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Conserved domains on  [gi|499364842|ref|WP_011052872|]
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MULTISPECIES: bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase [Xanthomonas]

Protein Classification

Fpg/Nei family DNA glycosylase( domain architecture ID 11479425)

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

CATH:  3.20.190.10
EC:  3.2.2.23
Gene Ontology:  GO:0140078|GO:0003684|GO:0008534|GO:0008270|GO:0006284
PubMed:  21486746|14607836
SCOP:  4000303

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-271 2.98e-164

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


:

Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 456.08  E-value: 2.98e-164
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   1 MPELPEVETTLRGLSPHLVGQRIHGVILRRPDLRWPIPEQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSL 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  81 RVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLLWQSGTQ--AHDLLAALGPEPLSDAFTGDYLHALAQGRRAAVKT 158
Cdd:PRK01103  81 RLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDleAHPLLAHLGPEPLSDAFDGEYLAAKLRKKKTAIKP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842 159 FLMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAYAIQRGGTTLRDFISPDGAPGYFEQELFV 238
Cdd:PRK01103 161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQV 240

                        250       260       270
                 ....*....|....*....|....*....|...
gi 499364842 239 YGREGEACKQCGRVLKHATIGQRATVWCGSCQR 271
Cdd:PRK01103 241 YGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-271 2.98e-164

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 456.08  E-value: 2.98e-164
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   1 MPELPEVETTLRGLSPHLVGQRIHGVILRRPDLRWPIPEQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSL 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  81 RVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLLWQSGTQ--AHDLLAALGPEPLSDAFTGDYLHALAQGRRAAVKT 158
Cdd:PRK01103  81 RLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDleAHPLLAHLGPEPLSDAFDGEYLAAKLRKKKTAIKP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842 159 FLMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAYAIQRGGTTLRDFISPDGAPGYFEQELFV 238
Cdd:PRK01103 161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQV 240

                        250       260       270
                 ....*....|....*....|....*....|...
gi 499364842 239 YGREGEACKQCGRVLKHATIGQRATVWCGSCQR 271
Cdd:PRK01103 241 YGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-271 7.18e-144

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 404.12  E-value: 7.18e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   2 PELPEVETTLRGLSPHLVGQRIHGVILRRPDLRWPIPEQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSLR 81
Cdd:COG0266    1 PELPEVETVRRGLAPALVGRTITRVEVRSPRLRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  82 VLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLLWQS--GTQAHDLLAALGPEPLSDAFTGDYLHALAQGRRAAVKTF 159
Cdd:COG0266   81 VVPPGEPPEKHDHVRLVLDDGTELRFADPRRFGALELLTpdELEVHPLLARLGPEPLDPDFDPEYLAARLRRRRRPIKAL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842 160 LMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAYAIQRGGTTLRDFISPDGAPGYFEQELFVY 239
Cdd:COG0266  161 LLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADGEPGYFQQRLYVY 240

                        250       260       270
                 ....*....|....*....|....*....|..
gi 499364842 240 GREGEACKQCGRVLKHATIGQRATVWCGSCQR 271
Cdd:COG0266  241 GREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-270 1.29e-110

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: 320.02  E-value: 1.29e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842    2 PELPEVETTLRGLSPHLVGQRIHGVI--LRRPDLRWPIPEQIERLLPGATITNVRRRAKYLLIDTDaGGSVLLHLGMSGS 79
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEvvLRNPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELD-DGALVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   80 LRVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLLWQSGTQAH--DLLAALGPEPLSDAFTGDYLHALAQGRRAAVK 157
Cdd:TIGR00577  80 YRLEAVPDAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQVEniPLLAKLGPEPLSEDFTAEYLFEKLAKSKRKIK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  158 TFLMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAYAIQRGGTTLRDFISPDGAPGYFEQELF 237
Cdd:TIGR00577 160 TALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQSDGHNGYFQQELQ 239

                         250       260       270
                  ....*....|....*....|....*....|...
gi 499364842  238 VYGREGEACKQCGRVLKHATIGQRATVWCGSCQ 270
Cdd:TIGR00577 240 VYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-118 1.56e-54

N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial 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. Escherichia coli Fpg mainly recognizes and excises damaged purines such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). It is bifunctional, having both a DNA glycosylase (recognition activity) and a AP lyase activity. In addition to this EcFpg-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif, which also contribute residues to the active site.


Pssm-ID: 176800  Cd Length: 120  Bit Score: 171.91  E-value: 1.56e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   2 PELPEVETTLRGLSPHLVGQRIHGVILRRPDLRWP-IPEQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSL 80
Cdd:cd08966    1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPpDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 499364842  81 RVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLLW 118
Cdd:cd08966   81 LVVPPDEPPEKHDHVIFELDDGRELRFNDPRRFGTLLL 118
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-116 1.80e-51

Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges.


Pssm-ID: 460082  Cd Length: 116  Bit Score: 164.22  E-value: 1.80e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842    1 MPELPEVETTLRGLSPHLVGQRIHGVILRRPD-LRWPIPEQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGS 79
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKnLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 499364842   80 LRVLPGDTLPRaHDHVDISLQSGRLLRFNDPRRFGCL 116
Cdd:pfam01149  81 LLIKTEEWPPK-HDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-117 3.05e-48

Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway. These enzymes are primarily from bacteria, and have both DNA glycosylase activity and AP lyase activity. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; ) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; ). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes. Fpg binds one ion of zinc at the C-terminus, which contains four conserved and essential cysteines.. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger (see PDB:1K82). The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger.


Pssm-ID: 214895 [Multi-domain]  Cd Length: 115  Bit Score: 155.80  E-value: 3.05e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842     2 PELPEVETTLRGLSPHLVGQRIHGV-ILRRPDLRWPIPeqIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSL 80
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVeVVRPPQLRFPDE--FAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSL 78

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 499364842    81 RVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLL 117
Cdd:smart00898  79 RVVPAGTPPPKHDHVRLVLDDGTELRFNDPRRFGAVR 115
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-271 2.98e-164

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 456.08  E-value: 2.98e-164
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   1 MPELPEVETTLRGLSPHLVGQRIHGVILRRPDLRWPIPEQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSL 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  81 RVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLLWQSGTQ--AHDLLAALGPEPLSDAFTGDYLHALAQGRRAAVKT 158
Cdd:PRK01103  81 RLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDleAHPLLAHLGPEPLSDAFDGEYLAAKLRKKKTAIKP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842 159 FLMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAYAIQRGGTTLRDFISPDGAPGYFEQELFV 238
Cdd:PRK01103 161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQV 240

                        250       260       270
                 ....*....|....*....|....*....|...
gi 499364842 239 YGREGEACKQCGRVLKHATIGQRATVWCGSCQR 271
Cdd:PRK01103 241 YGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-271 7.18e-144

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 404.12  E-value: 7.18e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   2 PELPEVETTLRGLSPHLVGQRIHGVILRRPDLRWPIPEQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSLR 81
Cdd:COG0266    1 PELPEVETVRRGLAPALVGRTITRVEVRSPRLRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  82 VLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLLWQS--GTQAHDLLAALGPEPLSDAFTGDYLHALAQGRRAAVKTF 159
Cdd:COG0266   81 VVPPGEPPEKHDHVRLVLDDGTELRFADPRRFGALELLTpdELEVHPLLARLGPEPLDPDFDPEYLAARLRRRRRPIKAL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842 160 LMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAYAIQRGGTTLRDFISPDGAPGYFEQELFVY 239
Cdd:COG0266  161 LLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADGEPGYFQQRLYVY 240

                        250       260       270
                 ....*....|....*....|....*....|..
gi 499364842 240 GREGEACKQCGRVLKHATIGQRATVWCGSCQR 271
Cdd:COG0266  241 GREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-270 1.29e-110

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: 320.02  E-value: 1.29e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842    2 PELPEVETTLRGLSPHLVGQRIHGVI--LRRPDLRWPIPEQIERLLPGATITNVRRRAKYLLIDTDaGGSVLLHLGMSGS 79
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEvvLRNPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELD-DGALVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   80 LRVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLLWQSGTQAH--DLLAALGPEPLSDAFTGDYLHALAQGRRAAVK 157
Cdd:TIGR00577  80 YRLEAVPDAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQVEniPLLAKLGPEPLSEDFTAEYLFEKLAKSKRKIK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  158 TFLMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAYAIQRGGTTLRDFISPDGAPGYFEQELF 237
Cdd:TIGR00577 160 TALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQSDGHNGYFQQELQ 239

                         250       260       270
                  ....*....|....*....|....*....|...
gi 499364842  238 VYGREGEACKQCGRVLKHATIGQRATVWCGSCQ 270
Cdd:TIGR00577 240 VYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 1-271 2.44e-73

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 225.58  E-value: 2.44e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   1 MPELPEVETTLRGLSPHLVGQRIHGV-ILRRPDLRWPI-PEQIERLLPGATITNVRRRAKYLL-----IDTDAGGSVLLH 73
Cdd:PRK13945   1 MPELPEVETVRRGLEQLLLNFIIKGVeVLLERTIASPGgVEEFIKGLKGSLIGQWQRRGKYLLaslkkEGSENAGWLGVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  74 LGMSGSLRVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLLWQSGTQAHDL----LAALGPEPLSDAFTGDYLHALA 149
Cdd:PRK13945  81 LRMTGQFLWVEQSTPPCKHTRVRLFFEKNQELRFVDIRSFGQMWWVPPGVSPESiitgLQKLGPEPFSPEFSVEYLKKKL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842 150 QGRRAAVKTFLMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAYAIQRGGTTLRDFISPDGAP 229
Cdd:PRK13945 161 KKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLKTSIGAGGTTFSDFRDLEGVN 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 499364842 230 GYFEQELFVYGREGEACKQCGRVLKHATIGQRATVWCGSCQR 271
Cdd:PRK13945 241 GNYGGQAWVYRRTGKPCRKCGTPIERIKLAGRSTHWCPNCQK 282
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-271 1.18e-65

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 205.91  E-value: 1.18e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   1 MPELPEVETTLRGLSPHLVGQRIHGVILRRpdLRWPI---PEQIERLLPGATITNVRRRAKYLLIDTDAG----GSVLLH 73
Cdd:PRK14810   1 MPELPEVETVARGLAPRAAGRRIATAEFRN--LRIPRkgdPDLMAARLAGRKILSVKRVGKHIVADLEGPgeprGQWIIH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  74 LGMSGSLRVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLLWQSGTQahDLLAALGPEPLSDAFtgDYLHALAQGRR 153
Cdd:PRK14810  79 LGMTGKLLLGGPDTPSPKHTHAVLTLSSGKELRFVDSRQFGCIEYSEAFP--KRFARPGPEPLEISF--EDFAALFRGRK 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842 154 AAVKTFLMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAYAIQRGGTTLRDFISPDGAPGYFE 233
Cdd:PRK14810 155 TRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAIELGGSSVSDYVDAEGRSGFFQ 234

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 499364842 234 QELFVYGREGEACKQCGRVLKHATIGQRATVWCGSCQR 271
Cdd:PRK14810 235 LSHRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHCQK 272
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-271 1.20e-65

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 205.80  E-value: 1.20e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   1 MPELPEVETTLRGLSPHLVGQRIHGVILRRPDlRWPIPEQIErllpGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSL 80
Cdd:PRK14811   1 MPELPEVETTRRKLEPLLLGQTIQQVVHDDPA-RYRNTELAE----GRRVLGLSRRGKYLLLHLPHDLELIVHLGMTGGF 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  81 RVLPGdtlprAHDHVDISLqSGRLLRFNDPRRFGCL-LWQSGTQAH-DLLAALGPEPLSDAFT-GDYLHALAQGRraAVK 157
Cdd:PRK14811  76 RLEPG-----PHTRVTLEL-PGRTLYFTDPRRFGKWwVVRAGDYREiPLLARMGPEPLSDDFTePEFVRALATAR--PVK 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842 158 TFLMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAYAIQRGGTTLRD--FISPDGAPGYFEQE 235
Cdd:PRK14811 148 PWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEAVEAGGSTLSDgsYRQPDGEPGGFQFQ 227

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 499364842 236 LFVYGREGEACKQCGRVLKHATIGQRATVWCGSCQR 271
Cdd:PRK14811 228 HAVYGREGQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-118 1.56e-54

N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial 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. Escherichia coli Fpg mainly recognizes and excises damaged purines such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). It is bifunctional, having both a DNA glycosylase (recognition activity) and a AP lyase activity. In addition to this EcFpg-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif, which also contribute residues to the active site.


Pssm-ID: 176800  Cd Length: 120  Bit Score: 171.91  E-value: 1.56e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   2 PELPEVETTLRGLSPHLVGQRIHGVILRRPDLRWP-IPEQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSL 80
Cdd:cd08966    1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPpDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 499364842  81 RVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLLW 118
Cdd:cd08966   81 LVVPPDEPPEKHDHVIFELDDGRELRFNDPRRFGTLLL 118
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-116 1.80e-51

Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges.


Pssm-ID: 460082  Cd Length: 116  Bit Score: 164.22  E-value: 1.80e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842    1 MPELPEVETTLRGLSPHLVGQRIHGVILRRPD-LRWPIPEQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGS 79
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKnLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 499364842   80 LRVLPGDTLPRaHDHVDISLQSGRLLRFNDPRRFGCL 116
Cdd:pfam01149  81 LLIKTEEWPPK-HDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-117 3.05e-48

Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway. These enzymes are primarily from bacteria, and have both DNA glycosylase activity and AP lyase activity. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; ) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; ). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes. Fpg binds one ion of zinc at the C-terminus, which contains four conserved and essential cysteines.. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger (see PDB:1K82). The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger.


Pssm-ID: 214895 [Multi-domain]  Cd Length: 115  Bit Score: 155.80  E-value: 3.05e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842     2 PELPEVETTLRGLSPHLVGQRIHGV-ILRRPDLRWPIPeqIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSL 80
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVeVVRPPQLRFPDE--FAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSL 78

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 499364842    81 RVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFGCLL 117
Cdd:smart00898  79 RVVPAGTPPPKHDHVRLVLDDGTELRFNDPRRFGAVR 115
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-114 3.47e-31

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: 112.07  E-value: 3.47e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   2 PELPEVETTLRGLSPHLVGQRIHGVILRRPDLRWPIPEQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSLR 81
Cdd:cd08773    1 PELPEVELLRRKLRRALKGKRVTRVEVSDPRRLFTPAAELAAALIGRRVRGAERRGKYLLLELSGGPWLVIHLGMTGRLR 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 499364842  82 VLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFG 114
Cdd:cd08773   81 VCPEGEPPPKHDRLVLRLANGSQLRFTDPRKFG 113
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 131-219 1.74e-30

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: 109.30  E-value: 1.74e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  131 LGPEPLSDAFTGDYLHALAQGRRAAVKTFLMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAY 210
Cdd:pfam06831   1 LGPEPLSEDFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVLQE 80


                  ....*....
gi 499364842  211 AIQRGGTTL 219
Cdd:pfam06831  81 AIEMGGGGI 89
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-271 1.32e-22

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 93.56  E-value: 1.32e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   1 MPELPEVETTLRGLSPHLVGQRIHGVILRRPDLRwpipeQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSL 80
Cdd:PRK10445   1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLK-----PYESQLIGQRVTHIETRGKALLTHFSNGLTLYSHNQLYGVW 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842  81 RVLPGDTLPrahdhvdislQSGRLLRFndprRFGC-----LLWQS---------GTQAHDLLAALGPEPLSDAFTGDYLH 146
Cdd:PRK10445  76 RVVDTGEEP----------QTTRVLRV----RLQTadktiLLYSAsdiemltpeQLTTHPFLQRVGPDVLDPNLTPEQVK 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842 147 A---LAQGRRAAVKTFLMDQAVVVGVGNIYAAESLHRAGISPLREAGKVSLERYRRLADAVKDILAYAIQRGGTTlrDFI 223
Cdd:PRK10445 142 ErllSPRFRNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRGQV--DEN 219

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 499364842 224 SPDGAPGYFeqelFVYGREGEACKQCGRVLKHATIGQRATVWCGSCQR 271
Cdd:PRK10445 220 KHHGALFRF----KVFHRDGEACERCGGIIEKTTLSSRPFYWCPGCQK 263
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-114 1.64e-18

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_4 domain, most enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176810  Cd Length: 117  Bit Score: 78.93  E-value: 1.64e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   2 PELPEVETTLRGLSPHLVGQRIHGVILRRPDLRWPIPEQIERLLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSLR 81
Cdd:cd08976    1 PELPEVEVQKQYLERTSLHRKIVEVEVGDDKILGEPKATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTGKLD 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 499364842  82 VLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFG 114
Cdd:cd08976   81 YYPDDEDPPKHARLLLHFEDGFRLAFECPRKFG 113
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-114 2.04e-17

N-terminal domain of the plant and fungal Nei and related proteins; This family contains the N-terminal domain of plant and Fungi Nei and related proteins. 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. The plant and fungal FpgNei glycosylases prefer the oxidized pyrimidines spiroiminodihydantoin (Sp), guanidinohydantoin (Gh) over 8-oxoguanine in double stranded oligonucleotides and also show weak activity on single stranded DNA. In addition to this domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a characteristic zincless finger motif. They share a common ancestor not shared with other eukaryotic members of the FpgNei family.


Pssm-ID: 176806  Cd Length: 137  Bit Score: 76.58  E-value: 2.04e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   1 MPELPEVETTLRGLSPHLVGQRIHGVILRRPDLRWP--IPEQIERLLPGATITNVRRRAKYLLIDTDAGG-SVLLHLGMS 77
Cdd:cd08972    1 MPELPEVERARRLLEEHCLGKKITKVDAQDDDKVFGgvTPGAFQKALLGRTITSAHRKGKYFWLTLDGDApVPVMHFGMT 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 499364842  78 GSL---------------RVLPGDTLPRAHDHVDISLQSGRLLRFNDPRRFG 114
Cdd:cd08972   81 GAIsikgvktiyykmlrpPKEEDQTWPPRFYKFVLTLEDGTELAFTDPRRLG 132
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-90 9.85e-15

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_1 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176807  Cd Length: 122  Bit Score: 68.81  E-value: 9.85e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   1 MPELPEVETTLRGLSPHLVGQRIHGVILRRPDLRWPIPEQIERLLpGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSL 80
Cdd:cd08973    1 MPELPEVEVYAENLERRLTGKTITRVELASKSLLVTPDPPLEALE-GRTVTGVRRHGKRLDFEFDNGLHLVLHLMLAGWL 79

                         90
                 ....*....|
gi 499364842  81 RVLPGDTLPR 90
Cdd:cd08973   80 YWTEAGALLP 89
AcNei2_N cd08971
N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains ...
 1-94 9.54e-08

N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains the N-terminal domain of the actinomycetal Nei2 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 Nei2 (MtuNei2). Complementation experiments in repair-deficient Escherichia coli (fpg mutY nei triple and nei nth double mutants), support that MtuNei2 is functionally active in vivo and recognizes both guanine and cytosine oxidation products. In addition to this AcNei2_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176805  Cd Length: 114  Bit Score: 49.51  E-value: 9.54e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   1 MPELPEVETTLRGLSPHLVGQrihgvILRRPDLRWPIPEQIErlLPGATITNVRRRAKYLLIDTDAGGSVLLHLGMSGSL 80
Cdd:cd08971    1 MPEGDTVHRAARRLRRALAGR-----VLTRADLRVPRLATAD--LAGRTVEEVVARGKHLLIRFDGGLTLHTHLRMDGSW 73

                         90
                 ....*....|....
gi 499364842  81 RVLPGDTLPRAHDH 94
Cdd:cd08971   74 HVYRPGERWRRPAH 87
MeNeil1_N cd08967
N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the ...
 1-121 7.87e-06

N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the N-terminal domain of metazoan NEIL1. 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. NEIL1 recognizes the oxidized pyrimidines 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino- 5-formamidopyrimidine (FapyA), thymine glycol (Tg) and 5-hydroxyuracil (5-OHU). However, even though it has weak activity on 8-oxo-7,8-dihydroguanine (8-oxoG), it does show strong preference for the products of its further oxidation: spiroiminodihydantoin and guanidinohydantoin. In addition to this MeNeil1_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zincless finger motif. This characteristic "zincless finger" motif, is a structural equivalent of the zinc finger common to other members of the Fpg/Nei family. Neil1 is one of three homologs found in eukaryotes and its lineage extends back as far as early metazoans.


Pssm-ID: 176801  Cd Length: 131  Bit Score: 44.37  E-value: 7.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499364842   1 MPELPEVEttlrgLSPHLVGQRIHGVIL----------RRPDLRWPIPEQierllpgaTITNVRRRAKYLLIDTDAGGS- 69
Cdd:cd08967    1 MPEGPELH-----LASLFVNKMCKGLIFtgavekssvsKNPEVPFACKAY--------TISAESRGKELRLILSPLPAAn 67

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499364842  70 ------------VLLHLGMSGSLRVLPGDTLPRaHDHVDI--SLQSGRLLRFNDPRRFGCllWQSG 121
Cdd:cd08967   68 gkkecksqeemrIVFRFGMSGSFQFTPVDEIPK-HAHLRFytKEEPKRVLSFVDIRRFGT--WQVG 130
zf-FPG_IleRS pfam06827
Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of ...
 243-270 1.85e-03

Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23.


Pssm-ID: 429140 [Multi-domain]  Cd Length: 28  Bit Score: 34.87  E-value: 1.85e-03
                          10        20
                  ....*....|....*....|....*...
gi 499364842  243 GEACKQCGRVLKHATIGQRATVWCGSCQ 270
Cdd:pfam06827   1 GEKCPRCWTYIEKVGVGGRSTYFCPRCQ 28
 
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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