NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|372114685|gb|AEX80743|]
View 

putative endonuclease [Corynebacterium diphtheriae HC04]

Protein Classification

Fpg/Nei family DNA glycosylase( domain architecture ID 1001686)

Fpg/Nei family DNA glycosylase similar to Mycobacterium tuberculosis bifunctional DNA-(apurinic or apyrimidinic site) lyase removes damaged bases from DNA, leaving an abasic site, and also probably cleaves 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

CATH:  3.20.190.10
Gene Ontology:  GO:0006281|GO:0008534|GO:0016799|GO:0003906|GO:0003684|GO:0008270|GO:0006284
PubMed:  22749143
SCOP:  4000303

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Nei super family cl33822
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-266 7.63e-46

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


The actual alignment was detected with superfamily member COG0266:

Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 154.51  E-value: 7.63e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   2 PEGDSVFQLARRLS-FMQGRTIT-----HTSLRVPAYATM--RFDGRTITKVWPYGKHLFMHIGS-EILHTHLKMEGTWA 72
Cdd:COG0266    1 PELPEVETVRRGLApALVGRTITrvevrSPRLRFPVPEDFaaRLTGRRITAVERRGKYLLLELDGgLTLLIHLGMSGRLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  73 VHRAGDRWRKpgHTaRVVLHLDDaphdpievvGHEL--------GFVRVFPDHEYPQR--IAHLGPDVLAESWptrgEAE 142
Cdd:COG0266   81 VVPPGEPPEK--HD-HVRLVLDD---------GTELrfadprrfGALELLTPDELEVHplLARLGPEPLDPDF----DPE 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685 143 ARKRLLGQPERAIGLALLDQKVLAGVGNEYRAEICFICGIHP---ATRIKDVDVDRVLSVTRRLMWA--------NRfSP 211
Cdd:COG0266  145 YLAARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPlrpAGSLSRAELERLAAAIREVLREaieaggttLR-DY 223

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 372114685 212 IRVTTGIRRPGETSYVFGRNHKPCRRCGTLIRKSTLVDDPTteleriiWWCPLCQ 266
Cdd:COG0266  224 VNADGEPGYFQQRLYVYGREGEPCPRCGTPIERIVLGGRST-------YYCPRCQ 271
 
Name Accession Description Interval E-value
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-266 7.63e-46

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 154.51  E-value: 7.63e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   2 PEGDSVFQLARRLS-FMQGRTIT-----HTSLRVPAYATM--RFDGRTITKVWPYGKHLFMHIGS-EILHTHLKMEGTWA 72
Cdd:COG0266    1 PELPEVETVRRGLApALVGRTITrvevrSPRLRFPVPEDFaaRLTGRRITAVERRGKYLLLELDGgLTLLIHLGMSGRLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  73 VHRAGDRWRKpgHTaRVVLHLDDaphdpievvGHEL--------GFVRVFPDHEYPQR--IAHLGPDVLAESWptrgEAE 142
Cdd:COG0266   81 VVPPGEPPEK--HD-HVRLVLDD---------GTELrfadprrfGALELLTPDELEVHplLARLGPEPLDPDF----DPE 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685 143 ARKRLLGQPERAIGLALLDQKVLAGVGNEYRAEICFICGIHP---ATRIKDVDVDRVLSVTRRLMWA--------NRfSP 211
Cdd:COG0266  145 YLAARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPlrpAGSLSRAELERLAAAIREVLREaieaggttLR-DY 223

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 372114685 212 IRVTTGIRRPGETSYVFGRNHKPCRRCGTLIRKSTLVDDPTteleriiWWCPLCQ 266
Cdd:COG0266  224 VNADGEPGYFQQRLYVYGREGEPCPRCGTPIERIVLGGRST-------YYCPRCQ 271
AcNei2_N cd08971
N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains ...
 1-117 9.68e-46

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: 149.27  E-value: 9.68e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   1 MPEGDSVFQLARRLSF-MQGRTITHTSLRVPAYATMRFDGRTITKVWPYGKHLFMHI-GSEILHTHLKMEGTWAVHRAGD 78
Cdd:cd08971    1 MPEGDTVHRAARRLRRaLAGRVLTRADLRVPRLATADLAGRTVEEVVARGKHLLIRFdGGLTLHTHLRMDGSWHVYRPGE 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 372114685  79 RWRKPGHTARVVLHLDDaphdpIEVVGHELGFVRVFPDH 117
Cdd:cd08971   81 RWRRPAHQARAVLATAD-----WTAVGFRLGVLELVPTR 114
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
16-266 4.85e-28

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 108.25  E-value: 4.85e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  16 FMQGRTITHTSLR-------VPAYATMRFDGRTITKVWPYGKHLFMHIGS-EILHTHLKMEGTWAVHRAGDRWRKpgHTa 87
Cdd:PRK01103  17 HLVGKTITRVEVRrpklrwpVPEDFAERLSGQTILAVGRRGKYLLLDLDDgGTLISHLGMSGSLRLLPEDTPPEK--HD- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  88 RVVLHLDDaphdpievvGHEL--------GFVRVFPDHEYPQR--IAHLGPDVLAESWptrgEAEARKRLLGQPERAIGL 157
Cdd:PRK01103  94 HVDFVLDD---------GTVLryndprrfGAMLLTPKGDLEAHplLAHLGPEPLSDAF----DGEYLAAKLRKKKTAIKP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685 158 ALLDQKVLAGVGNEYRAEICFICGIHPAT---RIKDVDVDRVLSVTRRLMwanrfspirvTTGIRRPGET--SY------ 226
Cdd:PRK01103 161 ALLDQTVVVGVGNIYADEALFRAGIHPERpagSLSRAEAERLVDAIKAVL----------AEAIEQGGTTlrDYvnadgk 230

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 372114685 227 ---------VFGRNHKPCRRCGTLIRK------STlvddptteleriiWWCPLCQ 266
Cdd:PRK01103 231 pgyfqqslqVYGREGEPCRRCGTPIEKikqggrST-------------FFCPRCQ 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 28-266 5.06e-23

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: 94.67  E-value: 5.06e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   28 RVPAYATMRFDGRTITKVWPYGKHLFMHIGSEILHTHLKMEGTWAVHRAGDRWRKpgHTaRVVLHLDDaphdpievvGHE 107
Cdd:TIGR00577  37 AGSEDLQKRLLGQTILSIQRRGKYLLFELDDGALVSHLRMEGKYRLEAVPDAPDK--HD-HVDFLFDD---------GTE 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  108 LGF--VRVF--------PDHEYPQRIAHLGPDVLAESWPTRGEAEArkrlLGQPERAIGLALLDQKVLAGVGNEYRAEIC 177
Cdd:TIGR00577 105 LRYhdPRRFgtwllldrGQVENIPLLAKLGPEPLSEDFTAEYLFEK----LAKSKRKIKTALLDQRLVAGIGNIYADEVL 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  178 FICGIHP---ATRIKDVDVDRVLSVTRRL------MWANRFSPIRVTTGIRRPGETSY-VFGRNHKPCRRCGTLIRKSTL 247
Cdd:TIGR00577 181 FRAGIHPerlASSLSKEECELLHRAIKEVlrkaieMGGTTIRDFSQSDGHNGYFQQELqVYGRKGEPCRRCGTTIEKEKV 260

                         250
                  ....*....|....*....
gi 372114685  248 VddpttelERIIWWCPLCQ 266
Cdd:TIGR00577 261 G-------GRGTHFCPQCQ 272
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-112 7.91e-18

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: 76.84  E-value: 7.91e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685     2 PEGDSVFQLARRLS-FMQGRTIT------HTSLRVPAYATMRFDGRTITKVWPYGKHLFMHIGSE-ILHTHLKMEGTWAV 73
Cdd:smart00898   1 PELPEVETVRRGLApALAGRTITrvevvrPPQLRFPDEFAAALSGRTITSVRRRGKYLLLRLLGGlTLVVHLGMSGSLRV 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 372114685    74 HRAGDRWRKPGHtarVVLHLDDaPHDPIEVVGHELGFVR 112
Cdd:smart00898  81 VPAGTPPPKHDH---VRLVLDD-GTELRFNDPRRFGAVR 115
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 126-204 1.11e-11

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: 59.61  E-value: 1.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  126 LGPDVLAESWptrGEAEARKRLLGQpERAIGLALLDQKVLAGVGNEYRAEICFICGIHP---ATRIKDVDVDRVLSVTRR 202
Cdd:pfam06831   1 LGPEPLSEDF---TVDYFAERLAKK-KRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPerlANSLSKEECELLHQAIKA 76


                  ..
gi 372114685  203 LM 204
Cdd:pfam06831  77 VL 78
 
Name Accession Description Interval E-value
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-266 7.63e-46

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 154.51  E-value: 7.63e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   2 PEGDSVFQLARRLS-FMQGRTIT-----HTSLRVPAYATM--RFDGRTITKVWPYGKHLFMHIGS-EILHTHLKMEGTWA 72
Cdd:COG0266    1 PELPEVETVRRGLApALVGRTITrvevrSPRLRFPVPEDFaaRLTGRRITAVERRGKYLLLELDGgLTLLIHLGMSGRLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  73 VHRAGDRWRKpgHTaRVVLHLDDaphdpievvGHEL--------GFVRVFPDHEYPQR--IAHLGPDVLAESWptrgEAE 142
Cdd:COG0266   81 VVPPGEPPEK--HD-HVRLVLDD---------GTELrfadprrfGALELLTPDELEVHplLARLGPEPLDPDF----DPE 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685 143 ARKRLLGQPERAIGLALLDQKVLAGVGNEYRAEICFICGIHP---ATRIKDVDVDRVLSVTRRLMWA--------NRfSP 211
Cdd:COG0266  145 YLAARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPlrpAGSLSRAELERLAAAIREVLREaieaggttLR-DY 223

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 372114685 212 IRVTTGIRRPGETSYVFGRNHKPCRRCGTLIRKSTLVDDPTteleriiWWCPLCQ 266
Cdd:COG0266  224 VNADGEPGYFQQRLYVYGREGEPCPRCGTPIERIVLGGRST-------YYCPRCQ 271
AcNei2_N cd08971
N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains ...
 1-117 9.68e-46

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: 149.27  E-value: 9.68e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   1 MPEGDSVFQLARRLSF-MQGRTITHTSLRVPAYATMRFDGRTITKVWPYGKHLFMHI-GSEILHTHLKMEGTWAVHRAGD 78
Cdd:cd08971    1 MPEGDTVHRAARRLRRaLAGRVLTRADLRVPRLATADLAGRTVEEVVARGKHLLIRFdGGLTLHTHLRMDGSWHVYRPGE 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 372114685  79 RWRKPGHTARVVLHLDDaphdpIEVVGHELGFVRVFPDH 117
Cdd:cd08971   81 RWRRPAHQARAVLATAD-----WTAVGFRLGVLELVPTR 114
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
16-266 4.85e-28

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 108.25  E-value: 4.85e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  16 FMQGRTITHTSLR-------VPAYATMRFDGRTITKVWPYGKHLFMHIGS-EILHTHLKMEGTWAVHRAGDRWRKpgHTa 87
Cdd:PRK01103  17 HLVGKTITRVEVRrpklrwpVPEDFAERLSGQTILAVGRRGKYLLLDLDDgGTLISHLGMSGSLRLLPEDTPPEK--HD- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  88 RVVLHLDDaphdpievvGHEL--------GFVRVFPDHEYPQR--IAHLGPDVLAESWptrgEAEARKRLLGQPERAIGL 157
Cdd:PRK01103  94 HVDFVLDD---------GTVLryndprrfGAMLLTPKGDLEAHplLAHLGPEPLSDAF----DGEYLAAKLRKKKTAIKP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685 158 ALLDQKVLAGVGNEYRAEICFICGIHPAT---RIKDVDVDRVLSVTRRLMwanrfspirvTTGIRRPGET--SY------ 226
Cdd:PRK01103 161 ALLDQTVVVGVGNIYADEALFRAGIHPERpagSLSRAEAERLVDAIKAVL----------AEAIEQGGTTlrDYvnadgk 230

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 372114685 227 ---------VFGRNHKPCRRCGTLIRK------STlvddptteleriiWWCPLCQ 266
Cdd:PRK01103 231 pgyfqqslqVYGREGEPCRRCGTPIEKikqggrST-------------FFCPRCQ 272
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-266 1.43e-23

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 96.25  E-value: 1.43e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   1 MPEGDSVFQLARRLS-FMQGRTITHTSLRVPA---YATMrFDGRTITKVWPYGKHLFMHIGSEI-LHTHLKMEGTWAVHR 75
Cdd:PRK10445   1 MPEGPEIRRAADNLEaAIKGKPLTDVWFAFPQlkpYESQ-LIGQRVTHIETRGKALLTHFSNGLtLYSHNQLYGVWRVVD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  76 AGDrwrKPGHTA--RVVLHLDD------APHDpIEVVGHElgfvrVFPDHEYPQRIahlGPDVLAESWPtrgEAEARKRL 147
Cdd:PRK10445  80 TGE---EPQTTRvlRVRLQTADktillySASD-IEMLTPE-----QLTTHPFLQRV---GPDVLDPNLT---PEQVKERL 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685 148 LGQP--ERAIGLALLDQKVLAGVGNEYRAEICFICGIHPATRIKDVDVDRVLSVTRRLMWANRFSpiRVTTGI----RRP 221
Cdd:PRK10445 145 LSPRfrNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLS--YATRGQvdenKHH 222

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 372114685 222 GE--TSYVFGRNHKPCRRCGTLIRKSTLVDDPtteleriIWWCPLCQ 266
Cdd:PRK10445 223 GAlfRFKVFHRDGEACERCGGIIEKTTLSSRP-------FYWCPGCQ 262
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 28-266 5.06e-23

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: 94.67  E-value: 5.06e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   28 RVPAYATMRFDGRTITKVWPYGKHLFMHIGSEILHTHLKMEGTWAVHRAGDRWRKpgHTaRVVLHLDDaphdpievvGHE 107
Cdd:TIGR00577  37 AGSEDLQKRLLGQTILSIQRRGKYLLFELDDGALVSHLRMEGKYRLEAVPDAPDK--HD-HVDFLFDD---------GTE 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  108 LGF--VRVF--------PDHEYPQRIAHLGPDVLAESWPTRGEAEArkrlLGQPERAIGLALLDQKVLAGVGNEYRAEIC 177
Cdd:TIGR00577 105 LRYhdPRRFgtwllldrGQVENIPLLAKLGPEPLSEDFTAEYLFEK----LAKSKRKIKTALLDQRLVAGIGNIYADEVL 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  178 FICGIHP---ATRIKDVDVDRVLSVTRRL------MWANRFSPIRVTTGIRRPGETSY-VFGRNHKPCRRCGTLIRKSTL 247
Cdd:TIGR00577 181 FRAGIHPerlASSLSKEECELLHRAIKEVlrkaieMGGTTIRDFSQSDGHNGYFQQELqVYGRKGEPCRRCGTTIEKEKV 260

                         250
                  ....*....|....*....
gi 372114685  248 VddpttelERIIWWCPLCQ 266
Cdd:TIGR00577 261 G-------GRGTHFCPQCQ 272
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-112 7.91e-18

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: 76.84  E-value: 7.91e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685     2 PEGDSVFQLARRLS-FMQGRTIT------HTSLRVPAYATMRFDGRTITKVWPYGKHLFMHIGSE-ILHTHLKMEGTWAV 73
Cdd:smart00898   1 PELPEVETVRRGLApALAGRTITrvevvrPPQLRFPDEFAAALSGRTITSVRRRGKYLLLRLLGGlTLVVHLGMSGSLRV 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 372114685    74 HRAGDRWRKPGHtarVVLHLDDaPHDPIEVVGHELGFVR 112
Cdd:smart00898  81 VPAGTPPPKHDH---VRLVLDD-GTELRFNDPRRFGAVR 115
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 85-266 4.57e-15

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 73.04  E-value: 4.57e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  85 HTaRVVLHLDDaphdpievvGHELGFV--RVF------PDHEYPQRI----AHLGPDVLAESWptrGEAEARKRLLGQpE 152
Cdd:PRK13945  99 HT-RVRLFFEK---------NQELRFVdiRSFgqmwwvPPGVSPESIitglQKLGPEPFSPEF---SVEYLKKKLKKR-T 164

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685 153 RAIGLALLDQKVLAGVGNEYRAEICFICGIHP---ATRIKDVDVDRV-LSVTRRLMWA-----NRFSPIRVTTGIR-RPG 222
Cdd:PRK13945 165 RSIKTALLDQSIVAGIGNIYADESLFKAGIHPttpAGQLKKKQLERLrEAIIEVLKTSigaggTTFSDFRDLEGVNgNYG 244

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 372114685 223 ETSYVFGRNHKPCRRCGTLIRKSTLVDdptteleRIIWWCPLCQ 266
Cdd:PRK13945 245 GQAWVYRRTGKPCRKCGTPIERIKLAG-------RSTHWCPNCQ 281
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-268 7.04e-14

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 69.44  E-value: 7.04e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   1 MPEGDSVFQLARRLS-FMQGRTITHTSLRVPAY--ATMRFDGRTITKVWPYGKHLFMHIGSEI-LHTHLKMEGtwavhra 76
Cdd:PRK14811   1 MPELPEVETTRRKLEpLLLGQTIQQVVHDDPARyrNTELAEGRRVLGLSRRGKYLLLHLPHDLeLIVHLGMTG------- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  77 GDRWRKPGHTaRVVLHLDDAP---HDPievvgHELGFVRVFPDHEYPQ--RIAHLGPDVLAESWPtrgEAEARKRLlgQP 151
Cdd:PRK14811  74 GFRLEPGPHT-RVTLELPGRTlyfTDP-----RRFGKWWVVRAGDYREipLLARMGPEPLSDDFT---EPEFVRAL--AT 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685 152 ERAIGLALLDQKVLAGVGNEYRAEICFICGIHP---ATRIKDVDVDRVLSVTRRLMWAnrfspiRVTTGIRRPGETSY-- 226
Cdd:PRK14811 143 ARPVKPWLLSQKPVAGVGNIYADESLWRARIHParpATSLKAPEARRLYRAIREVMAE------AVEAGGSTLSDGSYrq 216

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 372114685 227 -------------VFGRNHKPCRRCGTLIRKSTLVddpttelERIIWWCPLCQSE 268
Cdd:PRK14811 217 pdgepggfqfqhaVYGREGQPCPRCGTPIEKIVVG-------GRGTHFCPQCQPL 264
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 126-204 1.11e-11

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: 59.61  E-value: 1.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  126 LGPDVLAESWptrGEAEARKRLLGQpERAIGLALLDQKVLAGVGNEYRAEICFICGIHP---ATRIKDVDVDRVLSVTRR 202
Cdd:pfam06831   1 LGPEPLSEDF---TVDYFAERLAKK-KRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPerlANSLSKEECELLHQAIKA 76


                  ..
gi 372114685  203 LM 204
Cdd:pfam06831  77 VL 78
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-95 1.85e-11

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: 59.68  E-value: 1.85e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   2 PEGDSVFQLARRLS-FMQGRTITHTSLRVPAYA-------TMRFDGRTITKVWPYGKHLFMHIGSE-ILHTHLKMEGTWa 72
Cdd:cd08773    1 PELPEVELLRRKLRrALKGKRVTRVEVSDPRRLftpaaelAAALIGRRVRGAERRGKYLLLELSGGpWLVIHLGMTGRL- 79

                         90       100
                 ....*....|....*....|...
gi 372114685  73 vHRAGDRWRKPGHTaRVVLHLDD 95
Cdd:cd08773   80 -RVCPEGEPPPKHD-RLVLRLAN 100
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-266 7.38e-11

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 61.08  E-value: 7.38e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   1 MPEGDSVFQLARRLS-FMQGRTITHTSLR--------VPAYATMRFDGRTITKVWPYGKHLFMhigseILHTHLKMEGTW 71
Cdd:PRK14810   1 MPELPEVETVARGLApRAAGRRIATAEFRnlriprkgDPDLMAARLAGRKILSVKRVGKHIVA-----DLEGPGEPRGQW 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685  72 AVHRagdrwrkpGHTARVVLHLDDAPHDPIEVV------GHELGFV--RVFPDHEY----PQRIAHLGPDVLAESwPTRG 139
Cdd:PRK14810  76 IIHL--------GMTGKLLLGGPDTPSPKHTHAvltlssGKELRFVdsRQFGCIEYseafPKRFARPGPEPLEIS-FEDF 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685 140 EAEARKRLLgqperAIGLALLDQKVLAGVGNEYRAEICFICGIHPATRIKDVDVDRVL----SVTRRLMWANRFSPIRVT 215
Cdd:PRK14810 147 AALFRGRKT-----RIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRklhdAIGEVLREAIELGGSSVS 221

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 372114685 216 TGIRRPGETSY------VFGRNHKPCRRCGTLIRKSTLVddpttelERIIWWCPLCQ 266
Cdd:PRK14810 222 DYVDAEGRSGFfqlshrVYQRTGEPCLNCKTPIRRVVVA-------GRSSHYCPHCQ 271
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-111 3.11e-09

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: 53.66  E-value: 3.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685    1 MPEGDSVFQLARRLS-FMQGRTITHTSLR--------VPAYATMRFDGRTITKVWPYGKHLFMHIGSE-ILHTHLKMEGT 70
Cdd:pfam01149   1 MPELPEVETVRRGLRrHLVGKTIASVEVLddknlrgpSPEEFAAALTGRKVTSVGRRGKYLLLELDSGgHLVVHLGMTGW 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 372114685   71 WAVHRAGDRwrkPGHTaRVVLHLDDaphdpievvGHELGFV 111
Cdd:pfam01149  81 LLIKTEEWP---PKHD-HVRLELDD---------GRELRFT 108
AcNei1_N cd08970
N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases; This family contains ...
 1-81 8.54e-09

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


Pssm-ID: 176804 [Multi-domain]  Cd Length: 110  Bit Score: 52.26  E-value: 8.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   1 MPEGDSVFQLARRLSFMQGRTITHTSL---RVPAYATMrFDGRTITKVWPYGKHLFMHIGSE-ILHTHLKMEGTWAV--- 73
Cdd:cd08970    1 MPEGHVIHRLARDLNAAFAGQPVRVSSpqgRFADGAAL-LDGRVLADAEAHGKHLFLGFEGDrILHVHLGLYGKFRFggd 79

                         90
                 ....*....|..
gi 372114685  74 ----HRAGDRWR 81
Cdd:cd08970   80 ppppPRGQVRLR 91
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 39-95 2.93e-06

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: 45.18  E-value: 2.93e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 372114685  39 GRTITKVWPYGKHLFMHIGS-EILHTHLKMEGTWAVHRAGDRWRKpgHTaRVVLHLDD 95
Cdd:cd08966   47 GRRITGVERRGKYLLFELDDgLVLVIHLGMTGRLLVVPPDEPPEK--HD-HVIFELDD 101
BaFpgNei_N_2 cd08974
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-96 3.05e-06

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


Pssm-ID: 176808  Cd Length: 98  Bit Score: 44.62  E-value: 3.05e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372114685   1 MPEGDSVFQLARRLSFMQGRTIThtslRVPAYATM---RFDGRTITKVWPYGKHLFMHIGSEILHTHLKMEGTWAVHrag 77
Cdd:cd08974    1 MPEGPSIVILREAAAAFKGQTVI----RASGNAKIdkdRLAGQKVLAIRSWGKHFLLEFEDFTVRIHLLLFGSYRIN--- 73

                         90
                 ....*....|....*....
gi 372114685  78 drwRKPGHTARVVLHLDDA 96
Cdd:cd08974   74 ---ERKDAPPRLSLGFDNG 89
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH