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Conserved domains on  [gi|1083642139|gb|OGH32097|]
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MAG: DNA-formamidopyrimidine glycosylase [Candidatus Levybacteria bacterium RIFCSPHIGHO2_12_FULL_40_31]

Protein Classification

Fpg/Nei family DNA glycosylase( domain architecture ID 11415887)

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:  1.10.8.50|3.20.190.10
EC:  3.2.2.-|4.2.99.-
Gene Ontology:  GO:0140078|GO:0003684|GO:0008534|GO:0008270|GO:0006284|GO:0003906|GO:0006281
PubMed:  21486746|14607836
SCOP:  4000303

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-287 8.58e-104

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


:

Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 303.59  E-value: 8.58e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   2 PELPEVETLRLGLIKYVLGHKILDVEILHPK----VFQGEKEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQLI 77
Cdd:COG0266     1 PELPEVETVRRGLAPALVGRTITRVEVRSPRlrfpVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139  78 YRDEKTKnvslsakvggdlPNKFTHVIFKLSKLTAnsqkptayLYYNDQRRFGWIKVIKSDKVSKLPFFRDMGPEPF-KD 156
Cdd:COG0266    81 VVPPGEP------------PEKHDHVRLVLDDGTE--------LRFADPRRFGALELLTPDELEVHPLLARLGPEPLdPD 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 157 LTFARFKFVVGKKVTKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKKGLASRGASE 236
Cdd:COG0266   141 FDPEYLAARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTL 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1083642139 237 LSFVNILGQEGEYQNHTLVYGKRGQKCPNCGSTIKFIRIGGRGTYFCPNCQ 287
Cdd:COG0266   221 RDYVNADGEPGYFQQRLYVYGREGEPCPRCGTPIERIVLGGRSTYYCPRCQ 271
 
Name Accession Description Interval E-value
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-287 8.58e-104

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 303.59  E-value: 8.58e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   2 PELPEVETLRLGLIKYVLGHKILDVEILHPK----VFQGEKEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQLI 77
Cdd:COG0266     1 PELPEVETVRRGLAPALVGRTITRVEVRSPRlrfpVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139  78 YRDEKTKnvslsakvggdlPNKFTHVIFKLSKLTAnsqkptayLYYNDQRRFGWIKVIKSDKVSKLPFFRDMGPEPF-KD 156
Cdd:COG0266    81 VVPPGEP------------PEKHDHVRLVLDDGTE--------LRFADPRRFGALELLTPDELEVHPLLARLGPEPLdPD 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 157 LTFARFKFVVGKKVTKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKKGLASRGASE 236
Cdd:COG0266   141 FDPEYLAARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTL 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1083642139 237 LSFVNILGQEGEYQNHTLVYGKRGQKCPNCGSTIKFIRIGGRGTYFCPNCQ 287
Cdd:COG0266   221 RDYVNADGEPGYFQQRLYVYGREGEPCPRCGTPIERIVLGGRSTYYCPRCQ 271
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-288 2.22e-91

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 271.95  E-value: 2.22e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   1 MPELPEVETLRLGLIKYVLGHKILDVEILHPKV---FQGE-KEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQL 76
Cdd:PRK01103    1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLrwpVPEDfAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139  77 IYRDEKTKnvslsakvggdlPNKFTHVIFKLSKLTAnsqkptayLYYNDQRRFGWIKVIKSDKVSKLPFFRDMGPEPFKD 156
Cdd:PRK01103   81 RLLPEDTP------------PEKHDHVDFVLDDGTV--------LRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSD 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 157 -LTFARFKFVVGKKVTKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKKGLASRGAS 235
Cdd:PRK01103  141 aFDGEYLAAKLRKKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTT 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1083642139 236 ELSFVNILGQEGEYQNHTLVYGKRGQKCPNCGSTIKFIRIGGRGTYFCPNCQQ 288
Cdd:PRK01103  221 LRDYVNADGKPGYFQQSLQVYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-287 3.64e-79

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: 241.05  E-value: 3.64e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   2 PELPEVETLRLGLIKYVLGHKILDVEILHPKV------FQGEKEKVIGSTVKDARRVGKGLILELSNGYcLAIHIKLTGQ 75
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPvlrpagSEDLQKRLLGQTILSIQRRGKYLLFELDDGA-LVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139  76 liYRdektknvsLSAKvgGDLPNKFTHVIFKLSKLTAnsqkptayLYYNDQRRFGWIKVIKSDKVSKLPFFRDMGPEPF- 154
Cdd:TIGR00577  80 --YR--------LEAV--PDAPDKHDHVDFLFDDGTE--------LRYHDPRRFGTWLLLDRGQVENIPLLAKLGPEPLs 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 155 KDLTFARFKFVVGKKVTKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKKGLASRGA 234
Cdd:TIGR00577 140 EDFTAEYLFEKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGT 219

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1083642139 235 SELSFVNILGQEGEYQNHTLVYGKRGQKCPNCGSTIKFIRIGGRGTYFCPNCQ 287
Cdd:TIGR00577 220 TIRDFSQSDGHNGYFQQELQVYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-135 6.00e-33

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: 117.21  E-value: 6.00e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   2 PELPEVETLRLGLIKYVLGHKILDVEILHPKVFQGE-----KEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQL 76
Cdd:cd08966     1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPPdpeefAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1083642139  77 IYRDEKTKnvslsakvggdlPNKFTHVIFKLSKLTansqkptaYLYYNDQRRFGWIKVI 135
Cdd:cd08966    81 LVVPPDEP------------PEKHDHVIFELDDGR--------ELRFNDPRRFGTLLLV 119
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-132 2.37e-31

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: 112.99  E-value: 2.37e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   1 MPELPEVETLRLGLIKYVLGHKILDVEILHPKVFQGE-----KEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQ 75
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNLRGPspeefAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1083642139  76 LIYRDEktknvslsakvggDLPNKFTHVIFKLSkltansqkPTAYLYYNDQRRFGWI 132
Cdd:pfam01149  81 LLIKTE-------------EWPPKHDHVRLELD--------DGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-132 8.16e-28

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: 103.80  E-value: 8.16e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139    2 PELPEVETLRLGLIKYVLGHKILDVEILHPKVFQ---GEKEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQLIY 78
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQLRfpdEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSLRV 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1083642139   79 RDEktknvslsakvgGDLPNKFTHVIFKLSKLTAnsqkptayLYYNDQRRFGWI 132
Cdd:smart00898  81 VPA------------GTPPPKHDHVRLVLDDGTE--------LRFNDPRRFGAV 114
 
Name Accession Description Interval E-value
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-287 8.58e-104

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 303.59  E-value: 8.58e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   2 PELPEVETLRLGLIKYVLGHKILDVEILHPK----VFQGEKEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQLI 77
Cdd:COG0266     1 PELPEVETVRRGLAPALVGRTITRVEVRSPRlrfpVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139  78 YRDEKTKnvslsakvggdlPNKFTHVIFKLSKLTAnsqkptayLYYNDQRRFGWIKVIKSDKVSKLPFFRDMGPEPF-KD 156
Cdd:COG0266    81 VVPPGEP------------PEKHDHVRLVLDDGTE--------LRFADPRRFGALELLTPDELEVHPLLARLGPEPLdPD 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 157 LTFARFKFVVGKKVTKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKKGLASRGASE 236
Cdd:COG0266   141 FDPEYLAARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTL 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1083642139 237 LSFVNILGQEGEYQNHTLVYGKRGQKCPNCGSTIKFIRIGGRGTYFCPNCQ 287
Cdd:COG0266   221 RDYVNADGEPGYFQQRLYVYGREGEPCPRCGTPIERIVLGGRSTYYCPRCQ 271
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-288 2.22e-91

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 271.95  E-value: 2.22e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   1 MPELPEVETLRLGLIKYVLGHKILDVEILHPKV---FQGE-KEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQL 76
Cdd:PRK01103    1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLrwpVPEDfAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139  77 IYRDEKTKnvslsakvggdlPNKFTHVIFKLSKLTAnsqkptayLYYNDQRRFGWIKVIKSDKVSKLPFFRDMGPEPFKD 156
Cdd:PRK01103   81 RLLPEDTP------------PEKHDHVDFVLDDGTV--------LRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSD 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 157 -LTFARFKFVVGKKVTKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKKGLASRGAS 235
Cdd:PRK01103  141 aFDGEYLAAKLRKKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTT 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1083642139 236 ELSFVNILGQEGEYQNHTLVYGKRGQKCPNCGSTIKFIRIGGRGTYFCPNCQQ 288
Cdd:PRK01103  221 LRDYVNADGKPGYFQQSLQVYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-287 3.64e-79

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: 241.05  E-value: 3.64e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   2 PELPEVETLRLGLIKYVLGHKILDVEILHPKV------FQGEKEKVIGSTVKDARRVGKGLILELSNGYcLAIHIKLTGQ 75
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPvlrpagSEDLQKRLLGQTILSIQRRGKYLLFELDDGA-LVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139  76 liYRdektknvsLSAKvgGDLPNKFTHVIFKLSKLTAnsqkptayLYYNDQRRFGWIKVIKSDKVSKLPFFRDMGPEPF- 154
Cdd:TIGR00577  80 --YR--------LEAV--PDAPDKHDHVDFLFDDGTE--------LRYHDPRRFGTWLLLDRGQVENIPLLAKLGPEPLs 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 155 KDLTFARFKFVVGKKVTKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKKGLASRGA 234
Cdd:TIGR00577 140 EDFTAEYLFEKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGT 219

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1083642139 235 SELSFVNILGQEGEYQNHTLVYGKRGQKCPNCGSTIKFIRIGGRGTYFCPNCQ 287
Cdd:TIGR00577 220 TIRDFSQSDGHNGYFQQELQVYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 1-287 1.72e-60

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 193.61  E-value: 1.72e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   1 MPELPEVETLRLGLIKYVLGHKILDVEILHPK--VFQGEKEKVI----GSTVKDARRVGKGLILELS-----NGYCLAIH 69
Cdd:PRK13945    1 MPELPEVETVRRGLEQLLLNFIIKGVEVLLERtiASPGGVEEFIkglkGSLIGQWQRRGKYLLASLKkegseNAGWLGVH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139  70 IKLTGQLIYRDEKTKnvslsakvggdlPNKFTHVIFKLSKltaNSQkptayLYYNDQRRFG---WI-------KVIKSdk 139
Cdd:PRK13945   81 LRMTGQFLWVEQSTP------------PCKHTRVRLFFEK---NQE-----LRFVDIRSFGqmwWVppgvspeSIITG-- 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 140 VSKLpffrdmGPEPF-KDLTFARFKFVVGKKVTKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLY 218
Cdd:PRK13945  139 LQKL------GPEPFsPEFSVEYLKKKLKKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLR 212

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1083642139 219 DSILFVLKKGLASRGASELSFVNILGQEGEYQNHTLVYGKRGQKCPNCGSTIKFIRIGGRGTYFCPNCQ 287
Cdd:PRK13945  213 EAIIEVLKTSIGAGGTTFSDFRDLEGVNGNYGGQAWVYRRTGKPCRKCGTPIERIKLAGRSTHWCPNCQ 281
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-288 3.35e-57

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 184.61  E-value: 3.35e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   1 MPELPEVETLRLGLIKYVLGHKILDVEILHPKVFQgEKEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQliYRD 80
Cdd:PRK14811    1 MPELPEVETTRRKLEPLLLGQTIQQVVHDDPARYR-NTELAEGRRVLGLSRRGKYLLLHLPHDLELIVHLGMTGG--FRL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139  81 EktknvslsakvggdlPNKFTHVIFKLSKLTansqkptayLYYNDQRRFGWIKVIKSDKVSKLPFFRDMGPEPF-KDLTF 159
Cdd:PRK14811   78 E---------------PGPHTRVTLELPGRT---------LYFTDPRRFGKWWVVRAGDYREIPLLARMGPEPLsDDFTE 133

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 160 ARFkFVVGKKVTKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKKGLASRGA--SEL 237
Cdd:PRK14811  134 PEF-VRALATARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEAVEAGGStlSDG 212

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1083642139 238 SFVNILGQEGEYQNHTLVYGKRGQKCPNCGSTIKFIRIGGRGTYFCPNCQQ 288
Cdd:PRK14811  213 SYRQPDGEPGGFQFQHAVYGREGQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-288 2.03e-51

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 170.09  E-value: 2.03e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   1 MPELPEVETLRLGLIKYVLGHKILDVEILHPKVFQGEKEKVI-----GSTVKDARRVGKGLILELSNGYC----LAIHIK 71
Cdd:PRK14810    1 MPELPEVETVARGLAPRAAGRRIATAEFRNLRIPRKGDPDLMaarlaGRKILSVKRVGKHIVADLEGPGEprgqWIIHLG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139  72 LTGQLIYrdektknvslsakVGGDLPN-KFTHVIFKLSKltansqkpTAYLYYNDQRRFGWIKV--IKSDKVSKLpffrd 148
Cdd:PRK14810   81 MTGKLLL-------------GGPDTPSpKHTHAVLTLSS--------GKELRFVDSRQFGCIEYseAFPKRFARP----- 134

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 149 mGPEPFkDLTFARFKFVVGKKVTKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKKG 228
Cdd:PRK14810  135 -GPEPL-EISFEDFAALFRGRKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREA 212

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 229 LASRGASELSFVNILGQEGEYQNHTLVYGKRGQKCPNCGSTIKFIRIGGRGTYFCPNCQQ 288
Cdd:PRK14810  213 IELGGSSVSDYVDAEGRSGFFQLSHRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHCQK 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-135 6.00e-33

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: 117.21  E-value: 6.00e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   2 PELPEVETLRLGLIKYVLGHKILDVEILHPKVFQGE-----KEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQL 76
Cdd:cd08966     1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPPdpeefAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1083642139  77 IYRDEKTKnvslsakvggdlPNKFTHVIFKLSKLTansqkptaYLYYNDQRRFGWIKVI 135
Cdd:cd08966    81 LVVPPDEP------------PEKHDHVIFELDDGR--------ELRFNDPRRFGTLLLV 119
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-132 2.37e-31

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: 112.99  E-value: 2.37e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   1 MPELPEVETLRLGLIKYVLGHKILDVEILHPKVFQGE-----KEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQ 75
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNLRGPspeefAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1083642139  76 LIYRDEktknvslsakvggDLPNKFTHVIFKLSkltansqkPTAYLYYNDQRRFGWI 132
Cdd:pfam01149  81 LLIKTE-------------EWPPKHDHVRLELD--------DGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-132 8.16e-28

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: 103.80  E-value: 8.16e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139    2 PELPEVETLRLGLIKYVLGHKILDVEILHPKVFQ---GEKEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQLIY 78
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQLRfpdEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSLRV 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1083642139   79 RDEktknvslsakvgGDLPNKFTHVIFKLSKLTAnsqkptayLYYNDQRRFGWI 132
Cdd:smart00898  81 VPA------------GTPPPKHDHVRLVLDDGTE--------LRFNDPRRFGAV 114
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 149-235 5.56e-25

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: 95.44  E-value: 5.56e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 149 MGPEP-FKDLTFARFKFVVGKKVTKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKK 227
Cdd:pfam06831   1 LGPEPlSEDFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVLQE 80


                  ....*...
gi 1083642139 228 GLASRGAS 235
Cdd:pfam06831  81 AIEMGGGG 88
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-287 3.81e-19

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 84.70  E-value: 3.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   1 MPELPEVETLRLGLIKYVLGHKILDVEILHPKVfQGEKEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGqlIYRD 80
Cdd:PRK10445    1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQL-KPYESQLIGQRVTHIETRGKALLTHFSNGLTLYSHNQLYG--VWRV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139  81 EKTKNVSLSAKVggdlpnkfthvifklSKLTANSQKPTAYLYYNDQrrfgwIKVIKSDKVSKLPFFRDMGP--------- 151
Cdd:PRK10445   78 VDTGEEPQTTRV---------------LRVRLQTADKTILLYSASD-----IEMLTPEQLTTHPFLQRVGPdvldpnltp 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139 152 EPFKD-LTFARFKfvvgKKvtKIKPLLMDQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKKGLA 230
Cdd:PRK10445  138 EQVKErLLSPRFR----NR--QFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYA 211

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1083642139 231 SRGAselsfVNILGQEGEYQNHTlVYGKRGQKCPNCGSTIKFIRIGGRGTYFCPNCQ 287
Cdd:PRK10445  212 TRGQ-----VDENKHHGALFRFK-VFHRDGEACERCGGIIEKTTLSSRPFYWCPGCQ 262
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-107 2.88e-17

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: 76.13  E-value: 2.88e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   1 MPELPEVETLRLGLIKYVLGHKILDVEILHPKV---FQGEKEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQLI 77
Cdd:cd08973     1 MPELPEVEVYAENLERRLTGKTITRVELASKSLlvtPDPPLEALEGRTVTGVRRHGKRLDFEFDNGLHLVLHLMLAGWLY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1083642139  78 YRDEktknvslsakvGGDLPNKFTHVIFKL 107
Cdd:cd08973    81 WTEA-----------GALLPGKKGPIALRF 99
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-134 3.09e-16

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: 73.17  E-value: 3.09e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   2 PELPEVETLRLGLIKYVLGHKILDVEILHPKVFQGEKEKV----IGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQLI 77
Cdd:cd08773     1 PELPEVELLRRKLRRALKGKRVTRVEVSDPRRLFTPAAELaaalIGRRVRGAERRGKYLLLELSGGPWLVIHLGMTGRLR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1083642139  78 YRDEktknvslsakvgGDLPNKFTHVIFKLSkltansqkPTAYLYYNDQRRFGWIKV 134
Cdd:cd08773    81 VCPE------------GEPPPKHDRLVLRLA--------NGSQLRFTDPRKFGRVEL 117
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-134 5.05e-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_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: 64.29  E-value: 5.05e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   2 PELPEVETLRLGLIKYVLGHKILDVEILHPKVFQ----GEKEKVIGSTVKDARRVGKGLILELSNGYCLAIHIKLTGQLI 77
Cdd:cd08976     1 PELPEVEVQKQYLERTSLHRKIVEVEVGDDKILGepkaTLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTGKLD 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1083642139  78 YRDektknvslsakvGGDLPNKFTHVIFKLskltANSQKptayLYYNDQRRFGWIKV 134
Cdd:cd08976    81 YYP------------DDEDPPKHARLLLHF----EDGFR----LAFECPRKFGRVRL 117
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-134 2.77e-11

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: 60.01  E-value: 2.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083642139   1 MPELPEVETLRLGLIKYVLGHKILDVEILH-PKVFQGEK-----EKVIGSTVKDARRVGKGLILELS-NGYCLAIHIKLT 73
Cdd:cd08972     1 MPELPEVERARRLLEEHCLGKKITKVDAQDdDKVFGGVTpgafqKALLGRTITSAHRKGKYFWLTLDgDAPVPVMHFGMT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1083642139  74 GQLIYRDEKTKNVSLSAKVG---GDLPNKFTHVIFKLskltansQKPTAYLYYnDQRRFGWIKV 134
Cdd:cd08972    81 GAISIKGVKTIYYKMLRPPKeedQTWPPRFYKFVLTL-------EDGTELAFT-DPRRLGRVRL 136
zf-FPG_IleRS pfam06827
Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of ...
 260-287 1.04e-09

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: 52.59  E-value: 1.04e-09
                          10        20
                  ....*....|....*....|....*...
gi 1083642139 260 GQKCPNCGSTIKFIRIGGRGTYFCPNCQ 287
Cdd:pfam06827   1 GEKCPRCWTYIEKVGVGGRSTYFCPRCQ 28
RqcH COG1293
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) ...
 156-227 7.08e-07

Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) and RNA- (NFACT) binding domains [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440904 [Multi-domain]  Cd Length: 578  Bit Score: 50.22  E-value: 7.08e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1083642139 156 DLTFARFKFVVGKKVTKIKPLLMdqTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKK 227
Cdd:COG1293   174 ELSEEEFAELLSESDGDLVRTLA--TNFLGLSPLLAEEICYRAGLDKDTPTDELSEEDLEALYEALQELLEE 243
NFACT_N pfam05833
NFACT N-terminal and middle domains; This family contains the N-terminal and middle domains of ...
 150-227 2.37e-05

NFACT N-terminal and middle domains; This family contains the N-terminal and middle domains of NFACT (NEMF, FbpA, Caliban, and Tae2) proteins from eukaryotes, archaea and bacteria. Many members of this family act in ribosome quality control (RQC), including RqcH, which are involved in the addition of a poly-Ala tail to defective translated proteins to tag them for degradation. This process is analogous to the ssrA/tmRNA bacterial system. However, some other NFACT family members, such as bacterial proteins FbpA in Listeria or PavA in Streptococcus, are exported (despite lack of a classical signal peptide) and behave as fibronectin-binding adhesins associated with virulence.


Pssm-ID: 428644 [Multi-domain]  Cd Length: 451  Bit Score: 45.31  E-value: 2.37e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083642139 150 GPEPFKDLTFARFKFVVGKKvtKIKPLLmdQTNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSILFVLKK 227
Cdd:pfam05833 166 KLNPLTAEEFEEFKELLNDG--KLAKAL--VKAFQGLSPLLAEELCYRAGLDKETPAEELSDEDWERLYEAFQDLLNQ 239
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 261-286 9.86e-04

TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.


Pssm-ID: 400527 [Multi-domain]  Cd Length: 43  Bit Score: 36.13  E-value: 9.86e-04
                          10        20
                  ....*....|....*....|....*.
gi 1083642139 261 QKCPNCGSTiKFIRIGGRGTYFCPNC 286
Cdd:pfam08271   1 YKCPNCGST-NLVEDYERGELVCTDC 25
Prim_Zn_Ribbon smart00778
Zinc-binding domain of primase-helicase; This region represents the zinc binding domain. It is ...
 258-286 3.02e-03

Zinc-binding domain of primase-helicase; This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.


Pssm-ID: 129016 [Multi-domain]  Cd Length: 37  Bit Score: 34.62  E-value: 3.02e-03
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1083642139  258 KRGQKCPNCGST--IKFIRIGGRGTYFCPNC 286
Cdd:smart00778   1 GRHGPCPNCGGSdrFRFDDKDGRGTWFCSVC 31
Ribosomal_S13 pfam00416
Ribosomal protein S13/S18; This family includes ribosomal protein S13 from prokaryotes and S18 ...
 181-221 3.80e-03

Ribosomal protein S13/S18; This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.


Pssm-ID: 425669  Cd Length: 107  Bit Score: 36.14  E-value: 3.80e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1083642139 181 TNMGGIGNIYANDALFRAGIDPRKTGKSLSEEELKKLYDSI 221
Cdd:pfam00416  18 TYIKGIGRRRANIILKKAGIDRDKRAGELTEEEIDRLRDIV 58
Prim_Zn_Ribbon pfam08273
Zinc-binding domain of primase-helicase;
258-286 6.14e-03

Zinc-binding domain of primase-helicase;


Pssm-ID: 400529  Cd Length: 37  Bit Score: 33.89  E-value: 6.14e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1083642139 258 KRGQKCPNCGST--IKFIRIGGRGTYFCPNC 286
Cdd:pfam08273   1 GYHGPCPVCGGRdrFRFDDKDGRGTWFCRVC 31
 
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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