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Conserved domains on  [gi|21450800|ref|NP_659480|]
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endonuclease 8-like 2 isoform a [Homo sapiens]

Protein Classification

MeNeil2_N and Nei domain-containing protein( domain architecture ID 12963208)

MeNeil2_N and Nei domain-containing protein

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 ...
 1-185 9.59e-73

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: 220.79  E-value: 9.59e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800   1 MPEGPLVRKFHHLVSPFVGQQVVKTGGSSKKLQPASLQSLWLQDTQVHGKKLFLRFDLDEEMGPpgssptpeppqkevqk 80
Cdd:cd08968   1 MPEGPSVRKFHHLVSPFVGQRVVKVGGSSKKINPNDLQGLRLQDSQVHGKNLFLHFDLDEEMGP---------------- 64

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800  81 egaadpkqvgepsgqktldgssrsaelvpqgeddseylerdapAGDAGRWLRVSFGLFGSVWVNDFSRAKKANKRGDWRD 160
Cdd:cd08968  65 -------------------------------------------DRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKD 101

                       170       180
                ....*....|....*....|....*
gi 21450800 161 PSPRLVLHFGGGGFLAFYNCQLSWS 185
Cdd:cd08968 102 PNPRLVLHFESGGFLVFYNCRMSWC 126
Nei super family cl33822
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
126-320 1.73e-21

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: 92.11  E-value: 1.73e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800 126 DAGRWLRVSFGLFGSVWVNDfsrAKKANKRGDwrdpspRLVLHFGGGGFLAFYN------CQLSWSSSPVVTPTC----- 194
Cdd:COG0266  64 DGGLTLLIHLGMSGRLRVVP---PGEPPEKHD------HVRLVLDDGTELRFADprrfgaLELLTPDELEVHPLLarlgp 134

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800 195 DILSEKFHRGQALEAL-GQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVEFSTAWLQ 273
Cdd:COG0266 135 EPLDPDFDPEYLAARLrRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIE 214

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 21450800 274 ----------------GKFQgrpQHTQVYQK--EQCPA-GHQVMKEAFGpedglQRLTWWCPQCQP 320
Cdd:COG0266 215 aggttlrdyvnadgepGYFQ---QRLYVYGRegEPCPRcGTPIERIVLG-----GRSTYYCPRCQR 272
 
Name Accession Description Interval E-value
MeNeil2_N cd08968
N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the ...
 1-185 9.59e-73

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: 220.79  E-value: 9.59e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800   1 MPEGPLVRKFHHLVSPFVGQQVVKTGGSSKKLQPASLQSLWLQDTQVHGKKLFLRFDLDEEMGPpgssptpeppqkevqk 80
Cdd:cd08968   1 MPEGPSVRKFHHLVSPFVGQRVVKVGGSSKKINPNDLQGLRLQDSQVHGKNLFLHFDLDEEMGP---------------- 64

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800  81 egaadpkqvgepsgqktldgssrsaelvpqgeddseylerdapAGDAGRWLRVSFGLFGSVWVNDFSRAKKANKRGDWRD 160
Cdd:cd08968  65 -------------------------------------------DRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKD 101

                       170       180
                ....*....|....*....|....*
gi 21450800 161 PSPRLVLHFGGGGFLAFYNCQLSWS 185
Cdd:cd08968 102 PNPRLVLHFESGGFLVFYNCRMSWC 126
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
126-320 1.73e-21

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 92.11  E-value: 1.73e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800 126 DAGRWLRVSFGLFGSVWVNDfsrAKKANKRGDwrdpspRLVLHFGGGGFLAFYN------CQLSWSSSPVVTPTC----- 194
Cdd:COG0266  64 DGGLTLLIHLGMSGRLRVVP---PGEPPEKHD------HVRLVLDDGTELRFADprrfgaLELLTPDELEVHPLLarlgp 134

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800 195 DILSEKFHRGQALEAL-GQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVEFSTAWLQ 273
Cdd:COG0266 135 EPLDPDFDPEYLAARLrRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIE 214

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 21450800 274 ----------------GKFQgrpQHTQVYQK--EQCPA-GHQVMKEAFGpedglQRLTWWCPQCQP 320
Cdd:COG0266 215 aggttlrdyvnadgepGYFQ---QRLYVYGRegEPCPRcGTPIERIVLG-----GRSTYYCPRCQR 272
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
219-321 4.81e-17

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 79.74  E-value: 4.81e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800  219 TLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE---------------FSTAwlQGK---FQgrp 280
Cdd:PRK01103 161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAvlaeaieqggttlrdYVNA--DGKpgyFQ--- 235

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 21450800  281 QHTQVY--QKEQCPA-GHQVMKEAFGpedglQRLTWWCPQCQPQ 321
Cdd:PRK01103 236 QSLQVYgrEGEPCRRcGTPIEKIKQG-----GRSTFFCPRCQKR 274
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 220-319 8.03e-15

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: 73.49  E-value: 8.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800   220 LLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE------------FST----AWLQGKFQGRpqhT 283
Cdd:TIGR00577 162 LLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEvlrkaiemggttIRDfsqsDGHNGYFQQE---L 238

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 21450800   284 QVYQK--EQCPA-GHQVMKEAFGpedglQRLTWWCPQCQ 319
Cdd:TIGR00577 239 QVYGRkgEPCRRcGTTIEKEKVG-----GRGTHFCPQCQ 272
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 220-266 9.83e-12

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: 60.38  E-value: 9.83e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 21450800   220 LLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE 266
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 ...
 1-185 9.59e-73

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: 220.79  E-value: 9.59e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800   1 MPEGPLVRKFHHLVSPFVGQQVVKTGGSSKKLQPASLQSLWLQDTQVHGKKLFLRFDLDEEMGPpgssptpeppqkevqk 80
Cdd:cd08968   1 MPEGPSVRKFHHLVSPFVGQRVVKVGGSSKKINPNDLQGLRLQDSQVHGKNLFLHFDLDEEMGP---------------- 64

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800  81 egaadpkqvgepsgqktldgssrsaelvpqgeddseylerdapAGDAGRWLRVSFGLFGSVWVNDFSRAKKANKRGDWRD 160
Cdd:cd08968  65 -------------------------------------------DRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKD 101

                       170       180
                ....*....|....*....|....*
gi 21450800 161 PSPRLVLHFGGGGFLAFYNCQLSWS 185
Cdd:cd08968 102 PNPRLVLHFESGGFLVFYNCRMSWC 126
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
126-320 1.73e-21

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 92.11  E-value: 1.73e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800 126 DAGRWLRVSFGLFGSVWVNDfsrAKKANKRGDwrdpspRLVLHFGGGGFLAFYN------CQLSWSSSPVVTPTC----- 194
Cdd:COG0266  64 DGGLTLLIHLGMSGRLRVVP---PGEPPEKHD------HVRLVLDDGTELRFADprrfgaLELLTPDELEVHPLLarlgp 134

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800 195 DILSEKFHRGQALEAL-GQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVEFSTAWLQ 273
Cdd:COG0266 135 EPLDPDFDPEYLAARLrRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIE 214

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 21450800 274 ----------------GKFQgrpQHTQVYQK--EQCPA-GHQVMKEAFGpedglQRLTWWCPQCQP 320
Cdd:COG0266 215 aggttlrdyvnadgepGYFQ---QRLYVYGRegEPCPRcGTPIERIVLG-----GRSTYYCPRCQR 272
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
219-321 4.81e-17

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 79.74  E-value: 4.81e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800  219 TLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE---------------FSTAwlQGK---FQgrp 280
Cdd:PRK01103 161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAvlaeaieqggttlrdYVNA--DGKpgyFQ--- 235

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 21450800  281 QHTQVY--QKEQCPA-GHQVMKEAFGpedglQRLTWWCPQCQPQ 321
Cdd:PRK01103 236 QSLQVYgrEGEPCRRcGTPIEKIKQG-----GRSTFFCPRCQKR 274
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 220-319 8.03e-15

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: 73.49  E-value: 8.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800   220 LLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE------------FST----AWLQGKFQGRpqhT 283
Cdd:TIGR00577 162 LLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEvlrkaiemggttIRDfsqsDGHNGYFQQE---L 238

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 21450800   284 QVYQK--EQCPA-GHQVMKEAFGpedglQRLTWWCPQCQ 319
Cdd:TIGR00577 239 QVYGRkgEPCRRcGTTIEKEKVG-----GRGTHFCPQCQ 272
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 220-266 9.83e-12

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: 60.38  E-value: 9.83e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 21450800   220 LLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE 266
Cdd:pfam06831  30 LLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKA 76
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-179 2.75e-10

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: 56.99  E-value: 2.75e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800   2 PEGPLVRKFHHLVSP-FVGQQVVKTGGSSKKLQ-------PASLQSLWLQDTQVHGKKLFLRFdldeemgppgssptpep 73
Cdd:cd08773   1 PELPEVELLRRKLRRaLKGKRVTRVEVSDPRRLftpaaelAAALIGRRVRGAERRGKYLLLEL----------------- 63

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800  74 pqkevqkegaadpkqvgepsgqktldgssrsaelvpqgeddseylerdapagDAGRWLRVSFGLFGSVWVNDfsrakkan 153
Cdd:cd08773  64 ----------------------------------------------------SGGPWLVIHLGMTGRLRVCP-------- 83

                       170       180
                ....*....|....*....|....*.
gi 21450800 154 kRGDWRDPSPRLVLHFGGGGFLAFYN 179
Cdd:cd08773  84 -EGEPPPKHDRLVLRLANGSQLRFTD 108
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 197-320 1.30e-09

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 57.88  E-value: 1.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800  197 LSEKFHRGQALEALGQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASR--------REVLVDHVVEFS 268
Cdd:PRK14811 127 LSDDFTEPEFVRALATARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEarrlyraiREVMAEAVEAGG 206

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21450800  269 TAWLQGKFQ---GRPQHTQ----VYQKE--QCPA-GHQVMKEAFGpedglQRLTWWCPQCQP 320
Cdd:PRK14811 207 STLSDGSYRqpdGEPGGFQfqhaVYGREgqPCPRcGTPIEKIVVG-----GRGTHFCPQCQP 263
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 220-320 2.24e-07

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 51.47  E-value: 2.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800  220 LLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE------------FS----TAWLQGKFQGRpqhT 283
Cdd:PRK13945 171 LLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEvlktsigaggttFSdfrdLEGVNGNYGGQ---A 247

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 21450800  284 QVYQKEQCP---AGHQVMKEAFGpedglQRLTWWCPQCQP 320
Cdd:PRK13945 248 WVYRRTGKPcrkCGTPIERIKLA-----GRSTHWCPNCQK 282
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 123-319 2.85e-07

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 51.06  E-value: 2.85e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800  123 PAGDAGRWLrVSFGLFGSVWVndfsrakkankrGDWRDPSPR---LVLHFGGGGFLAFYNCQL-------SWSSSPVVTP 192
Cdd:PRK14810  68 PGEPRGQWI-IHLGMTGKLLL------------GGPDTPSPKhthAVLTLSSGKELRFVDSRQfgcieysEAFPKRFARP 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800  193 TCDILSEKFHRGQALeALGQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVEFSTAWL 272
Cdd:PRK14810 135 GPEPLEISFEDFAAL-FRGRKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAI 213

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21450800  273 Q----------------GKFQGRpqhTQVYQK--EQCPAGHQVMKEAFGPedglQRLTWWCPQCQ 319
Cdd:PRK14810 214 ElggssvsdyvdaegrsGFFQLS---HRVYQRtgEPCLNCKTPIRRVVVA----GRSSHYCPHCQ 271
PRK10445 PRK10445
endonuclease VIII; Provisional
 196-320 1.09e-05

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 46.18  E-value: 1.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21450800  196 ILSEKFHRGQaLEALgqaqpvcytLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVEFSTAWLQ-- 273
Cdd:PRK10445 144 LLSPRFRNRQ-FSGL---------LLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYAtr 213

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 21450800  274 -----GKFQGRPQHTQVYQK-----EQCpaGHQVMKEAFGpedglQRLTWWCPQCQP 320
Cdd:PRK10445 214 gqvdeNKHHGALFRFKVFHRdgeacERC--GGIIEKTTLS-----SRPFYWCPGCQK 263
BaFpgNei_N_2 cd08974
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 131-182 9.02e-03

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: 35.38  E-value: 9.02e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 21450800 131 LRVSFGLFGSVWVNDfsraKKankrgdwrDPSPRLVLHFGGGGfLAFYNCQL 182
Cdd:cd08974  60 VRIHLLLFGSYRINE----RK--------DAPPRLSLGFDNGE-LNFYTCSV 98
 
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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