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Conserved domains on  [gi|1720435943|ref|XP_030107378|]
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DNA-(apurinic or apyrimidinic site) endonuclease 2 isoform X2 [Mus musculus]

Protein Classification

exonuclease/endonuclease/phosphatase family protein( domain architecture ID 662)

exonuclease/endonuclease/phosphatase (EEP) family protein may cleave phosphodiester bonds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EEP super family cl00490
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-222 1.54e-102

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


The actual alignment was detected with superfamily member cd09088:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 309  Bit Score: 300.77  E-value: 1.54e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   3 RVVSWNINGIRSPLQGlacqEPSSCPTALRRVLDELDADIVCLQETKVTSehsriqdlygDVLTEPLAIVEGYNSYFSFS 82
Cdd:cd09088     1 RIVTWNVNGIRTRLQY----QPWNKENSLKSFLDSLDADIICLQETKLTR----------DELDEPSAIVEGYDSFFSFS 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  83 RSRSGYSGVATFCKDSA-TPVAAEEGLSGVFAT--------LNGDIGCYGNMDEFT-QEELRVLDSEGRALLTQHKirtl 152
Cdd:cd09088    67 RGRKGYSGVATYCRDSAaTPVAAEEGLTGVLSSpnqknelsENDDIGCYGEMLEFTdSKELLELDSEGRCVLTDHG---- 142

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943 153 egkekTLTLINVYCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPIDHCDASSL 222
Cdd:cd09088   143 -----TFVLINVYCPRADPEKEERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDS 207
 
Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 3-222 1.54e-102

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: 300.77  E-value: 1.54e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   3 RVVSWNINGIRSPLQGlacqEPSSCPTALRRVLDELDADIVCLQETKVTSehsriqdlygDVLTEPLAIVEGYNSYFSFS 82
Cdd:cd09088     1 RIVTWNVNGIRTRLQY----QPWNKENSLKSFLDSLDADIICLQETKLTR----------DELDEPSAIVEGYDSFFSFS 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  83 RSRSGYSGVATFCKDSA-TPVAAEEGLSGVFAT--------LNGDIGCYGNMDEFT-QEELRVLDSEGRALLTQHKirtl 152
Cdd:cd09088    67 RGRKGYSGVATYCRDSAaTPVAAEEGLTGVLSSpnqknelsENDDIGCYGEMLEFTdSKELLELDSEGRCVLTDHG---- 142

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943 153 egkekTLTLINVYCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPIDHCDASSL 222
Cdd:cd09088   143 -----TFVLINVYCPRADPEKEERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDS 207
XthA COG0708
Exonuclease III [Replication, recombination and repair];
2-215 5.33e-35

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 125.96  E-value: 5.33e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRSplqglacqepsscptALRRVLD---ELDADIVCLQETKVtsehsriQDlygDVLTEPLAIVEGYNSY 78
Cdd:COG0708     1 MKIASWNVNGIRA---------------RLPKLLDwlaEEDPDVLCLQETKA-------QD---EQFPLEAFEAAGYHVY 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  79 FSFSRsrsGYSGVATFCKDsaTPVAAEEGLSGvfatlngdigcygnmDEFtqeelrvlDSEGRALltqhkirtlEGKEKT 158
Cdd:COG0708    56 FHGQK---GYNGVAILSRL--PPEDVRRGLGG---------------DEF--------DAEGRYI---------EADFGG 98

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720435943 159 LTLINVYCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPID 215
Cdd:COG0708    99 VRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEID 155
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 2-215 7.94e-27

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: 104.77  E-value: 7.94e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRSplqglacqepssCPTALRRVLDELDADIVCLQETKVTSEHsriqdlygdvLTEPLAIVEGYNsyfSF 81
Cdd:TIGR00195   1 MKIISWNVNGLRA------------RPHKGLAWLKENQPDVLCLQETKVQDEQ----------FPLEPFHKEGYH---VF 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  82 SRSRSGYSGVATFCKDsaTPVAAEEGLsgvfatlngdigcygNMDEFtqeelrvlDSEGRALLtqhkirtleGKEKTLTL 161
Cdd:TIGR00195  56 FSGQKGYSGVAIFSKE--EPISVRRGF---------------GVEEE--------DAEGRIIM---------AEFDSFLV 101

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1720435943 162 INVYCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPID 215
Cdd:TIGR00195 102 INGYFPNGSRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEID 155
PRK11756 PRK11756
exonuclease III; Provisional
 2-215 1.73e-13

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 68.38  E-value: 1.73e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRS-PLQglacqepsscptaLRRVLDELDADIVCLQETKVTSEHSriqdlygdvltePLAIVE--GYNsy 78
Cdd:PRK11756    1 MKFVSFNINGLRArPHQ-------------LEAIIEKHQPDVIGLQETKVHDEMF------------PLEEVEalGYH-- 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  79 fSFSRSRSGYSGVATFCKdsATPVAAEEGLSGvfatlngdigcygnmDEFtqeelrvlDSEGRALLTqhkirTLEGKEKT 158
Cdd:PRK11756   54 -VFYHGQKGHYGVALLSK--QTPIAVRKGFPT---------------DDE--------EAQRRIIMA-----TIPTPNGN 102

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1720435943 159 LTLINVYCPHADPGK-PERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPID 215
Cdd:PRK11756  103 LTVINGYFPQGESRDhPTKFPAKRQFYQDLQNYLETELSPDNPLLIMGDMNISPTDLD 160
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 5-216 1.90e-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: 64.17  E-value: 1.90e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   5 VSWNINGIRSPLQGLACQepsscPTALRRVLDELDADIVCLQETKVTSEHsriqdlygdvLTEPLAIVEGYNSYFSFSRS 84
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRK-----LDALAALIRAYDPDVVALQETDDDDAS----------RLLLALLAYGGFLSYGGPGG 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  85 RSGYSGVATFCKDSATPVAAEEGLSGVFATLNGDIGCYGNmdeftqeelrvldsegralltqhkirtlegkektlTLINV 164
Cdd:pfam03372  66 GGGGGGVAILSRYPLSSVILVDLGEFGDPALRGAIAPFAG-----------------------------------VLVVP 110

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1720435943 165 YCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNtahrpIDH 216
Cdd:pfam03372 111 LVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN-----ADY 157
 
Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 3-222 1.54e-102

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: 300.77  E-value: 1.54e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   3 RVVSWNINGIRSPLQGlacqEPSSCPTALRRVLDELDADIVCLQETKVTSehsriqdlygDVLTEPLAIVEGYNSYFSFS 82
Cdd:cd09088     1 RIVTWNVNGIRTRLQY----QPWNKENSLKSFLDSLDADIICLQETKLTR----------DELDEPSAIVEGYDSFFSFS 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  83 RSRSGYSGVATFCKDSA-TPVAAEEGLSGVFAT--------LNGDIGCYGNMDEFT-QEELRVLDSEGRALLTQHKirtl 152
Cdd:cd09088    67 RGRKGYSGVATYCRDSAaTPVAAEEGLTGVLSSpnqknelsENDDIGCYGEMLEFTdSKELLELDSEGRCVLTDHG---- 142

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943 153 egkekTLTLINVYCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPIDHCDASSL 222
Cdd:cd09088   143 -----TFVLINVYCPRADPEKEERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDS 207
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 3-228 5.18e-50

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: 164.77  E-value: 5.18e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   3 RVVSWNINGIRSPLQglacqepsscpTALRRVLDELDADIVCLQETKVTSEhsriqdlygDVLTEPLAiVEGYNSYFSFS 82
Cdd:cd09073     1 KIISWNVNGLRARLK-----------KGVLKWLKEEKPDILCLQETKADED---------KLPEELQH-VEGYHSYWSPA 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  83 RSRsGYSGVATFCKDsaTPVAAEEGLSGvfatlngdigcygnmDEFtqeelrvlDSEGRALLTQHKirtlegkekTLTLI 162
Cdd:cd09073    60 RKK-GYSGVATLSKE--EPLDVSYGIGG---------------EEF--------DSEGRVITAEFD---------DFYLI 104

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720435943 163 NVYCPHADPGkPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPIDHCDASSLLPVAAC 228
Cdd:cd09073   105 NVYFPNGGRG-LERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEIDLARPKKNEKNAGF 169
XthA COG0708
Exonuclease III [Replication, recombination and repair];
2-215 5.33e-35

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 125.96  E-value: 5.33e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRSplqglacqepsscptALRRVLD---ELDADIVCLQETKVtsehsriQDlygDVLTEPLAIVEGYNSY 78
Cdd:COG0708     1 MKIASWNVNGIRA---------------RLPKLLDwlaEEDPDVLCLQETKA-------QD---EQFPLEAFEAAGYHVY 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  79 FSFSRsrsGYSGVATFCKDsaTPVAAEEGLSGvfatlngdigcygnmDEFtqeelrvlDSEGRALltqhkirtlEGKEKT 158
Cdd:COG0708    56 FHGQK---GYNGVAILSRL--PPEDVRRGLGG---------------DEF--------DAEGRYI---------EADFGG 98

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720435943 159 LTLINVYCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPID 215
Cdd:COG0708    99 VRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEID 155
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 2-215 6.29e-30

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: 112.76  E-value: 6.29e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRSPLQGlacqepsscptALRRVLDELDADIVCLQETKVTSEHsriqdlygdvLTEPLAIVEGYNSYFSF 81
Cdd:cd09085     1 MKIISWNVNGLRAVHKK-----------GFLDWFKEEKPDILCLQETKAQPEQ----------LPEDLRNIEGYHSYFNS 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  82 SRSRsGYSGVATFCKDSatPVAAEEGLsgvfatlngdigcygnmdeftqeELRVLDSEGRALltqhkirTLEGKEktLTL 161
Cdd:cd09085    60 AERK-GYSGVALYSKIE--PDSVREGL-----------------------GVEEFDNEGRIL-------IADFDD--FTL 104

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1720435943 162 INVYCPHADpGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPID 215
Cdd:cd09085   105 FNIYFPNGQ-MSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEID 157
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 2-215 7.94e-27

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: 104.77  E-value: 7.94e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRSplqglacqepssCPTALRRVLDELDADIVCLQETKVTSEHsriqdlygdvLTEPLAIVEGYNsyfSF 81
Cdd:TIGR00195   1 MKIISWNVNGLRA------------RPHKGLAWLKENQPDVLCLQETKVQDEQ----------FPLEPFHKEGYH---VF 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  82 SRSRSGYSGVATFCKDsaTPVAAEEGLsgvfatlngdigcygNMDEFtqeelrvlDSEGRALLtqhkirtleGKEKTLTL 161
Cdd:TIGR00195  56 FSGQKGYSGVAIFSKE--EPISVRRGF---------------GVEEE--------DAEGRIIM---------AEFDSFLV 101

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1720435943 162 INVYCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPID 215
Cdd:TIGR00195 102 INGYFPNGSRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEID 155
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 2-215 4.29e-25

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: 100.05  E-value: 4.29e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRSPLQGLACQepsscptalrrVLDELDADIVCLQETKVTSEhsriqdlygdVLTEPLAIVEGYNSYFSF 81
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLD-----------WLKEEQPDVLCLQETKVADE----------QFPAELFEELGYHVFFHG 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  82 SRSrsGYSGVATFCKdsATPVAAEEGLsgvfatlngdigcygNMDEFtqeelrvlDSEGRALLTqhkirTLEGkektLTL 161
Cdd:TIGR00633  60 AKK--GYSGVAILSK--VEPLDVRYGF---------------GGEPH--------DEEGRVITA-----EFDG----FTV 103

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1720435943 162 INVYCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPID 215
Cdd:TIGR00633 104 VNVYVPNGGSRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEID 157
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 2-215 7.90e-21

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: 88.44  E-value: 7.90e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRSplqglacqepsscptALRRVLDEL----DADIVCLQETKVTSEhsriqdlygdVLTEPLAIVEGYNS 77
Cdd:cd10281     1 MRVISVNVNGIRA---------------AAKKGFLEWlaaqDADVVCLQEVRAQEE----------QLDDDFFEPEGYNA 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  78 YFSFSRSRsGYSGVATFCKDsaTPVAAEEGLsgvfatlngdigcygNMDEFtqeelrvlDSEGRalltqhkirTLEGKEK 157
Cdd:cd10281    56 YFFDAEKK-GYAGVAIYSRT--QPKAVIYGL---------------GFEEF--------DDEGR---------YIEADFD 100

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1720435943 158 TLTLINVYCPHADPGKpERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPID 215
Cdd:cd10281   101 NVSVASLYVPSGSSGD-ERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEID 157
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 2-215 1.12e-20

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: 87.99  E-value: 1.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRSPLQglacqepsscpTALRRVLDELDADIVCLQETKVTSehsriqdlyGDVLTEPLAIVEGYnSYFSF 81
Cdd:cd09087     1 LKIISWNVNGLRALLK-----------KGLLDYVKKEDPDILCLQETKLQE---------GDVPKELKELLKGY-HQYWN 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  82 SRSRSGYSGVATFCKDSatPVAAEEGLsgvfatlngdigcygNMDEFtqeelrvlDSEGRALltqhkirTLEgkEKTLTL 161
Cdd:cd09087    60 AAEKKGYSGTAILSKKK--PLSVTYGI---------------GIEEH--------DQEGRVI-------TAE--FENFYL 105

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1720435943 162 INVYCPHADpGKPERLTFKMRFYRllQMRAE-ALLAAGSHVIILGDLNTAHRPID 215
Cdd:cd09087   106 VNTYVPNSG-RGLERLDRRKEWDV--DFRAYlKKLDSKKPVIWCGDLNVAHEEID 157
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 2-215 2.42e-20

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: 87.19  E-value: 2.42e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRSPLQglacqepsscptALRRVLDELDADIVCLQETKVTSEhsriqdlygdvlTEPLAIVE--GYNsyf 79
Cdd:cd09086     1 MKIATWNVNSIRARLE------------QVLDWLKEEDPDVLCLQETKVEDD------------QFPADAFEalGYH--- 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  80 SFSRSRSGYSGVATFCKdsatpvaaeEGLSGVFATLNGDIGcygnmdeftqeelrvlDSEGRAlltqhkirtLEGKEKTL 159
Cdd:cd09086    54 VAVHGQKAYNGVAILSR---------LPLEDVRTGFPGDPD----------------DDQARL---------IAARVGGV 99

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1720435943 160 TLINVYCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPID 215
Cdd:cd09086   100 RVINLYVPNGGDIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDID 155
PRK11756 PRK11756
exonuclease III; Provisional
 2-215 1.73e-13

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 68.38  E-value: 1.73e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRS-PLQglacqepsscptaLRRVLDELDADIVCLQETKVTSEHSriqdlygdvltePLAIVE--GYNsy 78
Cdd:PRK11756    1 MKFVSFNINGLRArPHQ-------------LEAIIEKHQPDVIGLQETKVHDEMF------------PLEEVEalGYH-- 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  79 fSFSRSRSGYSGVATFCKdsATPVAAEEGLSGvfatlngdigcygnmDEFtqeelrvlDSEGRALLTqhkirTLEGKEKT 158
Cdd:PRK11756   54 -VFYHGQKGHYGVALLSK--QTPIAVRKGFPT---------------DDE--------EAQRRIIMA-----TIPTPNGN 102

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1720435943 159 LTLINVYCPHADPGK-PERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPID 215
Cdd:PRK11756  103 LTVINGYFPQGESRDhPTKFPAKRQFYQDLQNYLETELSPDNPLLIMGDMNISPTDLD 160
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 5-216 1.90e-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: 64.17  E-value: 1.90e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   5 VSWNINGIRSPLQGLACQepsscPTALRRVLDELDADIVCLQETKVTSEHsriqdlygdvLTEPLAIVEGYNSYFSFSRS 84
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRK-----LDALAALIRAYDPDVVALQETDDDDAS----------RLLLALLAYGGFLSYGGPGG 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  85 RSGYSGVATFCKDSATPVAAEEGLSGVFATLNGDIGCYGNmdeftqeelrvldsegralltqhkirtlegkektlTLINV 164
Cdd:pfam03372  66 GGGGGGVAILSRYPLSSVILVDLGEFGDPALRGAIAPFAG-----------------------------------VLVVP 110

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1720435943 165 YCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNtahrpIDH 216
Cdd:pfam03372 111 LVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN-----ADY 157
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 4-215 1.85e-10

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: 59.42  E-value: 1.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   4 VVSWNINGIRSplqglacqepSSCPTALRRVLDELDADIVCLQETKvtsehsriqDLYGDVLTEPLAIVEGYNSYFSFSR 83
Cdd:cd08372     1 VASYNVNGLNA----------ATRASGIARWVRELDPDIVCLQEVK---------DSQYSAVALNQLLPEGYHQYQSGPS 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  84 SRSGYSGVATFCKDSATPVaaeeglsgvfatlngdigcygnmDEFTQEEL-RVLDSEGRALLTQhkirtLEGKEKTLTLI 162
Cdd:cd08372    62 RKEGYEGVAILSKTPKFKI-----------------------VEKHQYKFgEGDSGERRAVVVK-----FDVHDKELCVV 113

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1720435943 163 NVYCPHADPGKPERLTFKMRFYRLLQmraEALLAAGSHVIILGDLNTAHRPID 215
Cdd:cd08372   114 NAHLQAGGTRADVRDAQLKEVLEFLK---RLRQPNSAPVVICGDFNVRPSEVD 163
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 2-215 2.74e-10

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 59.32  E-value: 2.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRsplqglACQEpsscpTALRRVLDELDADIVCLQETKVTSEHSRIQdlygdvlteplaiVEGYnSYFSF 81
Cdd:PRK13911    1 MKLISWNVNGLR------ACMT-----KGFMDFFNSVDADVFCIQESKMQQEQNTFE-------------FKGY-FDFWN 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  82 SRSRSGYSGVATFCKDSatPVAAEEGLsgvfatlngdigcygNMDEFtqeelrvlDSEGRALLTQHkirtlegkeKTLTL 161
Cdd:PRK13911   56 CAIKKGYSGVVTFTKKE--PLSVSYGI---------------NIEEH--------DKEGRVITCEF---------ESFYL 101

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720435943 162 INVYCPHADPGKpERLTFKM-------RFYRLLQMRAEallaagshVIILGDLNTAHRPID 215
Cdd:PRK13911  102 VNVYTPNSQQAL-SRLSYRMswevefkKFLKALELKKP--------VIVCGDLNVAHNEID 153
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 4-209 3.62e-10

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: 58.52  E-value: 3.62e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943   4 VVSWNINGIRSPlqglacqepsscpTALRRVLDEL---DADIVCLQETKVTSEHSRIQDLYGD--VLTEPLAIVEGynsy 78
Cdd:cd09076     1 IGTLNVRGLRSP-------------GKRAQLLEELkrkKLDILGLQETHWTGEGELKKKREGGtiLYSGSDSGKSR---- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  79 fsfsrsrsgysGVATFCKDSATPVAaeeglsgVFATLngdigcygnmdeftqeelrvlDSEGRALLTqhkirTLEGKEKT 158
Cdd:cd09076    64 -----------GVAILLSKTAANKL-------LEYTK---------------------VVSGRIIMV-----RFKIKGKR 99

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1720435943 159 LTLINVYCPHADPGKperltFKMRFYRLLQmRAEALLAAGSHVIILGDLNT 209
Cdd:cd09076   100 LTIINVYAPTARDEE-----EKEEFYDQLQ-DVLDKVPRHDTLIIGGDFNA 144
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-47 2.18e-05

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 43.74  E-value: 2.18e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1720435943   1 MLRVVSWNINGIRSPlqglacqEPSSCPTALRRVLDELDADIVCLQE 47
Cdd:COG3568     7 TLRVMTYNIRYGLGT-------DGRADLERIARVIRALDPDVVALQE 46
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 2-47 5.92e-04

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: 40.40  E-value: 5.92e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1720435943   2 LRVVSWNINGIRSPlqglacqepssCP----TALRRVLDELDADIVCLQE 47
Cdd:cd09080     1 LKVLTWNVDFLDDV-----------NLaermRAILKLLEELDPDVIFLQE 39
RgfB-like cd09079
Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, ...
 30-209 1.63e-03

Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, and related proteins; This family includes Streptococcus agalactiae RgfB (for regulator of fibrinogen binding) and related proteins. The function of RgfB is unknown. It is part of a putative two component signal transduction system designated rgfBDAC (the rgf locus was identified in a screen for mutants of Streptococcus agalactiae with altered binding to fibrinogen). RgfA,-C,and -D do not belong to this superfamily: rgfA encodes a putative response regulator, and rgfC, a putative histidine kinase. All four genes are co-transcribed, and may be involved in regulating expression of bacterial cell surface components. 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: 197313 [Multi-domain]  Cd Length: 259  Bit Score: 39.17  E-value: 1.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943  30 ALRRVLDELDADIVCLQE------TKVTSEHSRiQDLYGDVLTEPLAivegynsyfsfsRSRSGYSGVATFCK---DSat 100
Cdd:cd09079    20 RLAKIIAEEDYDVIALQEvnqsidAPVSQVPIK-EDNFALLLYEKLR------------ELGATYYWTWILSHigyDK-- 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720435943 101 pvaAEEGLsgvfATLNGdigcyGNMDEFTQeelrVLDSEGRAlLTQHKIR-TLEGK-EKTLTLINVYCPHADPGKPERLT 178
Cdd:cd09079    85 ---YDEGL----AILSK-----RPIAEVED----FYVSKSQD-YTDYKSRkILGATiEINGQPIDVYSCHLGWWYDEEEP 147

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1720435943 179 FKmrfYRLLQMRAeALLAAGSHVIILGDLNT 209
Cdd:cd09079   148 FA---YEWSKLEK-ALAEAGRPVLLMGDFNN 174
 
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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