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Conserved domains on  [gi|41055919|ref|NP_956440|]
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DNA-(apurinic or apyrimidinic site) endonuclease 2 [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-311 4.23e-167

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: 476.42  E-value: 4.23e-167
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   2 KIVTWNINGIRTFK--------NGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSFSRGRSGYSGVATYCK 73
Cdd:cd09088   1 RIVTWNVNGIRTRLqyqpwnkeNSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGVATYCR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  74 -DAATPFLAEEGLTGLLSN--------QGAVIGCYGDQVELT-SEELLALDNEGRAVITQHHFIgqdglqklTVINVYCP 143
Cdd:cd09088  81 dSAATPVAAEEGLTGVLSSpnqknelsENDDIGCYGEMLEFTdSKELLELDSEGRCVLTDHGTF--------VLINVYCP 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 144 RADPDKPERKEFKLQFYRLLQCRAEAILSSGSHVIILGDVNTSHRPIDHCDPDDVDNF-----EDNPGRKWLDQFLFeta 218
Cdd:cd09088 153 RADPEKEERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFggesfEDNPSRQWLDQLLG--- 229

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 219 ensengnaadepAEDFQESASGGKFVDSFRYFHPKRSNAFTCWSTLTGARQTNYGTRIDYIFSNHSLVKTFFiGVDIMPE 298
Cdd:cd09088 230 ------------DSGEGGGSPGGLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVK-AADILPE 296

                       330
                ....*....|...
gi 41055919 299 VEGSDHCPVWAQL 311
Cdd:cd09088 297 VEGSDHCPVYADL 309
zf-GRF super family cl46396
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 506-557 3.01e-10

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


The actual alignment was detected with superfamily member pfam06839:

Pssm-ID: 480736  Cd Length: 45  Bit Score: 55.49  E-value: 3.01e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 41055919   506 PLCKsHNEPCVLRTVKKAGPNLGRQFFVCARPQGhasnpqARCNFFAWVEKG 557
Cdd:pfam06839   1 PLCP-CGQRAVLLTVRKTGPNPGRQFYKCPVGRE------KQCGFFQWADEV 45
 
Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-311 4.23e-167

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: 476.42  E-value: 4.23e-167
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   2 KIVTWNINGIRTFK--------NGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSFSRGRSGYSGVATYCK 73
Cdd:cd09088   1 RIVTWNVNGIRTRLqyqpwnkeNSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGVATYCR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  74 -DAATPFLAEEGLTGLLSN--------QGAVIGCYGDQVELT-SEELLALDNEGRAVITQHHFIgqdglqklTVINVYCP 143
Cdd:cd09088  81 dSAATPVAAEEGLTGVLSSpnqknelsENDDIGCYGEMLEFTdSKELLELDSEGRCVLTDHGTF--------VLINVYCP 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 144 RADPDKPERKEFKLQFYRLLQCRAEAILSSGSHVIILGDVNTSHRPIDHCDPDDVDNF-----EDNPGRKWLDQFLFeta 218
Cdd:cd09088 153 RADPEKEERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFggesfEDNPSRQWLDQLLG--- 229

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 219 ensengnaadepAEDFQESASGGKFVDSFRYFHPKRSNAFTCWSTLTGARQTNYGTRIDYIFSNHSLVKTFFiGVDIMPE 298
Cdd:cd09088 230 ------------DSGEGGGSPGGLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVK-AADILPE 296

                       330
                ....*....|...
gi 41055919 299 VEGSDHCPVWAQL 311
Cdd:cd09088 297 VEGSDHCPVYADL 309
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-311 6.90e-59

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 196.45  E-value: 6.90e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   1 MKIVTWNINGIRTFKNGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSfsrGRSGYSGVATYCKDAATpfl 80
Cdd:COG0708   1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFH---GQKGYNGVAILSRLPPE--- 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  81 aeegltgllsnqgAVIGCYGDQVEltseellalDNEGRAVITQhhfigqdgLQKLTVINVYCPRADPDKPERKEFKLQFY 160
Cdd:COG0708  75 -------------DVRRGLGGDEF---------DAEGRYIEAD--------FGGVRVVSLYVPNGGSVGSEKFDYKLRFL 124

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 161 RLLQCRAEAILSSGSHVIILGDVNTSHRPIDHCDPddvDNFEDNPG-----RKWLDQFLfetaensENGnaadepaedfq 235
Cdd:COG0708 125 DALRAYLAELLAPGRPLILCGDFNIAPTEIDVKNP---KANLKNAGflpeeRAWFDRLL-------ELG----------- 183

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055919 236 esasggkFVDSFRYFHPKRSNAFTCWSTLTGARQTNYGTRIDYIFSNHSL---VKTFFIGVDIMPEVEGSDHCPVWAQL 311
Cdd:COG0708 184 -------LVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALadrLKDAGIDREPRGDERPSDHAPVVVEL 255
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-311 4.61e-55

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: 186.33  E-value: 4.61e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919     1 MKIVTWNINGIRT-FKNGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSFSRGrsGYSGVAtyckdaatpf 79
Cdd:TIGR00633   1 MKIISWNVNGLRArLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAKK--GYSGVA---------- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919    80 laeegltgLLSNQGAVIGCYGDQVEltseellALDNEGRAVITQhhfigqdgLQKLTVINVYCPRADPDKPERKEFKLQF 159
Cdd:TIGR00633  69 --------ILSKVEPLDVRYGFGGE-------PHDEEGRVITAE--------FDGFTVVNVYVPNGGSRDLERLEYKLQF 125

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   160 YRLLQCRAEAILSSGSHVIILGDVNTSHRPIDHCDPDdvdNFEDNPG-----RKWLDQFLfetaensengnaadepaedf 234
Cdd:TIGR00633 126 WDALFQYLEKELDAGKPVVICGDMNVAHTEIDLGNPK---ENKGNAGftpeeREWFDELL-------------------- 182

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055919   235 qesasGGKFVDSFRYFHPKRSNAFTCWSTLTGARQTNYGTRIDYIFSNHSLVKTFfigVD--IMPEVEGSDHCPVWAQL 311
Cdd:TIGR00633 183 -----EAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERV---VDsyIDSEIRGSDHCPIVLEL 253
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-311 1.69e-30

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 119.80  E-value: 1.69e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919    1 MKIVTWNINGIRT-FKNGIKKILDSFDADIICVQETKVTRDlldEKTAIVDGYNSYFSFSRgRSGYSGVATYCKdaatpf 79
Cdd:PRK13911   1 MKLISWNVNGLRAcMTKGFMDFFNSVDADVFCIQESKMQQE---QNTFEFKGYFDFWNCAI-KKGYSGVVTFTK------ 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   80 laEEGLTGllsnqgavigCYGDQVEltseellALDNEGRAVITQhhfigqdgLQKLTVINVYCPRADPDKPE---RKEFK 156
Cdd:PRK13911  71 --KEPLSV----------SYGINIE-------EHDKEGRVITCE--------FESFYLVNVYTPNSQQALSRlsyRMSWE 123

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  157 LQFYRLLQCraeaiLSSGSHVIILGDVNTSHRPIDHCDPDdvdnfednpgrkwldqflfetaENSENGNAADEPAEDFQE 236
Cdd:PRK13911 124 VEFKKFLKA-----LELKKPVIVCGDLNVAHNEIDLENPK----------------------TNRKNAGFSDEERGKFSE 176

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41055919  237 SASGGkFVDSFRYFHPKRSNAFTCWSTLTGARQTNYGTRIDYIFSNHSLvKTFFIGVDIMPEVEGSDHCPVWAQL 311
Cdd:PRK13911 177 LLNAG-FIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPL-KTRLKDALIYKDILGSDHCPVGLEL 249
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-187 4.30e-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: 64.94  E-value: 4.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919     4 VTWNINGIRTFKNG-------IKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSFSRGRSGYSGVATYCKDaa 76
Cdd:pfam03372   1 LTWNVNGGNADAAGddrkldaLAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRY-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919    77 tpflaeegltgllsnqgavigcygdqvELTSEELLALDNEGRAVITQHHFIGqdglqKLTVINVYCPRADPDKPERKEFK 156
Cdd:pfam03372  79 ---------------------------PLSSVILVDLGEFGDPALRGAIAPF-----AGVLVVPLVLTLAPHASPRLARD 126

                         170       180       190
                  ....*....|....*....|....*....|.
gi 41055919   157 LQFYRLLQCRAEAILSSGSHVIILGDVNTSH 187
Cdd:pfam03372 127 EQRADLLLLLLALLAPRSEPVILAGDFNADY 157
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 506-557 3.01e-10

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 55.49  E-value: 3.01e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 41055919   506 PLCKsHNEPCVLRTVKKAGPNLGRQFFVCARPQGhasnpqARCNFFAWVEKG 557
Cdd:pfam06839   1 PLCP-CGQRAVLLTVRKTGPNPGRQFYKCPVGRE------KQCGFFQWADEV 45
 
Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-311 4.23e-167

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: 476.42  E-value: 4.23e-167
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   2 KIVTWNINGIRTFK--------NGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSFSRGRSGYSGVATYCK 73
Cdd:cd09088   1 RIVTWNVNGIRTRLqyqpwnkeNSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGVATYCR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  74 -DAATPFLAEEGLTGLLSN--------QGAVIGCYGDQVELT-SEELLALDNEGRAVITQHHFIgqdglqklTVINVYCP 143
Cdd:cd09088  81 dSAATPVAAEEGLTGVLSSpnqknelsENDDIGCYGEMLEFTdSKELLELDSEGRCVLTDHGTF--------VLINVYCP 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 144 RADPDKPERKEFKLQFYRLLQCRAEAILSSGSHVIILGDVNTSHRPIDHCDPDDVDNF-----EDNPGRKWLDQFLFeta 218
Cdd:cd09088 153 RADPEKEERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFggesfEDNPSRQWLDQLLG--- 229

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 219 ensengnaadepAEDFQESASGGKFVDSFRYFHPKRSNAFTCWSTLTGARQTNYGTRIDYIFSNHSLVKTFFiGVDIMPE 298
Cdd:cd09088 230 ------------DSGEGGGSPGGLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVK-AADILPE 296

                       330
                ....*....|...
gi 41055919 299 VEGSDHCPVWAQL 311
Cdd:cd09088 297 VEGSDHCPVYADL 309
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-311 2.22e-83

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: 259.91  E-value: 2.22e-83
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   2 KIVTWNINGIRT-FKNGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSFSRgRSGYSGVATYCKDaaTPFL 80
Cdd:cd09073   1 KIISWNVNGLRArLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPAR-KKGYSGVATLSKE--EPLD 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  81 AEEGLTGLlsnqgavigcygdqveltseellALDNEGRAVITQHhfigqdglQKLTVINVYCPRADPDkPERKEFKLQFY 160
Cdd:cd09073  78 VSYGIGGE-----------------------EFDSEGRVITAEF--------DDFYLINVYFPNGGRG-LERLDYKLRFY 125

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 161 RLLQCRAEAILSSGSHVIILGDVNTSHRPIDHCDPDDVDN---FEDnPGRKWLDQFLfetaensENGnaadepaedfqes 237
Cdd:cd09073 126 EAFLEFLEKLRKRGKPVVICGDFNVAHEEIDLARPKKNEKnagFTP-EERAWFDKLL-------SLG------------- 184

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41055919 238 asggkFVDSFRYFHPKrSNAFTCWSTLTGARQTNYGTRIDYIFSNHSLVKTFFiGVDIMPEVEGSDHCPVWAQL 311
Cdd:cd09073 185 -----YVDTFRHFHPE-PGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVK-DSGILSKVKGSDHAPVTLEL 251
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-311 4.50e-66

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: 215.22  E-value: 4.50e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   1 MKIVTWNINGIRT-FKNGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSFSRgRSGYSGVATYCKDAatPF 79
Cdd:cd09085   1 MKIISWNVNGLRAvHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAE-RKGYSGVALYSKIE--PD 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  80 LAEEGLTgllsnqgavigcygdqveltSEELlalDNEGRAVITqhHFigqdglQKLTVINVYCPRADpDKPERKEFKLQF 159
Cdd:cd09085  78 SVREGLG--------------------VEEF---DNEGRILIA--DF------DDFTLFNIYFPNGQ-MSEERLDYKLEF 125

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 160 YRLLQCRAEAILSSGSHVIILGDVNTSHRPIDHCDPDdvDNfEDNPG-----RKWLDQFLfetaensENGnaadepaedf 234
Cdd:cd09085 126 YDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLARPK--EN-EKVSGflpeeRAWMDKFI-------ENG---------- 185

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41055919 235 qesasggkFVDSFRYFHPKRSNaFTCWSTLTGARQTNYGTRIDYIFSNHSLvKTFFIGVDIMPEVEGSDHCPVWAQL 311
Cdd:cd09085 186 --------YVDTFRMFNKEPGQ-YTWWSYRTRARERNVGWRIDYFFVNEEF-KPKVKDAGILPDVMGSDHCPVSLEL 252
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-311 6.90e-59

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 196.45  E-value: 6.90e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   1 MKIVTWNINGIRTFKNGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSfsrGRSGYSGVATYCKDAATpfl 80
Cdd:COG0708   1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFH---GQKGYNGVAILSRLPPE--- 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  81 aeegltgllsnqgAVIGCYGDQVEltseellalDNEGRAVITQhhfigqdgLQKLTVINVYCPRADPDKPERKEFKLQFY 160
Cdd:COG0708  75 -------------DVRRGLGGDEF---------DAEGRYIEAD--------FGGVRVVSLYVPNGGSVGSEKFDYKLRFL 124

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 161 RLLQCRAEAILSSGSHVIILGDVNTSHRPIDHCDPddvDNFEDNPG-----RKWLDQFLfetaensENGnaadepaedfq 235
Cdd:COG0708 125 DALRAYLAELLAPGRPLILCGDFNIAPTEIDVKNP---KANLKNAGflpeeRAWFDRLL-------ELG----------- 183

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055919 236 esasggkFVDSFRYFHPKRSNAFTCWSTLTGARQTNYGTRIDYIFSNHSL---VKTFFIGVDIMPEVEGSDHCPVWAQL 311
Cdd:COG0708 184 -------LVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALadrLKDAGIDREPRGDERPSDHAPVVVEL 255
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-311 4.61e-55

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: 186.33  E-value: 4.61e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919     1 MKIVTWNINGIRT-FKNGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSFSRGrsGYSGVAtyckdaatpf 79
Cdd:TIGR00633   1 MKIISWNVNGLRArLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAKK--GYSGVA---------- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919    80 laeegltgLLSNQGAVIGCYGDQVEltseellALDNEGRAVITQhhfigqdgLQKLTVINVYCPRADPDKPERKEFKLQF 159
Cdd:TIGR00633  69 --------ILSKVEPLDVRYGFGGE-------PHDEEGRVITAE--------FDGFTVVNVYVPNGGSRDLERLEYKLQF 125

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   160 YRLLQCRAEAILSSGSHVIILGDVNTSHRPIDHCDPDdvdNFEDNPG-----RKWLDQFLfetaensengnaadepaedf 234
Cdd:TIGR00633 126 WDALFQYLEKELDAGKPVVICGDMNVAHTEIDLGNPK---ENKGNAGftpeeREWFDELL-------------------- 182

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055919   235 qesasGGKFVDSFRYFHPKRSNAFTCWSTLTGARQTNYGTRIDYIFSNHSLVKTFfigVD--IMPEVEGSDHCPVWAQL 311
Cdd:TIGR00633 183 -----EAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERV---VDsyIDSEIRGSDHCPIVLEL 253
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-311 1.62e-54

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: 184.89  E-value: 1.62e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919     1 MKIVTWNINGIRTFKNGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSfsrGRSGYSGVATYCKDaaTPFL 80
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFS---GQKGYSGVAIFSKE--EPIS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919    81 AEEGLtgllsnqgavigcyGDQVEltseellalDNEGRAVITQhhfigqdgLQKLTVINVYCPRADPDKPERKEFKLQFY 160
Cdd:TIGR00195  76 VRRGF--------------GVEEE---------DAEGRIIMAE--------FDSFLVINGYFPNGSRDDSEKLPYKLQWL 124

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   161 RLLQCRAEAILSSGSHVIILGDVNTSHRPIDHCDPDDVdnfEDNPG-----RKWLDQFLfetaensENGnaadepaedfq 235
Cdd:TIGR00195 125 EALQNYLEKLVDKDKPVLICGDMNIAPTEIDLHIPDEN---RNHTGflpeeREWLDRLL-------EAG----------- 183

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055919   236 esasggkFVDSFRYFHPKrSNAFTCWSTLTGARQTNYGTRIDYIFSNHSL---VKTFFIGVDIMPEVEGSDHCPVWAQL 311
Cdd:TIGR00195 184 -------LVDTFRKFNPD-EGAYSWWDYRTKARDRNRGWRIDYFLVSEPLkerCVDCGIDYDIRGSEKPSDHCPVVLEF 254
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-307 2.78e-48

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: 168.11  E-value: 2.78e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   1 MKIVTWNINGIRTF-KNGIKKILDSFDADIICVQETKVTR-DLLDEKTAIVDGYNSYFSFSRgRSGYSGVATYCKDAatp 78
Cdd:cd09087   1 LKIISWNVNGLRALlKKGLLDYVKKEDPDILCLQETKLQEgDVPKELKELLKGYHQYWNAAE-KKGYSGTAILSKKK--- 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  79 flaeegltgllsnqgaVIGC-YGDQVELtseellaLDNEGRaVITQHhfigqdgLQKLTVINVYCPRA--DPDKPE-RKE 154
Cdd:cd09087  77 ----------------PLSVtYGIGIEE-------HDQEGR-VITAE-------FENFYLVNTYVPNSgrGLERLDrRKE 125

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 155 FKLQFYRLLQCraeaiLSSGSHVIILGDVNTSHRPIDHCDPDdvdNFEDNPG-----RKWLDQFLfetaensENGnaade 229
Cdd:cd09087 126 WDVDFRAYLKK-----LDSKKPVIWCGDLNVAHEEIDLANPK---TNKKSAGftpeeRESFTELL-------EAG----- 185

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 230 paedfqesasggkFVDSFRYFHPKRSNAFTCWSTLTGARQTNYGTRIDYIF-SNH---SLVKTFfigvdIMPEVEGSDHC 305
Cdd:cd09087 186 -------------FVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLvSERlkdRVVDSF-----IRSDIMGSDHC 247


                ..
gi 41055919 306 PV 307
Cdd:cd09087 248 PI 249
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-311 1.62e-39

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: 144.58  E-value: 1.62e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   1 MKIVTWNINGIRTFKNGIKKILDSFDADIICVQETKVTRDL--LDEKTAIvdGYNSYFsfsRGRSGYSGVATyckdaATP 78
Cdd:cd09086   1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQfpADAFEAL--GYHVAV---HGQKAYNGVAI-----LSR 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  79 FLAEEGLTGLLSNQGavigcygdqveltseellalDNEGRAVITQHHFIgqdglqklTVINVYCPRADPDKPERKEFKLQ 158
Cdd:cd09086  71 LPLEDVRTGFPGDPD--------------------DDQARLIAARVGGV--------RVINLYVPNGGDIGSPKFAYKLD 122

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 159 FYRLLQCRAEAILSSGSHVIILGDVNTSHRPIDHCDPDdvdnfednpgrKWLDQFLFETAENsengnaadepaEDFQESA 238
Cdd:cd09086 123 WLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDVWDPK-----------QLLGKVLFTPEER-----------EALRALL 180

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41055919 239 SGGkFVDSFRYFHPKRsNAFTCWSTLTGARQTNYGTRIDYIFSNHSLVKTfFIGVDIMPEVEG----SDHCPVWAQL 311
Cdd:cd09086 181 DLG-FVDAFRALHPDE-KLFTWWDYRAGAFERNRGLRIDHILASPALADR-LKDVGIDREPRGwekpSDHAPVVAEL 254
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-308 1.26e-38

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: 141.98  E-value: 1.26e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   1 MKIVTWNINGIRT-FKNGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFsFSRGRSGYSGVATYCKDaaTPf 79
Cdd:cd10281   1 MRVISVNVNGIRAaAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYF-FDAEKKGYAGVAIYSRT--QP- 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  80 laeegltgllsnqGAVIgcYGdqveLTSEELlalDNEGRavitqhhFIGQDgLQKLTVINVYCPRADPDKpERKEFKLQF 159
Cdd:cd10281  77 -------------KAVI--YG----LGFEEF---DDEGR-------YIEAD-FDNVSVASLYVPSGSSGD-ERQEAKMAF 125

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 160 Y-----RLLQCRAEailssGSHVIILGDVNTSHRPIDhcdpddVDNFEDN---PG-----RKWLDQFLFETAensengna 226
Cdd:cd10281 126 LdafleHLKELRRK-----RREFIVCGDFNIAHTEID------IKNWKANqknSGflpeeRAWLDQVFGELG-------- 186

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 227 adepaedfqesasggkFVDSFRYFHPKrSNAFTCWSTLTGARQTNYGTRIDYIFSNHSL---VKTFFIGVDIMpeveGSD 303
Cdd:cd10281 187 ----------------YVDAFRELNPD-EGQYTWWSNRGQARANNVGWRIDYQIATPGLaskVVSAWIYREER----FSD 245


                ....*
gi 41055919 304 HCPVW 308
Cdd:cd10281 246 HAPLI 250
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-311 1.69e-30

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 119.80  E-value: 1.69e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919    1 MKIVTWNINGIRT-FKNGIKKILDSFDADIICVQETKVTRDlldEKTAIVDGYNSYFSFSRgRSGYSGVATYCKdaatpf 79
Cdd:PRK13911   1 MKLISWNVNGLRAcMTKGFMDFFNSVDADVFCIQESKMQQE---QNTFEFKGYFDFWNCAI-KKGYSGVVTFTK------ 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   80 laEEGLTGllsnqgavigCYGDQVEltseellALDNEGRAVITQhhfigqdgLQKLTVINVYCPRADPDKPE---RKEFK 156
Cdd:PRK13911  71 --KEPLSV----------SYGINIE-------EHDKEGRVITCE--------FESFYLVNVYTPNSQQALSRlsyRMSWE 123

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  157 LQFYRLLQCraeaiLSSGSHVIILGDVNTSHRPIDHCDPDdvdnfednpgrkwldqflfetaENSENGNAADEPAEDFQE 236
Cdd:PRK13911 124 VEFKKFLKA-----LELKKPVIVCGDLNVAHNEIDLENPK----------------------TNRKNAGFSDEERGKFSE 176

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41055919  237 SASGGkFVDSFRYFHPKRSNAFTCWSTLTGARQTNYGTRIDYIFSNHSLvKTFFIGVDIMPEVEGSDHCPVWAQL 311
Cdd:PRK13911 177 LLNAG-FIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPL-KTRLKDALIYKDILGSDHCPVGLEL 249
PRK11756 PRK11756
exonuclease III; Provisional
 1-312 1.80e-27

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 111.52  E-value: 1.80e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919    1 MKIVTWNINGIRTFKNGIKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFsfsRGRSGYSGVATYCKdaATPFL 80
Cdd:PRK11756   1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFY---HGQKGHYGVALLSK--QTPIA 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   81 AEEGLTGllsnqgavigcygdqveltseellalDNEGraviTQHHFIG---QDGLQKLTVINVYCPRADP-DKPERKEFK 156
Cdd:PRK11756  76 VRKGFPT--------------------------DDEE----AQRRIIMatiPTPNGNLTVINGYFPQGESrDHPTKFPAK 125

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  157 LQFYRLLQCRAEAILSSGSHVIILGDVNTShrPIDHcdpdDVDNFEDNPGRkWLDQ----FLFETAEnsengnaadepae 232
Cdd:PRK11756 126 RQFYQDLQNYLETELSPDNPLLIMGDMNIS--PTDL----DIGIGEENRKR-WLRTgkcsFLPEERE------------- 185

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  233 dFQESASGGKFVDSFRYFHPKRSNAFTCWSTLTGARQTNYGTRIDYIFSNHSLVKTfFIGVDIMPEVEG----SDHCPVW 308
Cdd:PRK11756 186 -WLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAER-CVETGIDYDIRGmekpSDHAPIW 263


                 ....
gi 41055919  309 AQLS 312
Cdd:PRK11756 264 ATFK 267
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-311 1.92e-22

Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197310 [Multi-domain]  Cd Length: 236  Bit Score: 96.27  E-value: 1.92e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   3 IVTWNINGIR-TFK-NGIKKILDSFDADIICVQETKVTRDllDEKTAIVDGYNSYFSFSRGRSGySGVATYCKDAATPfl 80
Cdd:cd09076   1 IGTLNVRGLRsPGKrAQLLEELKRKKLDILGLQETHWTGE--GELKKKREGGTILYSGSDSGKS-RGVAILLSKTAAN-- 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  81 aeegltGLLSNQgavigcygdqveltseellaLDNEGRAVITQhhFIGQDglQKLTVINVYCPRADPDkperkEFKLQFY 160
Cdd:cd09076  76 ------KLLEYT--------------------KVVSGRIIMVR--FKIKG--KRLTIINVYAPTARDE-----EEKEEFY 120

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 161 RLLQCRAEAIlSSGSHVIILGDVNTshrPIDhcdpddvdnfEDNPGRKWLDQflfetaENSENGNAADEPAEDFQesasg 240
Cdd:cd09076 121 DQLQDVLDKV-PRHDTLIIGGDFNA---VLG----------PKDDGRKGLDK------RNENGERALSALIEEHD----- 175

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41055919 241 gkFVDSFRYFHPKrSNAFTcWSTLTGarqtNYGTRIDYIFSNHSLVkTFFIGVDIMPEVeGSDHCPVWAQL 311
Cdd:cd09076 176 --LVDVWRENNPK-TREYT-WRSPDH----GSRSRIDRILVSKRLR-VKVKKTKITPGA-GSDHRLVTLKL 236
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-311 3.91e-20

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: 89.85  E-value: 3.91e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   3 IVTWNINGIRTFKN--GIKKILDSFDADIICVQETKV-TRDLLDEKTAIVDGYNSYFSFSRGRSGYSGVATYCKDaatpf 79
Cdd:cd08372   1 VASYNVNGLNAATRasGIARWVRELDPDIVCLQEVKDsQYSAVALNQLLPEGYHQYQSGPSRKEGYEGVAILSKT----- 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  80 laeegltgllsnqgavigCYGDQVELTSEEL-LALDNEGRAVITqhHFIGQDglQKLTVINVYCPRADPDKPERKEFKLQ 158
Cdd:cd08372  76 ------------------PKFKIVEKHQYKFgEGDSGERRAVVV--KFDVHD--KELCVVNAHLQAGGTRADVRDAQLKE 133

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 159 FYRLLQcraEAILSSGSHVIILGDVNTSHRpidhcdpddvdNFEDNPGRKWLDQFlfetaensengnaadepaedfqesa 238
Cdd:cd08372 134 VLEFLK---RLRQPNSAPVVICGDFNVRPS-----------EVDSENPSSMLRLF------------------------- 174

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41055919 239 SGGKFVDSFRYFHpkrsNAFTCWSTLTgarqtNYGTRIDYIFSNHSL---VKTFFIGVDIMPEVEGSDHCPVWAQL 311
Cdd:cd08372 175 VALNLVDSFETLP----HAYTFDTYMH-----NVKSRLDYIFVSKSLlpsVKSSKILSDAARARIPSDHYPIEVTL 241
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-187 4.30e-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: 64.94  E-value: 4.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919     4 VTWNINGIRTFKNG-------IKKILDSFDADIICVQETKVTRDLLDEKTAIVDGYNSYFSFSRGRSGYSGVATYCKDaa 76
Cdd:pfam03372   1 LTWNVNGGNADAAGddrkldaLAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRY-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919    77 tpflaeegltgllsnqgavigcygdqvELTSEELLALDNEGRAVITQHHFIGqdglqKLTVINVYCPRADPDKPERKEFK 156
Cdd:pfam03372  79 ---------------------------PLSSVILVDLGEFGDPALRGAIAPF-----AGVLVVPLVLTLAPHASPRLARD 126

                         170       180       190
                  ....*....|....*....|....*....|.
gi 41055919   157 LQFYRLLQCRAEAILSSGSHVIILGDVNTSH 187
Cdd:pfam03372 127 EQRADLLLLLLALLAPRSEPVILAGDFNADY 157
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 506-557 3.01e-10

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 55.49  E-value: 3.01e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 41055919   506 PLCKsHNEPCVLRTVKKAGPNLGRQFFVCARPQGhasnpqARCNFFAWVEKG 557
Cdd:pfam06839   1 PLCP-CGQRAVLLTVRKTGPNPGRQFYKCPVGRE------KQCGFFQWADEV 45
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 3-309 6.88e-06

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: 47.68  E-value: 6.88e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919   3 IVTWNINGIRTFK-----NGIKKILDSFDADIICVQETKVTRDLLDEKTA-IVDGYNSYFSFSRGRSGYSGVATYCKdaa 76
Cdd:cd09084   1 VMSYNVRSFNRYKwkddpDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRlLLKGYPYYYVVYKSDSGGTGLAIFSK--- 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919  77 TPFLAEEGLTGLLSNQGAVigcygdqveltseellaldnegRAVITqhhfIGQDglqKLTVINVYCP---------RADP 147
Cdd:cd09084  78 YPILNSGSIDFPNTNNNAI----------------------FADIR----VGGD---TIRVYNVHLEsfritpsdkELYK 128

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 148 DKPERKEFKLQFYRLLQCR-----------AEAILSSGSHVIILGDVNTS-----HRPIdhcdpddvdnfednpgrkwld 211
Cdd:cd09084 129 EEKKAKELSRNLLRKLAEAfkrraaqadllAADIAASPYPVIVCGDFNDTpasyvYRTL--------------------- 187

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055919 212 qflfetaenSENGNAAdepaedFQESASG-GKfvdSFRYFHPKrsnaftcWstltgarqtnygtRIDYIFSNHSL-VKTF 289
Cdd:cd09084 188 ---------KKGLTDA------FVEAGSGfGY---TFNGLFFP-------L-------------RIDYILTSKGFkVLRY 229

                       330       340
                ....*....|....*....|
gi 41055919 290 FIGVDIMpevegSDHCPVWA 309
Cdd:cd09084 230 RVDPGKY-----SDHYPIVA 244
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-34 1.34e-03

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 39.89  E-value: 1.34e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 41055919   1 MKIVTWNI-NGI----RTFKNGIKKILDSFDADIICVQE 34
Cdd:COG3568   8 LRVMTYNIrYGLgtdgRADLERIARVIRALDPDVVALQE 46
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 240-311 3.39e-03

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


Pssm-ID: 197317 [Multi-domain]  Cd Length: 252  Bit Score: 39.51  E-value: 3.39e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41055919 240 GGKFVDSFRYFHPKRSNAftcWSTLTGARQTNYGTRIDYIFSNHSL-VKTFFIGVDIMPEVEGSDHCPVWAQL 311
Cdd:cd09083 183 SGGLKDARDTAATTDGGP---EGTFHGFKGPPGGSRIDYIFVSPGVkVLSYEILTDRYDGRYPSDHFPVVADL 252
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 276-312 6.01e-03

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 37.97  E-value: 6.01e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 41055919 276 IDYIFSNHSL-VKTFFIgVDIMPEVEGSDHCPVWAQLS 312
Cdd:COG3568 129 IDYILVSPGLrVLSAEV-LDSPLGRAASDHLPVVADLE 165
 
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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