPGYYQYFNY-AERKGYSGTAIFTK 70
Cdd:cd09088    1 RIVTWNVNGIRTRLqyqpwnkENSLKSFLDSLDADIICLQETKLTRDELDEPsaiVEGYDSFFSFsRGRKGYSGVATYCR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  71 H---KPLNVTYGM-----------GIPEH---------------------DTEGRIITLEYPKFYLMTVYTP-NSGGELK 114
Cdd:cd09088   81 DsaaTPVAAEEGLtgvlsspnqknELSENddigcygemleftdskellelDSEGRCVLTDHGTFVLINVYCPrADPEKEE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 115 RLDYRqqwdRDFLAYTNE-----LAAKKPLVYCGDLNVAHEPIDLKNDKTNHHNAGFTDEE---RADFTKQLNSG----- 181
Cdd:cd09088  161 RLEFK----LDFYRLLEErvealLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLGDSgeggg 236

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 491998074 182 -----FIDTFRHFYPDTV-TYSWWSYRFHARANNAGWRIDYFVASSAFQSYIQDAKILTQIMGSDHCPVELV 247
Cdd:cd09088  237 spgglLIDSFRYFHPTRKgAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYAD 308
PRK11756 PRK11756
exonuclease III; Provisional
 1-244 8.90e-36

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 128.09  E-value: 8.90e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLKKdFMTIFNELDADWFCLQETKMQAGQVELDLP---GYYQYfnYAERKGYSGTAIFTKHKPLNVT 77
Cdd:PRK11756   1 MKFVSFNINGLRARPHQ-LEAIIEKHQPDVIGLQETKVHDEMFPLEEVealGYHVF--YHGQKGHYGVALLSKQTPIAVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  78 YGMGIPEHDTEGRIITLEYP-KFYLMTV---YTPNsgGE----LKRLDYRQQWDRDFLAY-TNELAAKKPLVYCGDLNVA 148
Cdd:PRK11756  78 KGFPTDDEEAQRRIIMATIPtPNGNLTVingYFPQ--GEsrdhPTKFPAKRQFYQDLQNYlETELSPDNPLLIMGDMNIS 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 149 HEPID-----------LKNDKTNhhnagFTDEERADFTKQLNSGFIDTFRHFYPDTV-TYSWWSYRFHARANNAGWRIDY 216
Cdd:PRK11756 156 PTDLDigigeenrkrwLRTGKCS-----FLPEEREWLDRLMDWGLVDTFRQLNPDVNdRFSWFDYRSKGFDDNRGLRIDL 230

                        250       260       270
                 ....*....|....*....|....*....|..
gi 491998074 217 FVASSAFQSYIQDAKILTQIMG----SDHCPV 244
Cdd:PRK11756 231 ILATQPLAERCVETGIDYDIRGmekpSDHAPI 262
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 4-246 2.01e-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: 118.35  E-value: 2.01e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   4 ISWNVNGLRAV-LKKDFMTIFNELDADWFCLQETK-MQAGQVELDLPGYYQYFNYA----ERKGYSGTAIFTK---HKPL 74
Cdd:cd08372    2 ASYNVNGLNAAtRASGIARWVRELDPDIVCLQEVKdSQYSAVALNQLLPEGYHQYQsgpsRKEGYEGVAILSKtpkFKIV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  75 NVTYGMGIPEHDTEGRI----ITLEYPKFYLMTVYTPNSGGelkRLDYRQQWDRDFLAYTNELAAKK--PLVYCGDLNVA 148
Cdd:cd08372   82 EKHQYKFGEGDSGERRAvvvkFDVHDKELCVVNAHLQAGGT---RADVRDAQLKEVLEFLKRLRQPNsaPVVICGDFNVR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 149 HEPIDLKNDKtnhhnagftdeERADFTKQLNsgFIDTFRHFypdTVTYSWWSYRfharaNNAGWRIDYFVASSAFQSYIQ 228
Cdd:cd08372  159 PSEVDSENPS-----------SMLRLFVALN--LVDSFETL---PHAYTFDTYM-----HNVKSRLDYIFVSKSLLPSVK 217

                        250       260
                 ....*....|....*....|..
gi 491998074 229 DAKILT----QIMGSDHCPVEL 246
Cdd:cd08372  218 SSKILSdaarARIPSDHYPIEV 239
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 4-244 2.27e-23

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: 94.73  E-value: 2.27e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   4 ISWNVNGLRAVLKkdFMTIFNEL---DADWFCLQETK-MQAGQVELDLPGYYQYFNYAERKGYSGTAIFTKHKPLN--VT 77
Cdd:cd09076    2 GTLNVRGLRSPGK--RAQLLEELkrkKLDILGLQETHwTGEGELKKKREGGTILYSGSDSGKSRGVAILLSKTAANklLE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  78 YgmgipEHDTEGRIITL----EYPKFYLMTVYTPNSGGELKRLDYRQQWDRdflaYTNELAAKKPLVYCGDLNVahePID 153
Cdd:cd09076   80 Y-----TKVVSGRIIMVrfkiKGKRLTIINVYAPTARDEEEKEEFYDQLQD----VLDKVPRHDTLIIGGDFNA---VLG 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 154 LKNDKTNHHNAGFTDEERADFTKQLNSGFIDTFRHFYPDTVTYSWWSYRFHARAnnagwRIDYFVASSAFQSYIQDAKIl 233
Cdd:cd09076  148 PKDDGRKGLDKRNENGERALSALIEEHDLVDVWRENNPKTREYTWRSPDHGSRS-----RIDRILVSKRLRVKVKKTKI- 221

                        250
                 ....*....|.
gi 491998074 234 TQIMGSDHCPV 244
Cdd:cd09076  222 TPGAGSDHRLV 232
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-147 1.37e-15

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: 72.64  E-value: 1.37e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074    4 ISWNVNGLRA------VLKKDFMTIFNELDADWFCLQETKMQAGQV----ELDLPGYYQYFNYAERKGYSGTAIFTKHKP 73
Cdd:pfam03372   1 LTWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASRlllaLLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491998074   74 LNVTYGMGIPEHDTEGRIIT-LEYPKFYLMTVYTPNSGGELKRLDYRQQWDRDFLAYTNELAAKKPLVYCGDLNV 147
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIaPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 3-244 1.67e-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: 50.76  E-value: 1.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   3 MISWNVNGLR----AVLKKDFMTIFNELDADWFCLQE--TKMQAGQVEL--DLPGY-YQYFNYAERKGYSGTAIFTKHKP 73
Cdd:cd09084    1 VMSYNVRSFNrykwKDDPDKILDFIKKQDPDILCLQEyyGSEGDKDDDLrlLLKGYpYYYVVYKSDSGGTGLAIFSKYPI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  74 LNVtyGMgIPEHDTEGRIITLEYPK------FYLM----TVYTPNSGGELKRLDYRQQWDRDFLAYTNELAAKK------ 137
Cdd:cd09084   81 LNS--GS-IDFPNTNNNAIFADIRVggdtirVYNVhlesFRITPSDKELYKEEKKAKELSRNLLRKLAEAFKRRaaqadl 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 138 ----------PLVYCGDLN------VAHEpidLKNDKTNhhnaGFTDEeradftkqlNSGFIDTFRHFYPdtvtyswwsy 201
Cdd:cd09084  158 laadiaaspyPVIVCGDFNdtpasyVYRT---LKKGLTD----AFVEA---------GSGFGYTFNGLFF---------- 211

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 491998074 202 rfharannaGWRIDYFVASSAFQSYiqDAKILTQIMgSDHCPV 244
Cdd:cd09084  212 ---------PLRIDYILTSKGFKVL--RYRVDPGKY-SDHYPI 242
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-244 3.20e-06

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 47.30  E-value: 3.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNG--------LRAVLkkdfmtifnELDADWFCLQETKMQAGQVELDLPGYYQYFNYAERKGYSGTAIFTKHK 72
Cdd:COG3021   95 LRVLTANVLFgnadaealAALVR---------EEDPDVLVLQETTPAWEEALAALEADYPYRVLCPLDNAYGMALLSRLP 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  73 PLNVTygmgiPEHDTEGRI------ITLEYPKFYLMTV--YTPnsggelkrLDYRQQWDRDFLAYTNELAA-KKPLVYCG 143
Cdd:COG3021  166 LTEAE-----VVYLVGDDIpsiratVELPGGPVRLVAVhpAPP--------VGGSAERDAELAALAKAVAAlDGPVIVAG 232

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074 144 DLN-VAHepidlkndktnHHNAgftdeerADFTKQlnSGFID--TFRHFYPdtvTyswwsyrFHARANNAGWRIDYFVAS 220
Cdd:COG3021  233 DFNaTPW-----------SPTL-------RRLLRA--SGLRDarAGRGLGP---T-------WPANLPFLRLPIDHVLVS 282

                        250       260
                 ....*....|....*....|....
gi 491998074 221 SAFQsyIQDAKILTQImGSDHCPV 244
Cdd:COG3021  283 RGLT--VVDVRVLPVI-GSDHRPL 303
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 1-168 1.30e-03

Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. 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: 197314 [Multi-domain]  Cd Length: 248  Bit Score: 39.25  E-value: 1.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074   1 MKMISWNVNGLRAVLKKDFMT----IFNELDADWFCLQEtkmqagqVEldlPGYYQYFNYAE--RKGYSGTAIftKHKPL 74
Cdd:cd09080    1 LKVLTWNVDFLDDVNLAERMRailkLLEELDPDVIFLQE-------VT---PPFLAYLLSQPwvRKNYYFSEG--PPSPA 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491998074  75 NVTYGMGI----PEHDTEGRIITLEYPKFYLMTVYTPNSGGELkRL------------DYRQQWDRDFLAYTNELAAKKP 138
Cdd:cd09080   69 VDPYGVLIlskkSLVVRRVPFTSTRMGRNLLAAEINLGSGEPL-RLatthleslkshsSERTAQLEEIAKKLKKPPGAAN 147

                        170       180       190
                 ....*....|....*....|....*....|
gi 491998074 139 LVYCGDLNvahepIDLKNDKTNHHNAGFTD 168
Cdd:cd09080  148 VILGGDFN-----LRDKEDDTGGLPNGFVD 172
 
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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