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Conserved domains on  [gi|1739696985|gb|KAA1480191|]
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hypothetical protein DENSPDRAFT_741686, partial [Dentipellis sp. KUC8613]

Protein Classification

endonuclease/exonuclease/phosphatase family protein( domain architecture ID 12043728)

endonuclease/exonuclease/phosphatase (EEP) family protein is among a diverse set of enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins

CATH:  3.60.10.10
EC:  3.1.-.-
Gene Ontology:  GO:0046872|GO:0016787|GO:0003677
PubMed:  10838565
SCOP:  4002213

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 71-213 8.19e-08

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: 51.07  E-value: 8.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985  71 LTLNINGFHSKKL-------QIVDLLLQMKVAVACFQETRVMDRHYP-----IRVNGYQTFVSDARAGFRGLAMLVDHRL 138
Cdd:pfam03372   1 LTWNVNGGNADAAgddrkldALAALIRAYDPDVVALQETDDDDASRLllallAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1739696985 139 AAYEVPHTLGIHGLYVKVAGLPGFECPVHIIGLYCPSGGNERSTRTTVLRGVCDLTASILeKDPEAHIVVLGDLN 213
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALL-APRSEPVILAGDFN 154
COG2374 super family cl28586
Predicted extracellular nuclease [General function prediction only];
174-259 4.48e-05

Predicted extracellular nuclease [General function prediction only];


The actual alignment was detected with superfamily member COG2374:

Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 44.24  E-value: 4.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985 174 PSGGNERS--TRT---TVLRgvcDLTASILEKDPEAHIVVLGDLNKEAGD--LDKFLGkrQCGLSRLVPTGSSLTRFPL- 245
Cdd:COG2374   222 PGDGQGASeaKRTaqaEALR---AFVDSLLAADPDAPVIVLGDFNDYPFEdpLRALLG--AGGLTNLAEKLPAAERYSYv 296

                          90
                  ....*....|....*
gi 1739696985 246 -RGRPTAIDHLLVSE 259
Cdd:COG2374   297 yDGNSGLLDHILVSP 311
 
Name Accession Description Interval E-value
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 71-213 8.19e-08

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: 51.07  E-value: 8.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985  71 LTLNINGFHSKKL-------QIVDLLLQMKVAVACFQETRVMDRHYP-----IRVNGYQTFVSDARAGFRGLAMLVDHRL 138
Cdd:pfam03372   1 LTWNVNGGNADAAgddrkldALAALIRAYDPDVVALQETDDDDASRLllallAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1739696985 139 AAYEVPHTLGIHGLYVKVAGLPGFECPVHIIGLYCPSGGNERSTRTTVLRGVCDLTASILeKDPEAHIVVLGDLN 213
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALL-APRSEPVILAGDFN 154
XthA COG0708
Exonuclease III [Replication, recombination and repair];
69-213 1.80e-07

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 50.85  E-value: 1.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985  69 TILTLNINGFHSKKLQIVDLLLQMKVAVACFQETRVMDRHYP---IRVNGYQTFVSDaRAGFRGLAMLVDHRLAAYEVph 145
Cdd:COG0708     2 KIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPleaFEAAGYHVYFHG-QKGYNGVAILSRLPPEDVRR-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985 146 tlgihglyvkvaGLPGFEC------------PVHIIGLYCPSGGNERSTR-----------TTVLRGvcdltasilEKDP 202
Cdd:COG0708    79 ------------GLGGDEFdaegryieadfgGVRVVSLYVPNGGSVGSEKfdyklrfldalRAYLAE---------LLAP 137

                         170
                  ....*....|.
gi 1739696985 203 EAHIVVLGDLN 213
Cdd:COG0708   138 GRPLILCGDFN 148
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 69-213 2.59e-07

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: 50.59  E-value: 2.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985  69 TILTLNINGFHSKKLQIVDLLLQMKVAVACFQETRVMDRHYP---IRVNGYQTFVS-----------------DARAGFR 128
Cdd:cd09086     2 KIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPadaFEALGYHVAVHgqkayngvailsrlpleDVRTGFP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985 129 GLAMLVDHRLaayevphtlgihgLYVKVAGlpgfecpVHIIGLYCPSGGNERSTR-TTVLRGVCDLTASILE-KDPEAHI 206
Cdd:cd09086    82 GDPDDDQARL-------------IAARVGG-------VRVINLYVPNGGDIGSPKfAYKLDWLDRLIRYLQKlLKPDDPL 141


                  ....*..
gi 1739696985 207 VVLGDLN 213
Cdd:cd09086   142 VLVGDFN 148
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
174-259 4.48e-05

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 44.24  E-value: 4.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985 174 PSGGNERS--TRT---TVLRgvcDLTASILEKDPEAHIVVLGDLNKEAGD--LDKFLGkrQCGLSRLVPTGSSLTRFPL- 245
Cdd:COG2374   222 PGDGQGASeaKRTaqaEALR---AFVDSLLAADPDAPVIVLGDFNDYPFEdpLRALLG--AGGLTNLAEKLPAAERYSYv 296

                          90
                  ....*....|....*
gi 1739696985 246 -RGRPTAIDHLLVSE 259
Cdd:COG2374   297 yDGNSGLLDHILVSP 311
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 70-133 1.86e-04

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: 41.98  E-value: 1.86e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1739696985  70 ILTLNINGFHSKKLQIVDLLLQMKVAVACFQETRVMDRHYP---IRVNGYQTFVSDARaGFRGLAML 133
Cdd:TIGR00195   3 IISWNVNGLRARPHKGLAWLKENQPDVLCLQETKVQDEQFPlepFHKEGYHVFFSGQK-GYSGVAIF 68
 
Name Accession Description Interval E-value
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 71-213 8.19e-08

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: 51.07  E-value: 8.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985  71 LTLNINGFHSKKL-------QIVDLLLQMKVAVACFQETRVMDRHYP-----IRVNGYQTFVSDARAGFRGLAMLVDHRL 138
Cdd:pfam03372   1 LTWNVNGGNADAAgddrkldALAALIRAYDPDVVALQETDDDDASRLllallAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1739696985 139 AAYEVPHTLGIHGLYVKVAGLPGFECPVHIIGLYCPSGGNERSTRTTVLRGVCDLTASILeKDPEAHIVVLGDLN 213
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALL-APRSEPVILAGDFN 154
XthA COG0708
Exonuclease III [Replication, recombination and repair];
69-213 1.80e-07

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 50.85  E-value: 1.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985  69 TILTLNINGFHSKKLQIVDLLLQMKVAVACFQETRVMDRHYP---IRVNGYQTFVSDaRAGFRGLAMLVDHRLAAYEVph 145
Cdd:COG0708     2 KIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPleaFEAAGYHVYFHG-QKGYNGVAILSRLPPEDVRR-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985 146 tlgihglyvkvaGLPGFEC------------PVHIIGLYCPSGGNERSTR-----------TTVLRGvcdltasilEKDP 202
Cdd:COG0708    79 ------------GLGGDEFdaegryieadfgGVRVVSLYVPNGGSVGSEKfdyklrfldalRAYLAE---------LLAP 137

                         170
                  ....*....|.
gi 1739696985 203 EAHIVVLGDLN 213
Cdd:COG0708   138 GRPLILCGDFN 148
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 69-213 2.59e-07

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: 50.59  E-value: 2.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985  69 TILTLNINGFHSKKLQIVDLLLQMKVAVACFQETRVMDRHYP---IRVNGYQTFVS-----------------DARAGFR 128
Cdd:cd09086     2 KIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPadaFEALGYHVAVHgqkayngvailsrlpleDVRTGFP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985 129 GLAMLVDHRLaayevphtlgihgLYVKVAGlpgfecpVHIIGLYCPSGGNERSTR-TTVLRGVCDLTASILE-KDPEAHI 206
Cdd:cd09086    82 GDPDDDQARL-------------IAARVGG-------VRVINLYVPNGGDIGSPKfAYKLDWLDRLIRYLQKlLKPDDPL 141


                  ....*..
gi 1739696985 207 VVLGDLN 213
Cdd:cd09086   142 VLVGDFN 148
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 70-213 2.01e-06

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: 47.73  E-value: 2.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985  70 ILTLNINGFHSK-KL-QIVDLLLQMKVAVACFQETRVMD--RHYPIRVNGYQTFVSDARAGFRGLAMLVDHRLAAYEVPH 145
Cdd:cd09076     1 IGTLNVRGLRSPgKRaQLLEELKRKKLDILGLQETHWTGegELKKKREGGTILYSGSDSGKSRGVAILLSKTAANKLLEY 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1739696985 146 TLGIHGLYVKVAGLpGFECPVHIIGLYCPSGGNErSTRTTVLRgvcDLTASILEKDPEAHIVVLGDLN 213
Cdd:cd09076    81 TKVVSGRIIMVRFK-IKGKRLTIINVYAPTARDE-EEKEEFYD---QLQDVLDKVPRHDTLIIGGDFN 143
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
174-259 4.48e-05

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 44.24  E-value: 4.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985 174 PSGGNERS--TRT---TVLRgvcDLTASILEKDPEAHIVVLGDLNKEAGD--LDKFLGkrQCGLSRLVPTGSSLTRFPL- 245
Cdd:COG2374   222 PGDGQGASeaKRTaqaEALR---AFVDSLLAADPDAPVIVLGDFNDYPFEdpLRALLG--AGGLTNLAEKLPAAERYSYv 296

                          90
                  ....*....|....*
gi 1739696985 246 -RGRPTAIDHLLVSE 259
Cdd:COG2374   297 yDGNSGLLDHILVSP 311
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 70-220 9.41e-05

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: 42.66  E-value: 9.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985  70 ILTLNINGFHSK-KLQIVDLLLQMKVAVACFQETRVMDRHYP---IRVNGYQTFVSDARA-GFRGLAMLVDhrlaayEVP 144
Cdd:cd09073     2 IISWNVNGLRARlKKGVLKWLKEEKPDILCLQETKADEDKLPeelQHVEGYHSYWSPARKkGYSGVATLSK------EEP 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985 145 HTL--GIHGLYVKVAG------LPGFecpvHIIGLYCPSGGnERSTRttvLRGVCDLTASILE-----KDPEAHIVVLGD 211
Cdd:cd09073    76 LDVsyGIGGEEFDSEGrvitaeFDDF----YLINVYFPNGG-RGLER---LDYKLRFYEAFLEfleklRKRGKPVVICGD 147


                  ....*....
gi 1739696985 212 LNKEAGDLD 220
Cdd:cd09073   148 FNVAHEEID 156
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 70-133 1.86e-04

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: 41.98  E-value: 1.86e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1739696985  70 ILTLNINGFHSKKLQIVDLLLQMKVAVACFQETRVMDRHYP---IRVNGYQTFVSDARaGFRGLAML 133
Cdd:TIGR00195   3 IISWNVNGLRARPHKGLAWLKENQPDVLCLQETKVQDEQFPlepFHKEGYHVFFSGQK-GYSGVAIF 68
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 34-262 3.06e-04

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 41.52  E-value: 3.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985  34 VLSKWRIAAWRPWQDRKGGPAPALaqgiserivgnTILTLNINGFHSKKLQIVDLLLQMKVAVACFQET--------RVM 105
Cdd:COG3021    72 VQAALILPYTLPAPKSAPAGGPDL-----------RVLTANVLFGNADAEALAALVREEDPDVLVLQETtpaweealAAL 140

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985 106 DRHYPirvngYQtfVSDARAGFRGLAMLVDHRLAAYEVPHTL--GIHGLYVKVAgLPGFecPVHIIGLYCPSGGNERSTR 183
Cdd:COG3021   141 EADYP-----YR--VLCPLDNAYGMALLSRLPLTEAEVVYLVgdDIPSIRATVE-LPGG--PVRLVAVHPAPPVGGSAER 210

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1739696985 184 TTVLRGVCDLTAsilekDPEAHIVVLGDLNKEAGD--LDKFLGKRQCGLSR----LVPTgssltrFPLRGRP--TAIDHL 255
Cdd:COG3021   211 DAELAALAKAVA-----ALDGPVIVAGDFNATPWSptLRRLLRASGLRDARagrgLGPT------WPANLPFlrLPIDHV 279


                  ....*..
gi 1739696985 256 LVSERVA 262
Cdd:COG3021   280 LVSRGLT 286
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 70-134 1.94e-03

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: 38.69  E-value: 1.94e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1739696985  70 ILTLNINGFHS--KKlQIVDLLLQMKVAVACFQETRVMDRHYPIRVN----GYQTFVSDA-RAGFRGLAMLV 134
Cdd:cd09087     3 IISWNVNGLRAllKK-GLLDYVKKEDPDILCLQETKLQEGDVPKELKellkGYHQYWNAAeKKGYSGTAILS 73
 
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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