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Conserved domains on  [gi|517258982|ref|WP_018447800|]
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MULTISPECIES: bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase [Rhizobium]

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

Graphical summary

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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;
1-301 4.80e-158

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


:

Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 441.44  E-value: 4.80e-158
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   1 MPELPEVETVKRGLTPAMEGTRITKLELRRGDLRFPFPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSF 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  81 RIeegrieeaaasaapgefHHARSKDEKHDHVVFHLEGAsgpRRVVYNDPRRFGFMDMVGRADLAAHPFFRDLGPEPTGN 160
Cdd:PRK01103  81 RL-----------------LPEDTPPEKHDHVDFVLDDG---TVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSD 140
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 161 ELGAAYLAERFRDKAQPLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLvtaggrPKAQLDLLVASIRDVIADAI 240
Cdd:PRK01103 141 AFDGEYLAAKLRKKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSL------SRAEAERLVDAIKAVLAEAI 214
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 517258982 241 AAGGSSLRDHIQTDGSLGYFQHSFSVYDRESQACrtPGCGGTVARIVQAGRSTFYCATCQK 301
Cdd:PRK01103 215 EQGGTTLRDYVNADGKPGYFQQSLQVYGREGEPC--RRCGTPIEKIKQGGRSTFFCPRCQK 273
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-301 4.80e-158

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 441.44  E-value: 4.80e-158
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   1 MPELPEVETVKRGLTPAMEGTRITKLELRRGDLRFPFPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSF 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  81 RIeegrieeaaasaapgefHHARSKDEKHDHVVFHLEGAsgpRRVVYNDPRRFGFMDMVGRADLAAHPFFRDLGPEPTGN 160
Cdd:PRK01103  81 RL-----------------LPEDTPPEKHDHVDFVLDDG---TVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSD 140
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 161 ELGAAYLAERFRDKAQPLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLvtaggrPKAQLDLLVASIRDVIADAI 240
Cdd:PRK01103 141 AFDGEYLAAKLRKKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSL------SRAEAERLVDAIKAVLAEAI 214
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 517258982 241 AAGGSSLRDHIQTDGSLGYFQHSFSVYDRESQACrtPGCGGTVARIVQAGRSTFYCATCQK 301
Cdd:PRK01103 215 EQGGTTLRDYVNADGKPGYFQQSLQVYGREGEPC--RRCGTPIEKIKQGGRSTFFCPRCQK 273
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-301 3.12e-136

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 386.40  E-value: 3.12e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   2 PELPEVETVKRGLTPAMEGTRITKLELRRGDLRFPFPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSFR 81
Cdd:COG0266    1 PELPEVETVRRGLAPALVGRTITRVEVRSPRLRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  82 IEEgrieeaaasaapgefhhARSKDEKHDHVVFHLEGAsgpRRVVYNDPRRFGFMDMVGRADLAAHPFFRDLGPEPTGNE 161
Cdd:COG0266   81 VVP-----------------PGEPPEKHDHVRLVLDDG---TELRFADPRRFGALELLTPDELEVHPLLARLGPEPLDPD 140
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 162 LGAAYLAERFRDKAQPLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLvtaggrPKAQLDLLVASIRDVIADAIA 241
Cdd:COG0266  141 FDPEYLAARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSL------SRAELERLAAAIREVLREAIE 214
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 242 AGGSSLRDHIQTDGSLGYFQHSFSVYDRESQACrtPGCGGTVARIVQAGRSTFYCATCQK 301
Cdd:COG0266  215 AGGTTLRDYVNADGEPGYFQQRLYVYGREGEPC--PRCGTPIERIVLGGRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
2-300 2.75e-94

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: 279.95  E-value: 2.75e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982    2 PELPEVETVKRGLTPAMEGTRITKLE--LRRGDLRFPFPDAFADRVSGRTIVGLGRRAKYLLVDLDDGnTLISHLGMSGS 79
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEvvLRNPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDDG-ALVSHLRMEGK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   80 FRIEEgrieeaaasaapgefhhARSKDEKHDHVVFHLEGASGPRrvvYNDPRRFGFMDMVGRADLAAHPFFRDLGPEPTG 159
Cdd:TIGR00577  80 YRLEA-----------------VPDAPDKHDHVDFLFDDGTELR---YHDPRRFGTWLLLDRGQVENIPLLAKLGPEPLS 139
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  160 NELGAAYLAERFRDKAQPLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLVtaggrpKAQLDLLVASIRDVIADA 239
Cdd:TIGR00577 140 EDFTAEYLFEKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLS------KEECELLHRAIKEVLRKA 213
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 517258982  240 IAAGGSSLRDHIQTDGSLGYFQHSFSVYDRESQACRtpGCGGTVARIVQAGRSTFYCATCQ 300
Cdd:TIGR00577 214 IEMGGTTIRDFSQSDGHNGYFQQELQVYGRKGEPCR--RCGTTIEKEKVGGRGTHFCPQCQ 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
2-139 9.16e-51

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: 163.44  E-value: 9.16e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   2 PELPEVETVKRGLTPAMEGTRITKLELRRGDLRFP-FPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSF 80
Cdd:cd08966    1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPpDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 517258982  81 RIEEgrieeaaasaapgefhhARSKDEKHDHVVFHLegaSGPRRVVYNDPRRFGFMDMV 139
Cdd:cd08966   81 LVVP-----------------PDEPPEKHDHVIFEL---DDGRELRFNDPRRFGTLLLV 119
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
1-136 9.64e-46

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: 150.35  E-value: 9.64e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982    1 MPELPEVETVKRGLTPAMEGTRITKLELRRGD-LRFPFPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGS 79
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKnLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 517258982   80 FRIEEgrieeaaASAAPgefhharskdeKHDHVVFHLEgasGPRRVVYNDPRRFGFM 136
Cdd:pfam01149  81 LLIKT-------EEWPP-----------KHDHVRLELD---DGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
2-137 2.31e-43

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: 144.25  E-value: 2.31e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982     2 PELPEVETVKRGLTPAMEGTRITKLE-LRRGDLRFPFPdaFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSF 80
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEvVRPPQLRFPDE--FAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSL 78
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 517258982    81 RIEEgrieeaaasaapgefhhARSKDEKHDHVVFHLEgasGPRRVVYNDPRRFGFMD 137
Cdd:smart00898  79 RVVP-----------------AGTPPPKHDHVRLVLD---DGTELRFNDPRRFGAVR 115
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-301 4.80e-158

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 441.44  E-value: 4.80e-158
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   1 MPELPEVETVKRGLTPAMEGTRITKLELRRGDLRFPFPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSF 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  81 RIeegrieeaaasaapgefHHARSKDEKHDHVVFHLEGAsgpRRVVYNDPRRFGFMDMVGRADLAAHPFFRDLGPEPTGN 160
Cdd:PRK01103  81 RL-----------------LPEDTPPEKHDHVDFVLDDG---TVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSD 140
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 161 ELGAAYLAERFRDKAQPLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLvtaggrPKAQLDLLVASIRDVIADAI 240
Cdd:PRK01103 141 AFDGEYLAAKLRKKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSL------SRAEAERLVDAIKAVLAEAI 214
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 517258982 241 AAGGSSLRDHIQTDGSLGYFQHSFSVYDRESQACrtPGCGGTVARIVQAGRSTFYCATCQK 301
Cdd:PRK01103 215 EQGGTTLRDYVNADGKPGYFQQSLQVYGREGEPC--RRCGTPIEKIKQGGRSTFFCPRCQK 273
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-301 3.12e-136

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 386.40  E-value: 3.12e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   2 PELPEVETVKRGLTPAMEGTRITKLELRRGDLRFPFPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSFR 81
Cdd:COG0266    1 PELPEVETVRRGLAPALVGRTITRVEVRSPRLRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  82 IEEgrieeaaasaapgefhhARSKDEKHDHVVFHLEGAsgpRRVVYNDPRRFGFMDMVGRADLAAHPFFRDLGPEPTGNE 161
Cdd:COG0266   81 VVP-----------------PGEPPEKHDHVRLVLDDG---TELRFADPRRFGALELLTPDELEVHPLLARLGPEPLDPD 140
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 162 LGAAYLAERFRDKAQPLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLvtaggrPKAQLDLLVASIRDVIADAIA 241
Cdd:COG0266  141 FDPEYLAARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSL------SRAELERLAAAIREVLREAIE 214
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 242 AGGSSLRDHIQTDGSLGYFQHSFSVYDRESQACrtPGCGGTVARIVQAGRSTFYCATCQK 301
Cdd:COG0266  215 AGGTTLRDYVNADGEPGYFQQRLYVYGREGEPC--PRCGTPIERIVLGGRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
2-300 2.75e-94

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: 279.95  E-value: 2.75e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982    2 PELPEVETVKRGLTPAMEGTRITKLE--LRRGDLRFPFPDAFADRVSGRTIVGLGRRAKYLLVDLDDGnTLISHLGMSGS 79
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEvvLRNPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDDG-ALVSHLRMEGK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   80 FRIEEgrieeaaasaapgefhhARSKDEKHDHVVFHLEGASGPRrvvYNDPRRFGFMDMVGRADLAAHPFFRDLGPEPTG 159
Cdd:TIGR00577  80 YRLEA-----------------VPDAPDKHDHVDFLFDDGTELR---YHDPRRFGTWLLLDRGQVENIPLLAKLGPEPLS 139
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  160 NELGAAYLAERFRDKAQPLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLVtaggrpKAQLDLLVASIRDVIADA 239
Cdd:TIGR00577 140 EDFTAEYLFEKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLS------KEECELLHRAIKEVLRKA 213
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 517258982  240 IAAGGSSLRDHIQTDGSLGYFQHSFSVYDRESQACRtpGCGGTVARIVQAGRSTFYCATCQ 300
Cdd:TIGR00577 214 IEMGGTTIRDFSQSDGHNGYFQQELQVYGRKGEPCR--RCGTTIEKEKVGGRGTHFCPQCQ 272
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
1-301 2.90e-67

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 210.81  E-value: 2.90e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   1 MPELPEVETVKRGLTPAMEGTRITKLELRRgdlrfpfPDAFAD--RVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSG 78
Cdd:PRK14811   1 MPELPEVETTRRKLEPLLLGQTIQQVVHDD-------PARYRNteLAEGRRVLGLSRRGKYLLLHLPHDLELIVHLGMTG 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  79 SFRIEEGRieeaaasaapgefhharskdekHDHVVFHLEGasgpRRVVYNDPRRFGFMDMVGRADLAAHPFFRDLGPEPT 158
Cdd:PRK14811  74 GFRLEPGP----------------------HTRVTLELPG----RTLYFTDPRRFGKWWVVRAGDYREIPLLARMGPEPL 127
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 159 GNELGAAYLAERFRdKAQPLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLVTAGGRPkaqldlLVASIRDVIAD 238
Cdd:PRK14811 128 SDDFTEPEFVRALA-TARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARR------LYRAIREVMAE 200
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 517258982 239 AIAAGGSSLRD--HIQTDGSLGYFQHSFSVYDRESQACrtPGCGGTVARIVQAGRSTFYCATCQK 301
Cdd:PRK14811 201 AVEAGGSTLSDgsYRQPDGEPGGFQFQHAVYGREGQPC--PRCGTPIEKIVVGGRGTHFCPQCQP 263
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
1-301 1.32e-55

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 181.28  E-value: 1.32e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   1 MPELPEVETVKRGLTPAMEGTRITKLE-LRRGDLRFPF-PDAFADRVSGRTIVGLGRRAKYLLVDLDD-----GNTLISH 73
Cdd:PRK13945   1 MPELPEVETVRRGLEQLLLNFIIKGVEvLLERTIASPGgVEEFIKGLKGSLIGQWQRRGKYLLASLKKegsenAGWLGVH 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  74 LGMSGSFrieegrieeaaasaapgEFHHARSKDEKHDHVVFHLEGASGPRRVvynDPRRFGFMDMV--GRADLAAHPFFR 151
Cdd:PRK13945  81 LRMTGQF-----------------LWVEQSTPPCKHTRVRLFFEKNQELRFV---DIRSFGQMWWVppGVSPESIITGLQ 140
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 152 DLGPEPTGNELGAAYLAERFRDKAQPLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLvtaggrPKAQLDLLVAS 231
Cdd:PRK13945 141 KLGPEPFSPEFSVEYLKKKLKKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQL------KKKQLERLREA 214
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 232 IRDVIADAIAAGGSSLRDHIQTDGSLGYFQHSFSVYDRESQACRTpgCGGTVARIVQAGRSTFYCATCQK 301
Cdd:PRK13945 215 IIEVLKTSIGAGGTTFSDFRDLEGVNGNYGGQAWVYRRTGKPCRK--CGTPIERIKLAGRSTHWCPNCQK 282
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
1-301 1.21e-51

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 170.86  E-value: 1.21e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   1 MPELPEVETVKRGLTPAMEGTRITKLELRRgdLRFPF---PDAFADRVSGRTIVGLGRRAKYLLVDLDDGNT----LISH 73
Cdd:PRK14810   1 MPELPEVETVARGLAPRAAGRRIATAEFRN--LRIPRkgdPDLMAARLAGRKILSVKRVGKHIVADLEGPGEprgqWIIH 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  74 LGMSGSFRIEegrieeAAASAAPgefhharskdeKHDHVVFHLegaSGPRRVVYNDPRRFGFMDM-VGRADLAAHPffrd 152
Cdd:PRK14810  79 LGMTGKLLLG------GPDTPSP-----------KHTHAVLTL---SSGKELRFVDSRQFGCIEYsEAFPKRFARP---- 134
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 153 lGPEPTgnELGAAYLAERFRDKAQPLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLvtaggrPKAQLDLLVASI 232
Cdd:PRK14810 135 -GPEPL--EISFEDFAALFRGRKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSL------SRERLRKLHDAI 205
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517258982 233 RDVIADAIAAGGSSLRDHIQTDGSLGYFQHSFSVYDRESQACRTpgCGGTVARIVQAGRSTFYCATCQK 301
Cdd:PRK14810 206 GEVLREAIELGGSSVSDYVDAEGRSGFFQLSHRVYQRTGEPCLN--CKTPIRRVVVAGRSSHYCPHCQK 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
2-139 9.16e-51

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: 163.44  E-value: 9.16e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   2 PELPEVETVKRGLTPAMEGTRITKLELRRGDLRFP-FPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSF 80
Cdd:cd08966    1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPpDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 517258982  81 RIEEgrieeaaasaapgefhhARSKDEKHDHVVFHLegaSGPRRVVYNDPRRFGFMDMV 139
Cdd:cd08966   81 LVVP-----------------PDEPPEKHDHVIFEL---DDGRELRFNDPRRFGTLLLV 119
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
1-136 9.64e-46

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: 150.35  E-value: 9.64e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982    1 MPELPEVETVKRGLTPAMEGTRITKLELRRGD-LRFPFPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGS 79
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKnLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 517258982   80 FRIEEgrieeaaASAAPgefhharskdeKHDHVVFHLEgasGPRRVVYNDPRRFGFM 136
Cdd:pfam01149  81 LLIKT-------EEWPP-----------KHDHVRLELD---DGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
2-137 2.31e-43

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: 144.25  E-value: 2.31e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982     2 PELPEVETVKRGLTPAMEGTRITKLE-LRRGDLRFPFPdaFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSF 80
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEvVRPPQLRFPDE--FAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSL 78
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 517258982    81 RIEEgrieeaaasaapgefhhARSKDEKHDHVVFHLEgasGPRRVVYNDPRRFGFMD 137
Cdd:smart00898  79 RVVP-----------------AGTPPPKHDHVRLVLD---DGTELRFNDPRRFGAVR 115
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
153-247 8.60e-26

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: 97.75  E-value: 8.60e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  153 LGPEPTGNELGAAYLAERFRDKAQPLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLvtaggrPKAQLDLLVASI 232
Cdd:pfam06831   1 LGPEPLSEDFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSL------SKEECELLHQAI 74
                          90
                  ....*....|....*
gi 517258982  233 RDVIADAIAAGGSSL 247
Cdd:pfam06831  75 KAVLQEAIEMGGGGI 89
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
2-138 1.06e-25

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: 98.59  E-value: 1.06e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   2 PELPEVETVKRGLTPAMEGTRITKLELRRGDLRFPFPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSFR 81
Cdd:cd08773    1 PELPEVELLRRKLRRALKGKRVTRVEVSDPRRLFTPAAELAAALIGRRVRGAERRGKYLLLELSGGPWLVIHLGMTGRLR 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 517258982  82 IEEgrieeaaasaapgefhhARSKDEKHDHVVFHLEGAsgpRRVVYNDPRRFGFMDM 138
Cdd:cd08773   81 VCP-----------------EGEPPPKHDRLVLRLANG---SQLRFTDPRKFGRVEL 117
PRK10445 PRK10445
endonuclease VIII; Provisional
1-301 6.27e-24

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 97.79  E-value: 6.27e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   1 MPELPEVETVKRGLTPAMEGTRITklelrrgDLRFPFPD--AFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSG 78
Cdd:PRK10445   1 MPEGPEIRRAADNLEAAIKGKPLT-------DVWFAFPQlkPYESQLIGQRVTHIETRGKALLTHFSNGLTLYSHNQLYG 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982  79 SFRIeegrieeAAASAAPGEFHHARSKDEKHDHVVFhLEGASGprrvvyndprrfgfMDMVGRADLAAHPFFRDLGP--- 155
Cdd:PRK10445  74 VWRV-------VDTGEEPQTTRVLRVRLQTADKTIL-LYSASD--------------IEMLTPEQLTTHPFLQRVGPdvl 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982 156 --EPTGNELGAAYLAERFRDKAqpLKSALLDQKNIAGLGNIYVCEALWRAHLSPIRAAGTLvtaggrPKAQLDLLVASIR 233
Cdd:PRK10445 132 dpNLTPEQVKERLLSPRFRNRQ--FSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDL------NEAQLDALAHALL 203
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 517258982 234 DVIADAIAAGGssLRDHIQTDGSLgyfqHSFSVYDRESQACRTpgCGGTVARIVQAGRSTFYCATCQK 301
Cdd:PRK10445 204 DIPRLSYATRG--QVDENKHHGAL----FRFKVFHRDGEACER--CGGIIEKTTLSSRPFYWCPGCQK 263
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
1-134 5.08e-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: 75.81  E-value: 5.08e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   1 MPELPEVETVKRGLTPAMEGTRITKLELRRGDLRFP--FPDAFADRVSGRTIVGLGRRAKYLLVDLD-DGNTLISHLGMS 77
Cdd:cd08972    1 MPELPEVERARRLLEEHCLGKKITKVDAQDDDKVFGgvTPGAFQKALLGRTITSAHRKGKYFWLTLDgDAPVPVMHFGMT 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 517258982  78 GSFRIEEGRIEEAAASAAPGEfhhaRSKDEKHDHVVFHLEGASGpRRVVYNDPRRFG 134
Cdd:cd08972   81 GAISIKGVKTIYYKMLRPPKE----EDQTWPPRFYKFVLTLEDG-TELAFTDPRRLG 132
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
1-84 4.83e-13

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: 64.58  E-value: 4.83e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   1 MPELPEVETVKRGLTPAMEGTRITKLELRRGDLRFPfPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSF 80
Cdd:cd08973    1 MPELPEVEVYAENLERRLTGKTITRVELASKSLLVT-PDPPLEALEGRTVTGVRRHGKRLDFEFDNGLHLVLHLMLAGWL 79

                 ....
gi 517258982  81 RIEE 84
Cdd:cd08973   80 YWTE 83
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
2-134 1.15e-10

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: 57.75  E-value: 1.15e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   2 PELPEVETVKRGLTPAMEGTRITKLELRRGDLRFPFPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSFr 81
Cdd:cd08976    1 PELPEVEVQKQYLERTSLHRKIVEVEVGDDKILGEPKATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTGKL- 79
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 517258982  82 ieegrieeaaasaapgEFHHARSKDEKHDHVVFHLEGAsgpRRVVYNDPRRFG 134
Cdd:cd08976   80 ----------------DYYPDDEDPPKHARLLLHFEDG---FRLAFECPRKFG 113
AcNei2_N cd08971
N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains ...
1-82 1.75e-09

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: 54.52  E-value: 1.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517258982   1 MPELPEVETVKRGLTPAMEGTRITKLELRRgdlrfpfPDAFADRVSGRTIVGLGRRAKYLLVDLDDGNTLISHLGMSGSF 80
Cdd:cd08971    1 MPEGDTVHRAARRLRRALAGRVLTRADLRV-------PRLATADLAGRTVEEVVARGKHLLIRFDGGLTLHTHLRMDGSW 73

                 ..
gi 517258982  81 RI 82
Cdd:cd08971   74 HV 75
zf-FPG_IleRS pfam06827
Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of ...
279-300 2.71e-04

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: 37.57  E-value: 2.71e-04
                          10        20
                  ....*....|....*....|..
gi 517258982  279 CGGTVARIVQAGRSTFYCATCQ 300
Cdd:pfam06827   7 CWTYIEKVGVGGRSTYFCPRCQ 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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