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Conserved domains on  [gi|2077599933|ref|XP_042739463|]
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endonuclease 8-like 2 [Lagopus leucura]

Protein Classification

DNA glycosylase( domain architecture ID 12963208)

Fpg/Nei family DNA glycosylase similar to Escherichia coli DNA-formamidopyrimidine glycosylase (Fpg), a DNA repair enzyme that excises oxidized purines from damaged DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MeNeil2_N cd08968
N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the ...
 1-178 1.85e-72

N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the N-terminal domain of the metazoan protein Neil2. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL2 repairs 5-hydroxyuracil (5-OHU) and other oxidized derivatives of cytosine, but it shows preference for DNA bubble structures. In addition to this MeNeil2_N domain, NEIL2 contains a helix-two turn-helix (H2TH) domain and a characteristic CHCC zinc finger motif. Neil2 is one of three homologs found in eukaryotes.


:

Pssm-ID: 176802  Cd Length: 126  Bit Score: 220.02  E-value: 1.85e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933   1 MPEGPSVRKFQLLTSRFVGQVVAKVGGSSKKINVNDLNALRLQDSQVHGKNLFLAFVAASSPLEpsveetelqkeaatgs 80
Cdd:cd08968     1 MPEGPSVRKFHHLVSPFVGQRVVKVGGSSKKINPNDLQGLRLQDSQVHGKNLFLHFDLDEEMGP---------------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933  81 rslvqgkqgqvcapltptqeeelqelqnsrpgapsaAGGPGSWLRFHFGLFGSVRANEFSRASRANKRGDWKDPIPRLVL 160
Cdd:cd08968    65 ------------------------------------DRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKDPNPRLVL 108

                         170
                  ....*....|....*...
gi 2077599933 161 YFESGGFLVFYNCRMHWC 178
Cdd:cd08968   109 HFESGGFLVFYNCRMSWC 126
Nei super family cl33822
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
119-313 5.92e-19

Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0266:

Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 84.79  E-value: 5.92e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 119 GPGSWLRFHFGLFGSVRaneFSRASRANKRGDwkdpipRLVLYFESGGFLVFYNCR----MHWCSSPVAD---------P 185
Cdd:COG0266    64 DGGLTLLIHLGMSGRLR---VVPPGEPPEKHD------HVRLVLDDGTELRFADPRrfgaLELLTPDELEvhpllarlgP 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 186 tsDILSAEFHRGRALDALCTSH-PICYTLLDQRYFSGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDC-------A 257
Cdd:COG0266   135 --EPLDPDFDPEYLAARLRRRRrPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAirevlreA 212

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2077599933 258 IQF----TSDWLQSklQGK----GLHLQIYQK--EHCPL-GHVVMKGALGppGgwkRLTWWCPQCQP 313
Cdd:COG0266   213 IEAggttLRDYVNA--DGEpgyfQQRLYVYGRegEPCPRcGTPIERIVLG--G---RSTYYCPRCQR 272
 
Name Accession Description Interval E-value
MeNeil2_N cd08968
N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the ...
 1-178 1.85e-72

N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the N-terminal domain of the metazoan protein Neil2. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL2 repairs 5-hydroxyuracil (5-OHU) and other oxidized derivatives of cytosine, but it shows preference for DNA bubble structures. In addition to this MeNeil2_N domain, NEIL2 contains a helix-two turn-helix (H2TH) domain and a characteristic CHCC zinc finger motif. Neil2 is one of three homologs found in eukaryotes.


Pssm-ID: 176802  Cd Length: 126  Bit Score: 220.02  E-value: 1.85e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933   1 MPEGPSVRKFQLLTSRFVGQVVAKVGGSSKKINVNDLNALRLQDSQVHGKNLFLAFVAASSPLEpsveetelqkeaatgs 80
Cdd:cd08968     1 MPEGPSVRKFHHLVSPFVGQRVVKVGGSSKKINPNDLQGLRLQDSQVHGKNLFLHFDLDEEMGP---------------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933  81 rslvqgkqgqvcapltptqeeelqelqnsrpgapsaAGGPGSWLRFHFGLFGSVRANEFSRASRANKRGDWKDPIPRLVL 160
Cdd:cd08968    65 ------------------------------------DRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKDPNPRLVL 108

                         170
                  ....*....|....*...
gi 2077599933 161 YFESGGFLVFYNCRMHWC 178
Cdd:cd08968   109 HFESGGFLVFYNCRMSWC 126
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
119-313 5.92e-19

Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 84.79  E-value: 5.92e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 119 GPGSWLRFHFGLFGSVRaneFSRASRANKRGDwkdpipRLVLYFESGGFLVFYNCR----MHWCSSPVAD---------P 185
Cdd:COG0266    64 DGGLTLLIHLGMSGRLR---VVPPGEPPEKHD------HVRLVLDDGTELRFADPRrfgaLELLTPDELEvhpllarlgP 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 186 tsDILSAEFHRGRALDALCTSH-PICYTLLDQRYFSGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDC-------A 257
Cdd:COG0266   135 --EPLDPDFDPEYLAARLRRRRrPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAirevlreA 212

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2077599933 258 IQF----TSDWLQSklQGK----GLHLQIYQK--EHCPL-GHVVMKGALGppGgwkRLTWWCPQCQP 313
Cdd:COG0266   213 IEAggttLRDYVNA--DGEpgyfQQRLYVYGRegEPCPRcGTPIERIVLG--G---RSTYYCPRCQR 272
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
157-313 7.76e-13

bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 67.41  E-value: 7.76e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 157 RLVLYFESGGFLVFYNCR----MHWCSS-------PVA----DPTSDILSAE-FHRgraldALCTSH-PICYTLLDQRYF 219
Cdd:PRK01103   94 HVDFVLDDGTVLRYNDPRrfgaMLLTPKgdleahpLLAhlgpEPLSDAFDGEyLAA-----KLRKKKtAIKPALLDQTVV 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 220 SGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDCAIQF---------TSdwLQSKLQGKG------LHLQIYQKE-- 282
Cdd:PRK01103  169 VGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVlaeaieqggTT--LRDYVNADGkpgyfqQSLQVYGREge 246

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2077599933 283 ---HCplGHVVMKGALGppggwKRLTWWCPQCQP 313
Cdd:PRK01103  247 pcrRC--GTPIEKIKQG-----GRSTFFCPRCQK 273
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 123-312 7.48e-11

DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). 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: 273150 [Multi-domain]  Cd Length: 272  Bit Score: 61.55  E-value: 7.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 123 WLRFHFGLFGSVRANEfsrasrankRGDWKDPIPRLVLYFESGGFLVFYNCR----MHWCSSPVADPTS-------DILS 191
Cdd:TIGR00577  69 ALVSHLRMEGKYRLEA---------VPDAPDKHDHVDFLFDDGTELRYHDPRrfgtWLLLDRGQVENIPllaklgpEPLS 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 192 AEFHRGRALDALCTSH-PICYTLLDQRYFSGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDC-------AIQFTSD 263
Cdd:TIGR00577 140 EDFTAEYLFEKLAKSKrKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAikevlrkAIEMGGT 219

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2077599933 264 WLQSKLQGKGL------HLQIYQK--EHCPL-GHVVMKGALGppggwKRLTWWCPQCQ 312
Cdd:TIGR00577 220 TIRDFSQSDGHngyfqqELQVYGRkgEPCRRcGTTIEKEKVG-----GRGTHFCPQCQ 272
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 213-259 4.39e-09

Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.


Pssm-ID: 399664 [Multi-domain]  Cd Length: 89  Bit Score: 52.68  E-value: 4.39e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2077599933 213 LLDQRYFSGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDCAIQ 259
Cdd:pfam06831  30 LLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKA 76
 
Name Accession Description Interval E-value
MeNeil2_N cd08968
N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the ...
 1-178 1.85e-72

N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the N-terminal domain of the metazoan protein Neil2. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL2 repairs 5-hydroxyuracil (5-OHU) and other oxidized derivatives of cytosine, but it shows preference for DNA bubble structures. In addition to this MeNeil2_N domain, NEIL2 contains a helix-two turn-helix (H2TH) domain and a characteristic CHCC zinc finger motif. Neil2 is one of three homologs found in eukaryotes.


Pssm-ID: 176802  Cd Length: 126  Bit Score: 220.02  E-value: 1.85e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933   1 MPEGPSVRKFQLLTSRFVGQVVAKVGGSSKKINVNDLNALRLQDSQVHGKNLFLAFVAASSPLEpsveetelqkeaatgs 80
Cdd:cd08968     1 MPEGPSVRKFHHLVSPFVGQRVVKVGGSSKKINPNDLQGLRLQDSQVHGKNLFLHFDLDEEMGP---------------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933  81 rslvqgkqgqvcapltptqeeelqelqnsrpgapsaAGGPGSWLRFHFGLFGSVRANEFSRASRANKRGDWKDPIPRLVL 160
Cdd:cd08968    65 ------------------------------------DRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKDPNPRLVL 108

                         170
                  ....*....|....*...
gi 2077599933 161 YFESGGFLVFYNCRMHWC 178
Cdd:cd08968   109 HFESGGFLVFYNCRMSWC 126
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
119-313 5.92e-19

Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 84.79  E-value: 5.92e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 119 GPGSWLRFHFGLFGSVRaneFSRASRANKRGDwkdpipRLVLYFESGGFLVFYNCR----MHWCSSPVAD---------P 185
Cdd:COG0266    64 DGGLTLLIHLGMSGRLR---VVPPGEPPEKHD------HVRLVLDDGTELRFADPRrfgaLELLTPDELEvhpllarlgP 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 186 tsDILSAEFHRGRALDALCTSH-PICYTLLDQRYFSGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDC-------A 257
Cdd:COG0266   135 --EPLDPDFDPEYLAARLRRRRrPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAirevlreA 212

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2077599933 258 IQF----TSDWLQSklQGK----GLHLQIYQK--EHCPL-GHVVMKGALGppGgwkRLTWWCPQCQP 313
Cdd:COG0266   213 IEAggttLRDYVNA--DGEpgyfQQRLYVYGRegEPCPRcGTPIERIVLG--G---RSTYYCPRCQR 272
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
157-313 7.76e-13

bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 67.41  E-value: 7.76e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 157 RLVLYFESGGFLVFYNCR----MHWCSS-------PVA----DPTSDILSAE-FHRgraldALCTSH-PICYTLLDQRYF 219
Cdd:PRK01103   94 HVDFVLDDGTVLRYNDPRrfgaMLLTPKgdleahpLLAhlgpEPLSDAFDGEyLAA-----KLRKKKtAIKPALLDQTVV 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 220 SGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDCAIQF---------TSdwLQSKLQGKG------LHLQIYQKE-- 282
Cdd:PRK01103  169 VGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVlaeaieqggTT--LRDYVNADGkpgyfqQSLQVYGREge 246

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2077599933 283 ---HCplGHVVMKGALGppggwKRLTWWCPQCQP 313
Cdd:PRK01103  247 pcrRC--GTPIEKIKQG-----GRSTFFCPRCQK 273
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-175 9.99e-12

N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In addition to this FpgNei_N domain, FpgNei proteins have a helix-two-turn-helix (H2TH) domain and a zinc (or zincless)-finger motif which also contribute residues to the active site. FpgNei DNA glycosylases have a broad substrate specificity. They are bifunctional, in addition to the glycosylase (recognition) activity, they have a lyase (cleaving) activity on the phosphodiester backbone of the DNA at the AP site. This superfamily includes eukaryotic, bacterial, and viral proteins.


Pssm-ID: 176798  Cd Length: 117  Bit Score: 61.22  E-value: 9.99e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933   2 PEGPSVRKF-QLLTSRFVGQVVAKVGGSSKKIN-------VNDLNALRLQDSQVHGKNLFLAFvaassplepsveetelq 73
Cdd:cd08773     1 PELPEVELLrRKLRRALKGKRVTRVEVSDPRRLftpaaelAAALIGRRVRGAERRGKYLLLEL----------------- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933  74 keaatgsrslvqgkqgqvcapltptqeeelqelqnsrpgapsaagGPGSWLRFHFGLFGSVRANEfsrasrankRGDWKD 153
Cdd:cd08773    64 ---------------------------------------------SGGPWLVIHLGMTGRLRVCP---------EGEPPP 89

                         170       180
                  ....*....|....*....|..
gi 2077599933 154 PIPRLVLYFESGGFLVFYNCRM 175
Cdd:cd08773    90 KHDRLVLRLANGSQLRFTDPRK 111
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 123-312 7.48e-11

DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). 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: 273150 [Multi-domain]  Cd Length: 272  Bit Score: 61.55  E-value: 7.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 123 WLRFHFGLFGSVRANEfsrasrankRGDWKDPIPRLVLYFESGGFLVFYNCR----MHWCSSPVADPTS-------DILS 191
Cdd:TIGR00577  69 ALVSHLRMEGKYRLEA---------VPDAPDKHDHVDFLFDDGTELRYHDPRrfgtWLLLDRGQVENIPllaklgpEPLS 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 192 AEFHRGRALDALCTSH-PICYTLLDQRYFSGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDC-------AIQFTSD 263
Cdd:TIGR00577 140 EDFTAEYLFEKLAKSKrKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAikevlrkAIEMGGT 219

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2077599933 264 WLQSKLQGKGL------HLQIYQK--EHCPL-GHVVMKGALGppggwKRLTWWCPQCQ 312
Cdd:TIGR00577 220 TIRDFSQSDGHngyfqqELQVYGRkgEPCRRcGTTIEKEKVG-----GRGTHFCPQCQ 272
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 213-259 4.39e-09

Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.


Pssm-ID: 399664 [Multi-domain]  Cd Length: 89  Bit Score: 52.68  E-value: 4.39e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2077599933 213 LLDQRYFSGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDCAIQ 259
Cdd:pfam06831  30 LLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKA 76
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 149-312 5.36e-07

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 50.29  E-value: 5.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 149 GDWKDPIPR---LVLYFESGGFLVFYNCRMHWC-------SSPVADPTSDILSAEFH------RGRALdalctshPICYT 212
Cdd:PRK14810   88 GGPDTPSPKhthAVLTLSSGKELRFVDSRQFGCieyseafPKRFARPGPEPLEISFEdfaalfRGRKT-------RIKSA 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 213 LLDQRYFSGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDC-------AIQFTSDWLQSKLQGKG------LHLQIY 279
Cdd:PRK14810  161 LLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAigevlreAIELGGSSVSDYVDAEGrsgffqLSHRVY 240

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2077599933 280 QK--EHC-----PLGHVVMKGalgppggwkRLTWWCPQCQ 312
Cdd:PRK14810  241 QRtgEPClncktPIRRVVVAG---------RSSHYCPHCQ 271
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 208-313 8.19e-06

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 46.46  E-value: 8.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 208 PICYTLLDQRYFSGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDCAIQ------------FtSDWLQSK-LQGK-G 273
Cdd:PRK13945  166 SIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEvlktsigaggttF-SDFRDLEgVNGNyG 244

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2077599933 274 LHLQIYQK--EHCPL-GHVVMKGALGppggwKRLTWWCPQCQP 313
Cdd:PRK13945  245 GQAWVYRRtgKPCRKcGTPIERIKLA-----GRSTHWCPNCQK 282
BaFpgNei_N_2 cd08974
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-173 8.24e-06

Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines, and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_2 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain. Most also contain a zinc-finger motif.


Pssm-ID: 176808  Cd Length: 98  Bit Score: 43.85  E-value: 8.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933   1 MPEGPSVRKFQLLTSRFVGQVVAKVGGSSKkINVNDLNALRLQDSQVHGKNLFLAFVAASsplepsveetelqkeaatgs 80
Cdd:cd08974     1 MPEGPSIVILREAAAAFKGQTVIRASGNAK-IDKDRLAGQKVLAIRSWGKHFLLEFEDFT-------------------- 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933  81 rslvqgkqgqvcapltptqeeelqelqnsrpgapsaaggpgswLRFHFGLFGSVRANEfsrasrankrgdWKDPIPRLVL 160
Cdd:cd08974    60 -------------------------------------------VRIHLLLFGSYRINE------------RKDAPPRLSL 84

                         170
                  ....*....|...
gi 2077599933 161 YFEsGGFLVFYNC 173
Cdd:cd08974    85 GFD-NGELNFYTC 96
PRK10445 PRK10445
endonuclease VIII; Provisional
 189-313 8.89e-06

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 46.56  E-value: 8.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 189 ILSAEFHRgRALDALctshpicytLLDQRYFSGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHLLDCAIQF-------- 260
Cdd:PRK10445  144 LLSPRFRN-RQFSGL---------LLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIprlsyatr 213

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2077599933 261 -TSDwlQSKLQG-----KGLHLQIYQKEHCplGHVVMKGALGppggwKRLTWWCPQCQP 313
Cdd:PRK10445  214 gQVD--ENKHHGalfrfKVFHRDGEACERC--GGIIEKTTLS-----SRPFYWCPGCQK 263
AcNei1_N cd08970
N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases; This family contains ...
 1-59 3.65e-04

N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases; This family contains the N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This family contains mostly actinomycetes and includes Mycobacterium tuberculosis Nei1 (MtuNei1). MtuNei1 recognizes oxidized pyrimidines such as thymine glycol (Tg) and 5,6-dihydrouracil on both double stranded and single stranded DNA, it has a strong preference for the 5R isomer of Tg. In addition to this domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176804 [Multi-domain]  Cd Length: 110  Bit Score: 39.55  E-value: 3.65e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2077599933   1 MPEGPSVRKF-QLLTSRFVGQVVAKvggSSKKINVND----LNALRLQDSQVHGKNLFLAFVAA 59
Cdd:cd08970     1 MPEGHVIHRLaRDLNAAFAGQPVRV---SSPQGRFADgaalLDGRVLADAEAHGKHLFLGFEGD 61
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 190-313 1.02e-03

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 40.16  E-value: 1.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077599933 190 LSAEFHRGRALDALCTSHPICYTLLDQRYFSGLGNIIKNEVLYLVKIHPLTQGSLLAQSDLEHL-------LDCAIQFTS 262
Cdd:PRK14811  127 LSDDFTEPEFVRALATARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLyrairevMAEAVEAGG 206

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2077599933 263 DWL--QSKLQGKGLHlQIYQKEH---------CP-LGHVVMKGALGppggwKRLTWWCPQCQP 313
Cdd:PRK14811  207 STLsdGSYRQPDGEP-GGFQFQHavygregqpCPrCGTPIEKIVVG-----GRGTHFCPQCQP 263
 
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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