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Conserved domains on  [gi|386780804|ref|NP_001248294|]
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DNA-(apurinic or apyrimidinic site) endonuclease 2 [Macaca mulatta]

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 ...
 3-311 2.10e-169

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: 480.66  E-value: 2.10e-169
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   3 RVVSWNINGIRRPVQGVANQEPsncaaVAVGRILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFSRNRSGYSGV 82
Cdd:cd09088    1 RIVTWNVNGIRTRLQYQPWNKE-----NSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  83 ATFCKDNA-TPVAAEEGLSGLFAT--------QNGNVGCYGNMDEFT-QEELRALDSEGRALLTQHKIrtwegkeriLTL 152
Cdd:cd09088   76 ATYCRDSAaTPVAAEEGLTGVLSSpnqknelsENDDIGCYGEMLEFTdSKELLELDSEGRCVLTDHGT---------FVL 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 153 INVYCPHADPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLECF-----EEDPGRKWMDS 227
Cdd:cd09088  147 INVYCPRADPEKEERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFggesfEDNPSRQWLDQ 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 228 LLSNLGCQSASHVGPFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLVIDTFrASFLLPEVMGSDHCPV 307
Cdd:cd09088  227 LLGDSGEGGGSPGGLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVK-AADILPEVEGSDHCPV 305


                 ....
gi 386780804 308 GAVL 311
Cdd:cd09088  306 YADL 309
zf-GRF super family cl46396
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 467-514 1.46e-09

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: 53.56  E-value: 1.46e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 386780804  467 PLCGGHRePCVMRTVKKPGPNLGRRFYMCARPRGpptdpsSRCNFFLW 514
Cdd:pfam06839   1 PLCPCGQ-RAVLLTVRKTGPNPGRQFYKCPVGRE------KQCGFFQW 41
 
Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 3-311 2.10e-169

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: 480.66  E-value: 2.10e-169
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   3 RVVSWNINGIRRPVQGVANQEPsncaaVAVGRILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFSRNRSGYSGV 82
Cdd:cd09088    1 RIVTWNVNGIRTRLQYQPWNKE-----NSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  83 ATFCKDNA-TPVAAEEGLSGLFAT--------QNGNVGCYGNMDEFT-QEELRALDSEGRALLTQHKIrtwegkeriLTL 152
Cdd:cd09088   76 ATYCRDSAaTPVAAEEGLTGVLSSpnqknelsENDDIGCYGEMLEFTdSKELLELDSEGRCVLTDHGT---------FVL 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 153 INVYCPHADPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLECF-----EEDPGRKWMDS 227
Cdd:cd09088  147 INVYCPRADPEKEERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFggesfEDNPSRQWLDQ 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 228 LLSNLGCQSASHVGPFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLVIDTFrASFLLPEVMGSDHCPV 307
Cdd:cd09088  227 LLGDSGEGGGSPGGLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVK-AADILPEVEGSDHCPV 305


                 ....
gi 386780804 308 GAVL 311
Cdd:cd09088  306 YADL 309
XthA COG0708
Exonuclease III [Replication, recombination and repair];
2-311 1.36e-60

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 199.92  E-value: 1.36e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   2 LRVVSWNINGIRrpvqgvanqepsncAAV-AVGRILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFsrnRSGYS 80
Cdd:COG0708    1 MKIASWNVNGIR--------------ARLpKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHG---QKGYN 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  81 GVATFCKDnaTPVAAEEGLSGlfatqngnvgcygnmDEFtqeelralDSEGRALLTqhkirTWEGkeriLTLINVYCPHA 160
Cdd:COG0708   64 GVAILSRL--PPEDVRRGLGG---------------DEF--------DAEGRYIEA-----DFGG----VRVVSLYVPNG 109

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 161 DPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLE---CF--EEdpgRKWMDSLLsNLGcq 235
Cdd:COG0708  110 GSVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVKNPKANLknaGFlpEE---RAWFDRLL-ELG-- 183

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 236 sashvgpFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLViDTFRASFLLPE----VMGSDHCPVGAVL 311
Cdd:COG0708  184 -------LVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALA-DRLKDAGIDREprgdERPSDHAPVVVEL 255
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 2-311 1.31e-50

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: 173.62  E-value: 1.31e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804    2 LRVVSWNINGIR-RPVQGVANqepsncaavavgrILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFSRnrSGYS 80
Cdd:TIGR00633   1 MKIISWNVNGLRaRLHKLFLD-------------WLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAK--KGYS 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   81 GVATFCKdnATPVAAEEGLsglfatqngnvgcygNMDEFtqeelralDSEGRALLTqhkirTWEGkeriLTLINVYCPHA 160
Cdd:TIGR00633  66 GVAILSK--VEPLDVRYGF---------------GGEPH--------DEEGRVITA-----EFDG----FTVVNVYVPNG 111

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  161 DPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLE---CF--EEdpgRKWMDSLLSNlgcq 235
Cdd:TIGR00633 112 GSRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLGNPKENKgnaGFtpEE---REWFDELLEA---- 184

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 386780804  236 sashvgPFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTL---VIDtfraSFLLPEVMGSDHCPVGAVL 311
Cdd:TIGR00633 185 ------GFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLaerVVD----SYIDSEIRGSDHCPIVLEL 253
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 2-308 2.33e-26

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 107.47  E-value: 2.33e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   2 LRVVSWNINGIRRpvqgvanqepsnCAAVAVGRILDELDADIVCLQETKVTRDALTEPlaivegYNSYFSF--SRNRSGY 79
Cdd:PRK13911   1 MKLISWNVNGLRA------------CMTKGFMDFFNSVDADVFCIQESKMQQEQNTFE------FKGYFDFwnCAIKKGY 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  80 SGVATFCKDNatPVAAEEGLsglfatqngnvgcygNMDEFtqeelralDSEGRALLTQHKIrtwegkeriLTLINVYCPH 159
Cdd:PRK13911  63 SGVVTFTKKE--PLSVSYGI---------------NIEEH--------DKEGRVITCEFES---------FYLVNVYTPN 108

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 160 ADPGRpERLVFKM-------RFYRLLQIRAEallaagshVIILGDLNTAHRPIDHwdavnlecfeEDPGRKWMDSLLSNL 232
Cdd:PRK13911 109 SQQAL-SRLSYRMswevefkKFLKALELKKP--------VIVCGDLNVAHNEIDL----------ENPKTNRKNAGFSDE 169

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 386780804 233 GCQSASHV--GPFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLVIdTFRASFLLPEVMGSDHCPVG 308
Cdd:PRK13911 170 ERGKFSELlnAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKT-RLKDALIYKDILGSDHCPVG 246
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 5-207 1.13e-15

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 75.34  E-value: 1.13e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804    5 VSWNINGIRRPVQGVANQepsncaAVAVGRILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFSRNRSGYSGVAT 84
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRK------LDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGGGGGGVAI 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   85 FCKDNATPVAAEEGLSGLfatqngnvgcygnmdeftqeelraldsegralltqHKIRTWEGKERILTLINVYCPHADPGR 164
Cdd:pfam03372  75 LSRYPLSSVILVDLGEFG-----------------------------------DPALRGAIAPFAGVLVVPLVLTLAPHA 119

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 386780804  165 PERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNtahrpIDH 207
Cdd:pfam03372 120 SPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN-----ADY 157
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 467-514 1.46e-09

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: 53.56  E-value: 1.46e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 386780804  467 PLCGGHRePCVMRTVKKPGPNLGRRFYMCARPRGpptdpsSRCNFFLW 514
Cdd:pfam06839   1 PLCPCGQ-RAVLLTVRKTGPNPGRQFYKCPVGRE------KQCGFFQW 41
 
Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 3-311 2.10e-169

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: 480.66  E-value: 2.10e-169
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   3 RVVSWNINGIRRPVQGVANQEPsncaaVAVGRILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFSRNRSGYSGV 82
Cdd:cd09088    1 RIVTWNVNGIRTRLQYQPWNKE-----NSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  83 ATFCKDNA-TPVAAEEGLSGLFAT--------QNGNVGCYGNMDEFT-QEELRALDSEGRALLTQHKIrtwegkeriLTL 152
Cdd:cd09088   76 ATYCRDSAaTPVAAEEGLTGVLSSpnqknelsENDDIGCYGEMLEFTdSKELLELDSEGRCVLTDHGT---------FVL 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 153 INVYCPHADPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLECF-----EEDPGRKWMDS 227
Cdd:cd09088  147 INVYCPRADPEKEERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFggesfEDNPSRQWLDQ 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 228 LLSNLGCQSASHVGPFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLVIDTFrASFLLPEVMGSDHCPV 307
Cdd:cd09088  227 LLGDSGEGGGSPGGLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVK-AADILPEVEGSDHCPV 305


                 ....
gi 386780804 308 GAVL 311
Cdd:cd09088  306 YADL 309
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 3-311 1.03e-98

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: 298.43  E-value: 1.03e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   3 RVVSWNINGIRRPVQgvanqepsncaaVAVGRILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFSRnRSGYSGV 82
Cdd:cd09073    1 KIISWNVNGLRARLK------------KGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPAR-KKGYSGV 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  83 ATFCKDnaTPVAAEEGLSGLFatqngnvgcygnmdeftqeelraLDSEGRALLTQHKIrtwegkeriLTLINVYCPHADP 162
Cdd:cd09073   68 ATLSKE--EPLDVSYGIGGEE-----------------------FDSEGRVITAEFDD---------FYLINVYFPNGGR 113

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 163 GrPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLECF--EEDPGRKWMDSLLSNlgcqsashv 240
Cdd:cd09073  114 G-LERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEIDLARPKKNEKNagFTPEERAWFDKLLSL--------- 183

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 386780804 241 gPFIDSYRCFQPkQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLVIDTFrASFLLPEVMGSDHCPVGAVL 311
Cdd:cd09073  184 -GYVDTFRHFHP-EPGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVK-DSGILSKVKGSDHAPVTLEL 251
XthA COG0708
Exonuclease III [Replication, recombination and repair];
2-311 1.36e-60

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 199.92  E-value: 1.36e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   2 LRVVSWNINGIRrpvqgvanqepsncAAV-AVGRILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFsrnRSGYS 80
Cdd:COG0708    1 MKIASWNVNGIR--------------ARLpKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHG---QKGYN 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  81 GVATFCKDnaTPVAAEEGLSGlfatqngnvgcygnmDEFtqeelralDSEGRALLTqhkirTWEGkeriLTLINVYCPHA 160
Cdd:COG0708   64 GVAILSRL--PPEDVRRGLGG---------------DEF--------DAEGRYIEA-----DFGG----VRVVSLYVPNG 109

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 161 DPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLE---CF--EEdpgRKWMDSLLsNLGcq 235
Cdd:COG0708  110 GSVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVKNPKANLknaGFlpEE---RAWFDRLL-ELG-- 183

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 236 sashvgpFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLViDTFRASFLLPE----VMGSDHCPVGAVL 311
Cdd:COG0708  184 -------LVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALA-DRLKDAGIDREprgdERPSDHAPVVVEL 255
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 2-311 5.04e-59

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: 195.57  E-value: 5.04e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   2 LRVVSWNINGIRrpvqgvanqepsncaavAVGR-----ILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFSRnR 76
Cdd:cd09085    1 MKIISWNVNGLR-----------------AVHKkgfldWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAE-R 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  77 SGYSGVATFCKDNatPVAAEEGLsglfatqngnvgcygnmdeftqeELRALDSEGRALLTQHKIrtwegkeriLTLINVY 156
Cdd:cd09085   63 KGYSGVALYSKIE--PDSVREGL-----------------------GVEEFDNEGRILIADFDD---------FTLFNIY 108

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 157 CPHADPGRpERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIdhwDAVNLECFEEDPG-----RKWMDSLLSN 231
Cdd:cd09085  109 FPNGQMSE-ERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEI---DLARPKENEKVSGflpeeRAWMDKFIEN 184

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 232 lGcqsashvgpFIDSYRCFQpKQEGAFTCWSAVTGARHLNYGSRLDYVLGDrTLVIDTFRASFLLPEVMGSDHCPVGAVL 311
Cdd:cd09085  185 -G---------YVDTFRMFN-KEPGQYTWWSYRTRARERNVGWRIDYFFVN-EEFKPKVKDAGILPDVMGSDHCPVSLEL 252
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 2-311 1.31e-50

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: 173.62  E-value: 1.31e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804    2 LRVVSWNINGIR-RPVQGVANqepsncaavavgrILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFSRnrSGYS 80
Cdd:TIGR00633   1 MKIISWNVNGLRaRLHKLFLD-------------WLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAK--KGYS 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   81 GVATFCKdnATPVAAEEGLsglfatqngnvgcygNMDEFtqeelralDSEGRALLTqhkirTWEGkeriLTLINVYCPHA 160
Cdd:TIGR00633  66 GVAILSK--VEPLDVRYGF---------------GGEPH--------DEEGRVITA-----EFDG----FTVVNVYVPNG 111

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  161 DPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLE---CF--EEdpgRKWMDSLLSNlgcq 235
Cdd:TIGR00633 112 GSRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLGNPKENKgnaGFtpEE---REWFDELLEA---- 184

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 386780804  236 sashvgPFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTL---VIDtfraSFLLPEVMGSDHCPVGAVL 311
Cdd:TIGR00633 185 ------GFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLaerVVD----SYIDSEIRGSDHCPIVLEL 253
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 2-311 1.17e-48

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: 168.33  E-value: 1.17e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804    2 LRVVSWNINGIR-RPVQGVAnqepsncaavavgrILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFSRnrsGYS 80
Cdd:TIGR00195   1 MKIISWNVNGLRaRPHKGLA--------------WLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQK---GYS 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   81 GVATFCKDnaTPVAAEEGLsglfatqngnvgcygNMDEFtqeelralDSEGRALLTQhkirtWEGkeriLTLINVYCPHA 160
Cdd:TIGR00195  64 GVAIFSKE--EPISVRRGF---------------GVEEE--------DAEGRIIMAE-----FDS----FLVINGYFPNG 109

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  161 DPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLE---CFEEDPgRKWMDSLLsNLGcqsa 237
Cdd:TIGR00195 110 SRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDLHIPDENRnhtGFLPEE-REWLDRLL-EAG---- 183

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 386780804  238 shvgpFIDSYRCFQPkQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLViDTFRASFLLPEVMG----SDHCPVGAVL 311
Cdd:TIGR00195 184 -----LVDTFRKFNP-DEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLK-ERCVDCGIDYDIRGsekpSDHCPVVLEF 254
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 2-311 1.45e-45

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: 160.03  E-value: 1.45e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   2 LRVVSWNINGIRrpvqgvanqepsncAAVAVG--RILDELDADIVCLQETKVTRDALT-EPLAIVEGYNSYFSFSRnRSG 78
Cdd:cd09087    1 LKIISWNVNGLR--------------ALLKKGllDYVKKEDPDILCLQETKLQEGDVPkELKELLKGYHQYWNAAE-KKG 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  79 YSGVATFCKDnaTPVAAEEGLsglfatqngnvgcygNMDEFtqeelralDSEGRalltqhkirtwegkerILT------- 151
Cdd:cd09087   66 YSGTAILSKK--KPLSVTYGI---------------GIEEH--------DQEGR----------------VITaefenfy 104

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 152 LINVYCPHAdpGRP-ERLVFKMRFYRLLQ--IRAealLAAGSHVIILGDLNTAHRPIDHWDAvnlECFEEDPG-----RK 223
Cdd:cd09087  105 LVNTYVPNS--GRGlERLDRRKEWDVDFRayLKK---LDSKKPVIWCGDLNVAHEEIDLANP---KTNKKSAGftpeeRE 176

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 224 WMDSLLSNlgcqsashvgPFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLViDTFRASFLLPEVMGSD 303
Cdd:cd09087  177 SFTELLEA----------GFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLK-DRVVDSFIRSDIMGSD 245


                 ....*...
gi 386780804 304 HCPVGAVL 311
Cdd:cd09087  246 HCPIGLEL 253
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 2-311 1.58e-37

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: 138.42  E-value: 1.58e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   2 LRVVSWNINGIR-RPVQgvanqepsncaavaVGRILDELDADIVCLQETKVTRDALtePLAIVE--GYNSYFsfsRNRSG 78
Cdd:cd09086    1 MKIATWNVNSIRaRLEQ--------------VLDWLKEEDPDVLCLQETKVEDDQF--PADAFEalGYHVAV---HGQKA 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  79 YSGVATFCKdnatpvaaeeglSGLFATQNGNVGCYGnmdeftqeelralDSEGRALltqhkirtwEGKERILTLINVYCP 158
Cdd:cd09086   62 YNGVAILSR------------LPLEDVRTGFPGDPD-------------DDQARLI---------AARVGGVRVINLYVP 107

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 159 HADPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLE---CF--EEdpgRKWMDSLLsNLG 233
Cdd:cd09086  108 NGGDIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDVWDPKQLLgkvLFtpEE---REALRALL-DLG 183

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 234 cqsashvgpFIDSYRCFQPkQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLViDTFRASFLLPEVMG----SDHCPVGA 309
Cdd:cd09086  184 ---------FVDAFRALHP-DEKLFTWWDYRAGAFERNRGLRIDHILASPALA-DRLKDVGIDREPRGwekpSDHAPVVA 252


                 ..
gi 386780804 310 VL 311
Cdd:cd09086  253 EL 254
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 2-307 8.85e-36

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: 133.89  E-value: 8.85e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   2 LRVVSWNINGIRrpvqgvanqepsncAAVAVGRI--LDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFsFSRNRSGY 79
Cdd:cd10281    1 MRVISVNVNGIR--------------AAAKKGFLewLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYF-FDAEKKGY 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  80 SGVATFCKDnaTPVAAEEGLsglfatqngnvgcygNMDEFtqeelralDSEGRALltQHKIRTwegkeriLTLINVYCPH 159
Cdd:cd10281   66 AGVAIYSRT--QPKAVIYGL---------------GFEEF--------DDEGRYI--EADFDN-------VSVASLYVPS 111

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 160 ADPGRpERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPID--HWDAvNlecfEEDPG-----RKWMDSLLSNL 232
Cdd:cd10281  112 GSSGD-ERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDikNWKA-N----QKNSGflpeeRAWLDQVFGEL 185

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 386780804 233 GcqsashvgpFIDSYRCFQPkQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLViDTFRASFLLPEVMGSDHCPV 307
Cdd:cd10281  186 G---------YVDAFRELNP-DEGQYTWWSNRGQARANNVGWRIDYQIATPGLA-SKVVSAWIYREERFSDHAPL 249
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 2-308 2.33e-26

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 107.47  E-value: 2.33e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   2 LRVVSWNINGIRRpvqgvanqepsnCAAVAVGRILDELDADIVCLQETKVTRDALTEPlaivegYNSYFSF--SRNRSGY 79
Cdd:PRK13911   1 MKLISWNVNGLRA------------CMTKGFMDFFNSVDADVFCIQESKMQQEQNTFE------FKGYFDFwnCAIKKGY 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  80 SGVATFCKDNatPVAAEEGLsglfatqngnvgcygNMDEFtqeelralDSEGRALLTQHKIrtwegkeriLTLINVYCPH 159
Cdd:PRK13911  63 SGVVTFTKKE--PLSVSYGI---------------NIEEH--------DKEGRVITCEFES---------FYLVNVYTPN 108

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 160 ADPGRpERLVFKM-------RFYRLLQIRAEallaagshVIILGDLNTAHRPIDHwdavnlecfeEDPGRKWMDSLLSNL 232
Cdd:PRK13911 109 SQQAL-SRLSYRMswevefkKFLKALELKKP--------VIVCGDLNVAHNEIDL----------ENPKTNRKNAGFSDE 169

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 386780804 233 GCQSASHV--GPFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLVIdTFRASFLLPEVMGSDHCPVG 308
Cdd:PRK13911 170 ERGKFSELlnAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKT-RLKDALIYKDILGSDHCPVG 246
PRK11756 PRK11756
exonuclease III; Provisional
 2-313 6.66e-21

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 92.26  E-value: 6.66e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   2 LRVVSWNINGIR-RPVQGVAnqepsncaavavgrILDELDADIVCLQETKVTRDALtePLAIVE--GYNSYFsfsRNRSG 78
Cdd:PRK11756   1 MKFVSFNINGLRaRPHQLEA--------------IIEKHQPDVIGLQETKVHDEMF--PLEEVEalGYHVFY---HGQKG 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  79 YSGVATFCKdnATPVAAEEGLSGlfatqngnvgcygnmDEFtqeelralDSEGRALLTqhkirTWEGKERILTLINVYCP 158
Cdd:PRK11756  62 HYGVALLSK--QTPIAVRKGFPT---------------DDE--------EAQRRIIMA-----TIPTPNGNLTVINGYFP 111

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 159 HADP-GRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPID---------HWDAVNLECF--EEdpgRKWMD 226
Cdd:PRK11756 112 QGESrDHPTKFPAKRQFYQDLQNYLETELSPDNPLLIMGDMNISPTDLDigigeenrkRWLRTGKCSFlpEE---REWLD 188

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 227 SLLsNLGcqsashvgpFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGDRTLViDTFRASFLLPEVMG----S 302
Cdd:PRK11756 189 RLM-DWG---------LVDTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLILATQPLA-ERCVETGIDYDIRGmekpS 257

                        330
                 ....*....|.
gi 386780804 303 DHCPVGAVLSV 313
Cdd:PRK11756 258 DHAPIWATFKL 268
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 4-311 1.18e-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: 91.00  E-value: 1.18e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   4 VVSWNINGIRrpvqgvANQEPSNcaavaVGRILDELDADIVCLQETKV-TRDALTEPLAIVEGYNSYFSFSRNRSGYSGV 82
Cdd:cd08372    1 VASYNVNGLN------AATRASG-----IARWVRELDPDIVCLQEVKDsQYSAVALNQLLPEGYHQYQSGPSRKEGYEGV 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  83 ATFCKDNATPVaaeeglsglfatqngnvgcygnmDEFTQEEL-RALDSEGRALLTQHKIRTWEgkeriLTLINVYCPHAD 161
Cdd:cd08372   70 AILSKTPKFKI-----------------------VEKHQYKFgEGDSGERRAVVVKFDVHDKE-----LCVVNAHLQAGG 121

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 162 PGRPERLVFKMRFYRLLQiraEALLAAGSHVIILGDLNTAHRpidHWDAVNlecfeedpgRKWMDSLLsnlgcqsasHVG 241
Cdd:cd08372  122 TRADVRDAQLKEVLEFLK---RLRQPNSAPVVICGDFNVRPS---EVDSEN---------PSSMLRLF---------VAL 177

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 386780804 242 PFIDSYRcfqpKQEGAFTCWSAVTgarhlNYGSRLDYVLGDRTLVIDTFRASFLLPEV---MGSDHCPVGAVL 311
Cdd:cd08372  178 NLVDSFE----TLPHAYTFDTYMH-----NVKSRLDYIFVSKSLLPSVKSSKILSDAArarIPSDHYPIEVTL 241
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 4-307 1.92e-16

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: 78.55  E-value: 1.92e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   4 VVSWNINGIRrpvqgvanqEPSNCAAVAvgRILDELDADIVCLQETKVTRDalTEPLAIVEGYNSYFSFSRNRSGySGVA 83
Cdd:cd09076    1 IGTLNVRGLR---------SPGKRAQLL--EELKRKKLDILGLQETHWTGE--GELKKKREGGTILYSGSDSGKS-RGVA 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  84 TFCKDNAtpvaaeeglsglfatQNGNVgcygnmdEFTqeelraLDSEGRALLTQHKIrtwegKERILTLINVYCPHADPG 163
Cdd:cd09076   67 ILLSKTA---------------ANKLL-------EYT------KVVSGRIIMVRFKI-----KGKRLTIINVYAPTARDE 113

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804 164 RperlvFKMRFYRLLQIRAEAlLAAGSHVIILGDLNTahrPIDhwdavnlecfEEDPGRKWMDSL---LSNLGCQSASHV 240
Cdd:cd09076  114 E-----EKEEFYDQLQDVLDK-VPRHDTLIIGGDFNA---VLG----------PKDDGRKGLDKRnenGERALSALIEEH 174

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 386780804 241 GpFIDSYRCFQPKQEGaFTcWSAVTGarhlNYGSRLDYVLGDRTLVIdTFRASFLLPEVmGSDHCPV 307
Cdd:cd09076  175 D-LVDVWRENNPKTRE-YT-WRSPDH----GSRSRIDRILVSKRLRV-KVKKTKITPGA-GSDHRLV 232
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 5-207 1.13e-15

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 75.34  E-value: 1.13e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804    5 VSWNINGIRRPVQGVANQepsncaAVAVGRILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYFSFSRNRSGYSGVAT 84
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRK------LDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGGGGGGVAI 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   85 FCKDNATPVAAEEGLSGLfatqngnvgcygnmdeftqeelraldsegralltqHKIRTWEGKERILTLINVYCPHADPGR 164
Cdd:pfam03372  75 LSRYPLSSVILVDLGEFG-----------------------------------DPALRGAIAPFAGVLVVPLVLTLAPHA 119

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 386780804  165 PERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNtahrpIDH 207
Cdd:pfam03372 120 SPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN-----ADY 157
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 467-514 1.46e-09

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: 53.56  E-value: 1.46e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 386780804  467 PLCGGHRePCVMRTVKKPGPNLGRRFYMCARPRGpptdpsSRCNFFLW 514
Cdd:pfam06839   1 PLCPCGQ-RAVLLTVRKTGPNPGRQFYKCPVGRE------KQCGFFQW 41
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 4-87 3.98e-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: 48.06  E-value: 3.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   4 VVSWNINGIRRpvqgvaNQEPSNCAAVAvgRILDELDADIVCLQETKVTRDALTEPLA-IVEGYNSYFSFSRNRSGYSGV 82
Cdd:cd09084    1 VMSYNVRSFNR------YKWKDDPDKIL--DFIKKQDPDILCLQEYYGSEGDKDDDLRlLLKGYPYYYVVYKSDSGGTGL 72


                 ....*
gi 386780804  83 ATFCK 87
Cdd:cd09084   73 AIFSK 77
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 2-56 3.04e-05

Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197314 [Multi-domain]  Cd Length: 248  Bit Score: 45.41  E-value: 3.04e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 386780804   2 LRVVSWNINGIRRpvqgVANQEpsncAAVAVGRILDELDADIVCLQEtkVTRDAL 56
Cdd:cd09080    1 LKVLTWNVDFLDD----VNLAE----RMRAILKLLEELDPDVIFLQE--VTPPFL 45
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-207 6.23e-05

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 43.36  E-value: 6.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804   1 MLRVVSWNINGirrpvqGVANQEPSNCAAVAvgRILDELDADIVCLQEtkvtrdaltepLAIvegynsyfsFSRnrsgys 80
Cdd:COG3568    7 TLRVMTYNIRY------GLGTDGRADLERIA--RVIRALDPDVVALQE-----------NAI---------LSR------ 52

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  81 gvatfckdnaTPVAAEEglsglfatqngnvgcygnmdeftQEELRALDSEGRALLTqHKIRtWEGKEriLTLINVycpHA 160
Cdd:COG3568   53 ----------YPIVSSG-----------------------TFDLPDPGGEPRGALW-ADVD-VPGKP--LRVVNT---HL 92

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 386780804 161 DPGRPERlvfkmrfyRLLQIR--AEAL--LAAGSHVIILGDLNTahrpIDH 207
Cdd:COG3568   93 DLRSAAA--------RRRQARalAELLaeLPAGAPVILAGDFND----IDY 131
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 150-307 3.90e-03

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 37.34  E-value: 3.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  150 LTLINVYCPhadPGRPERLVFKmrfyrllQIRAEALLAAGSHVIILGDLNtAHRPIdhW-----DAVNLECFEEdpgrkw 224
Cdd:pfam14529   1 ILIISVYCP---PSDQLRNLLD-------TLEDILRSLDRPPIIIGGDFN-AHHPL--WgsnstDVSRGEELIE------ 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386780804  225 mdsLLSNLGCQSASHVGPFIdsyrcfqpkqegafTCWSAvtgarhlNYGSRLDYVLGDRTLVIDTfraSFLLPEVMGSDH 304
Cdd:pfam14529  62 ---FLNEHGLNLLNLPKSGP--------------TFISS-------NGDSTIDLTLTSDPLAVRV---LSDLGPDSGSDH 114


                  ...
gi 386780804  305 CPV 307
Cdd:pfam14529 115 RPI 117
 
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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