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Conserved domains on  [gi|697052345|ref|WP_033144951|]
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MULTISPECIES: endonuclease VIII [Enterobacter]

Protein Classification

endonuclease VIII( domain architecture ID 11484730)

endonuclease VIII is a DNA-(apurinic or apyrimidinic site) lyase involved in base excision repair of DNA damaged by oxidation or by mutagenic agents; acts as DNA glycosylase that recognizes and removes damaged bases with a preference for oxidized pyrimidines

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-263 0e+00

endonuclease VIII; Provisional


:

Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 550.02  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPEIRRAADSLEAAIKGKPLTDVWFAFPQLKPFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWRVVEA 80
Cdd:PRK10445   1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYESQLIGQRVTHIETRGKALLTHFSNGLTLYSHNQLYGVWRVVDT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345  81 DEQPQTTRVLRVRLQTADKAILLYSASDIEMLTPEQLLTHPFLQRVGPDVLDMRLTASDVKARLLSPKFRNRQFSGLFLD 160
Cdd:PRK10445  81 GEEPQTTRVLRVRLQTADKTILLYSASDIEMLTPEQLTTHPFLQRVGPDVLDPNLTPEQVKERLLSPRFRNRQFSGLLLD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345 161 QAFLAGLGNYLRVEILWEVGLAPQHKASQLSDEQLEALSHALLDIPRLSYNTRGVADENTHHGALFRFKVFHQAGKKCER 240
Cdd:PRK10445 161 QAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRGQVDENKHHGALFRFKVFHRDGEACER 240

                        250       260
                 ....*....|....*....|...
gi 697052345 241 CGGIIDRIMLSSRPFYWCPHCQK 263
Cdd:PRK10445 241 CGGIIEKTTLSSRPFYWCPGCQK 263
 
Name Accession Description Interval E-value
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-263 0e+00

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 550.02  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPEIRRAADSLEAAIKGKPLTDVWFAFPQLKPFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWRVVEA 80
Cdd:PRK10445   1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYESQLIGQRVTHIETRGKALLTHFSNGLTLYSHNQLYGVWRVVDT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345  81 DEQPQTTRVLRVRLQTADKAILLYSASDIEMLTPEQLLTHPFLQRVGPDVLDMRLTASDVKARLLSPKFRNRQFSGLFLD 160
Cdd:PRK10445  81 GEEPQTTRVLRVRLQTADKTILLYSASDIEMLTPEQLTTHPFLQRVGPDVLDPNLTPEQVKERLLSPRFRNRQFSGLLLD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345 161 QAFLAGLGNYLRVEILWEVGLAPQHKASQLSDEQLEALSHALLDIPRLSYNTRGVADENTHHGALFRFKVFHQAGKKCER 240
Cdd:PRK10445 161 QAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRGQVDENKHHGALFRFKVFHRDGEACER 240

                        250       260
                 ....*....|....*....|...
gi 697052345 241 CGGIIDRIMLSSRPFYWCPHCQK 263
Cdd:PRK10445 241 CGGIIEKTTLSSRPFYWCPGCQK 263
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-263 4.27e-87

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 260.06  E-value: 4.27e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   2 PEGPEIRRAADSLEAAIKGKPLTDVWFAFPQLK-----PFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWR 76
Cdd:COG0266    1 PELPEVETVRRGLAPALVGRTITRVEVRSPRLRfpvpeDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345  77 VVEADEQPQttRVLRVRLQTADKAIL----LYSASDIEMLTPEQLLTHPFLQRVGPDVLDMRLTASDVKARLlspKFRNR 152
Cdd:COG0266   81 VVPPGEPPE--KHDHVRLVLDDGTELrfadPRRFGALELLTPDELEVHPLLARLGPEPLDPDFDPEYLAARL---RRRRR 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345 153 QFSGLFLDQAFLAGLGNYLRVEILWEVGLAPQHKASQLSDEQLEALSHALLDIPRLSYNTRGVADENTHHGA------LF 226
Cdd:COG0266  156 PIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADgepgyfQQ 235

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 697052345 227 RFKVFHQAGKKCERCGGIIDRIMLSSRPFYWCPHCQK 263
Cdd:COG0266  236 RLYVYGREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
EcNei-like_N cd08965
N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases; This ...
 2-116 9.36e-73

N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases; This family contains the N-terminal domain of proteobacteria Nei and related DNA glycosylases. It includes Escherichia coli Nei, and 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 Nei has been well studied, it is a DNA glycosylase/AP lyase that excises damaged pyrimidines, including 5-hydroxycytosine, 5-hydroxyuracil, and uracil glycol. In addition to this EcNei-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a canonical zinc-finger motif.


Pssm-ID: 176799  Cd Length: 115  Bit Score: 218.00  E-value: 9.36e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   2 PEGPEIRRAADSLEAAIKGKPLTDVWFAFPQLKPFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWRVVEAD 81
Cdd:cd08965    1 PEGPEIRRAADRIEAAIKGRPLEEVWFAFPHLKEYEAQLKGQNVTRVETRGKALLTHFDNGLSIYSHNQLYGVWRVRKRG 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 697052345  82 EQPQTTRVLRVRLQTADKAILLYSASDIEMLTPEQ 116
Cdd:cd08965   81 NYPKTNRQLRVALHTAKKSALLYSASDIDVLPTEE 115
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-262 8.38e-30

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: 112.78  E-value: 8.38e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345    2 PEGPEIRRAADSLEAAIKGKPLTDVWFAFPQLK-------PFESQLVGQTVTHIETRGKALLTHFSHNLtLYSHNQLYGV 74
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVlrpagseDLQKRLLGQTILSIQRRGKYLLFELDDGA-LVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   75 WRVVEADEQPQTTRVLRVRLQT------ADK----AILLYSASDIEMLTPeqllthpfLQRVGPDVLDMRLTASDVKARL 144
Cdd:TIGR00577  80 YRLEAVPDAPDKHDHVDFLFDDgtelryHDPrrfgTWLLLDRGQVENIPL--------LAKLGPEPLSEDFTAEYLFEKL 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345  145 LSpkfRNRQFSGLFLDQAFLAGLGNYLRVEILWEVGLAPQHKASQLSDEQLEALSHALLDIPRLSYNTRG--------VA 216
Cdd:TIGR00577 152 AK---SKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGttirdfsqSD 228

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 697052345  217 DENTHHGAlfRFKVFHQAGKKCERCGGIIDRIMLSSRPFYWCPHCQ 262
Cdd:TIGR00577 229 GHNGYFQQ--ELQVYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-104 1.34e-23

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: 91.86  E-value: 1.34e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345     2 PEGPEIRRAADSLEAAIKGKPLTDVW-FAFPQLK---PFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWRV 77
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEvVRPPQLRfpdEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSLRV 80

                           90       100
                   ....*....|....*....|....*..
gi 697052345    78 VEADEQPQttRVLRVRLQTADKAILLY 104
Cdd:smart00898  81 VPAGTPPP--KHDHVRLVLDDGTELRF 105
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-104 4.11e-16

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: 72.15  E-value: 4.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345    1 MPEGPEIRRAADSLEAAIKGKPLTDVWF------AFPQLKPFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGV 74
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVlddknlRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 697052345   75 WRVVEADEQPQTTrvlRVRLQTADKAILLY 104
Cdd:pfam01149  81 LLIKTEEWPPKHD---HVRLELDDGRELRF 107
 
Name Accession Description Interval E-value
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-263 0e+00

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 550.02  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPEIRRAADSLEAAIKGKPLTDVWFAFPQLKPFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWRVVEA 80
Cdd:PRK10445   1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYESQLIGQRVTHIETRGKALLTHFSNGLTLYSHNQLYGVWRVVDT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345  81 DEQPQTTRVLRVRLQTADKAILLYSASDIEMLTPEQLLTHPFLQRVGPDVLDMRLTASDVKARLLSPKFRNRQFSGLFLD 160
Cdd:PRK10445  81 GEEPQTTRVLRVRLQTADKTILLYSASDIEMLTPEQLTTHPFLQRVGPDVLDPNLTPEQVKERLLSPRFRNRQFSGLLLD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345 161 QAFLAGLGNYLRVEILWEVGLAPQHKASQLSDEQLEALSHALLDIPRLSYNTRGVADENTHHGALFRFKVFHQAGKKCER 240
Cdd:PRK10445 161 QAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRGQVDENKHHGALFRFKVFHRDGEACER 240

                        250       260
                 ....*....|....*....|...
gi 697052345 241 CGGIIDRIMLSSRPFYWCPHCQK 263
Cdd:PRK10445 241 CGGIIEKTTLSSRPFYWCPGCQK 263
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-263 4.27e-87

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 260.06  E-value: 4.27e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   2 PEGPEIRRAADSLEAAIKGKPLTDVWFAFPQLK-----PFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWR 76
Cdd:COG0266    1 PELPEVETVRRGLAPALVGRTITRVEVRSPRLRfpvpeDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345  77 VVEADEQPQttRVLRVRLQTADKAIL----LYSASDIEMLTPEQLLTHPFLQRVGPDVLDMRLTASDVKARLlspKFRNR 152
Cdd:COG0266   81 VVPPGEPPE--KHDHVRLVLDDGTELrfadPRRFGALELLTPDELEVHPLLARLGPEPLDPDFDPEYLAARL---RRRRR 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345 153 QFSGLFLDQAFLAGLGNYLRVEILWEVGLAPQHKASQLSDEQLEALSHALLDIPRLSYNTRGVADENTHHGA------LF 226
Cdd:COG0266  156 PIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADgepgyfQQ 235

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 697052345 227 RFKVFHQAGKKCERCGGIIDRIMLSSRPFYWCPHCQK 263
Cdd:COG0266  236 RLYVYGREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
EcNei-like_N cd08965
N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases; This ...
 2-116 9.36e-73

N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases; This family contains the N-terminal domain of proteobacteria Nei and related DNA glycosylases. It includes Escherichia coli Nei, and 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 Nei has been well studied, it is a DNA glycosylase/AP lyase that excises damaged pyrimidines, including 5-hydroxycytosine, 5-hydroxyuracil, and uracil glycol. In addition to this EcNei-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a canonical zinc-finger motif.


Pssm-ID: 176799  Cd Length: 115  Bit Score: 218.00  E-value: 9.36e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   2 PEGPEIRRAADSLEAAIKGKPLTDVWFAFPQLKPFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWRVVEAD 81
Cdd:cd08965    1 PEGPEIRRAADRIEAAIKGRPLEEVWFAFPHLKEYEAQLKGQNVTRVETRGKALLTHFDNGLSIYSHNQLYGVWRVRKRG 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 697052345  82 EQPQTTRVLRVRLQTADKAILLYSASDIEMLTPEQ 116
Cdd:cd08965   81 NYPKTNRQLRVALHTAKKSALLYSASDIDVLPTEE 115
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-263 2.01e-33

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 122.11  E-value: 2.01e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPE---IRRaadSLEAAIKGKPLTDV---W----FAFPQLkpFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQ 70
Cdd:PRK01103   1 MPELPEvetVRR---GLEPHLVGKTITRVevrRpklrWPVPED--FAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLG 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345  71 LYGVWRVVEADEQPQttRVLRVRLQTADKAILLYSasD------IEMLTPEQLLTHPFLQRVGPDVLDMRLTASDVKARL 144
Cdd:PRK01103  76 MSGSLRLLPEDTPPE--KHDHVDFVLDDGTVLRYN--DprrfgaMLLTPKGDLEAHPLLAHLGPEPLSDAFDGEYLAAKL 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345 145 lspkfRNRQFS--GLFLDQAFLAGLGN-YlrV-EILWEVGLAPQHKASQLSDEQLEALSHALLDIprLsynTRGVAdent 220
Cdd:PRK01103 152 -----RKKKTAikPALLDQTVVVGVGNiY--AdEALFRAGIHPERPAGSLSRAEAERLVDAIKAV--L---AEAIE---- 215

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 697052345 221 HHGALFR---------------FKVFHQAGKKCERCGGIIDRIMLSSRPFYWCPHCQK 263
Cdd:PRK01103 216 QGGTTLRdyvnadgkpgyfqqsLQVYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-262 8.38e-30

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: 112.78  E-value: 8.38e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345    2 PEGPEIRRAADSLEAAIKGKPLTDVWFAFPQLK-------PFESQLVGQTVTHIETRGKALLTHFSHNLtLYSHNQLYGV 74
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVlrpagseDLQKRLLGQTILSIQRRGKYLLFELDDGA-LVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   75 WRVVEADEQPQTTRVLRVRLQT------ADK----AILLYSASDIEMLTPeqllthpfLQRVGPDVLDMRLTASDVKARL 144
Cdd:TIGR00577  80 YRLEAVPDAPDKHDHVDFLFDDgtelryHDPrrfgTWLLLDRGQVENIPL--------LAKLGPEPLSEDFTAEYLFEKL 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345  145 LSpkfRNRQFSGLFLDQAFLAGLGNYLRVEILWEVGLAPQHKASQLSDEQLEALSHALLDIPRLSYNTRG--------VA 216
Cdd:TIGR00577 152 AK---SKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGttirdfsqSD 228

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 697052345  217 DENTHHGAlfRFKVFHQAGKKCERCGGIIDRIMLSSRPFYWCPHCQ 262
Cdd:TIGR00577 229 GHNGYFQQ--ELQVYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-105 9.42e-24

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: 92.43  E-value: 9.42e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   2 PEGPEIRRAADSLEAAIKGKPLTDVWFAFPQL-----KPFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWR 76
Cdd:cd08773    1 PELPEVELLRRKLRRALKGKRVTRVEVSDPRRlftpaAELAAALIGRRVRGAERRGKYLLLELSGGPWLVIHLGMTGRLR 80

                         90       100
                 ....*....|....*....|....*....
gi 697052345  77 VVEADEQPqtTRVLRVRLQTADKAILLYS 105
Cdd:cd08773   81 VCPEGEPP--PKHDRLVLRLANGSQLRFT 107
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-104 1.34e-23

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: 91.86  E-value: 1.34e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345     2 PEGPEIRRAADSLEAAIKGKPLTDVW-FAFPQLK---PFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWRV 77
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEvVRPPQLRfpdEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSLRV 80

                           90       100
                   ....*....|....*....|....*..
gi 697052345    78 VEADEQPQttRVLRVRLQTADKAILLY 104
Cdd:smart00898  81 VPAGTPPP--KHDHVRLVLDDGTELRF 105
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 1-263 4.19e-23

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 94.99  E-value: 4.19e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPEI---RRAadsLEAAIKGKPLTDV------WFAFPQ-LKPFESQLVGQTVTHIETRGKALLTHFSHnltlySHNQ 70
Cdd:PRK13945   1 MPELPEVetvRRG---LEQLLLNFIIKGVevllerTIASPGgVEEFIKGLKGSLIGQWQRRGKYLLASLKK-----EGSE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345  71 LYGVWRV----------VEADEQPQT-TRVlrvRLQTADKAILLYSasDI----EM------LTPEQLLTHpfLQRVGPD 129
Cdd:PRK13945  73 NAGWLGVhlrmtgqflwVEQSTPPCKhTRV---RLFFEKNQELRFV--DIrsfgQMwwvppgVSPESIITG--LQKLGPE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345 130 VLDMRLTASDVKARLlspKFRNRQFSGLFLDQAFLAGLGNYLRVEILWEVGLAPQHKASQLSDEQLEALSHALLDIPRLS 209
Cdd:PRK13945 146 PFSPEFSVEYLKKKL---KKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLKTS 222

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 697052345 210 Y--------NTRGVADENTHHG--ALfrfkVFHQAGKKCERCGGIIDRIMLSSRPFYWCPHCQK 263
Cdd:PRK13945 223 IgaggttfsDFRDLEGVNGNYGgqAW----VYRRTGKPCRKCGTPIERIKLAGRSTHWCPNCQK 282
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-263 5.39e-19

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 83.69  E-value: 5.39e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPEIRRAADSLEAAIKGKPLTDVWFAFPQLKPFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWRVvea 80
Cdd:PRK14811   1 MPELPEVETTRRKLEPLLLGQTIQQVVHDDPARYRNTELAEGRRVLGLSRRGKYLLLHLPHDLELIVHLGMTGGFRL--- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345  81 DEQPQTtrvlRVRLQTaDKAILLYSAS----DIEMLTPEQLLTHPFLQRVGPDVLDMRLTASDVKARLLSPkfrnRQFSG 156
Cdd:PRK14811  78 EPGPHT----RVTLEL-PGRTLYFTDPrrfgKWWVVRAGDYREIPLLARMGPEPLSDDFTEPEFVRALATA----RPVKP 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345 157 LFLDQAFLAGLGNYLRVEILWEVGLAPQHKASQLSDEQLEALSHALLDIPRLSYNTRG--VADEN--THHGA--LFRFK- 229
Cdd:PRK14811 149 WLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEAVEAGGstLSDGSyrQPDGEpgGFQFQh 228

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 697052345 230 -VFHQAGKKCERCGGIIDRIMLSSRPFYWCPHCQK 263
Cdd:PRK14811 229 aVYGREGQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263
AcNei2_N cd08971
N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains ...
 1-115 4.14e-17

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: 74.93  E-value: 4.14e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPEIRRAADSLEAAIKGKPLTDVWFAFPQLKPfeSQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWRVVEA 80
Cdd:cd08971    1 MPEGDTVHRAARRLRRALAGRVLTRADLRVPRLAT--ADLAGRTVEEVVARGKHLLIRFDGGLTLHTHLRMDGSWHVYRP 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 697052345  81 DEQPQT-TRVLRVRLQTADKAILLYSASDIEMLTPE 115
Cdd:cd08971   79 GERWRRpAHQARAVLATADWTAVGFRLGVLELVPTR 114
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-104 4.11e-16

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: 72.15  E-value: 4.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345    1 MPEGPEIRRAADSLEAAIKGKPLTDVWF------AFPQLKPFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGV 74
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVlddknlRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 697052345   75 WRVVEADEQPQTTrvlRVRLQTADKAILLY 104
Cdd:pfam01149  81 LLIKTEEWPPKHD---HVRLELDDGRELRF 107
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-263 2.23e-13

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 68.01  E-value: 2.23e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPEIRRAADSLEAAIKGKPLTDVWFAFPQlKPFESQ-------LVGQTVTHIETRGKALLTHFS----HNLTLYSHN 69
Cdd:PRK14810   1 MPELPEVETVARGLAPRAAGRRIATAEFRNLR-IPRKGDpdlmaarLAGRKILSVKRVGKHIVADLEgpgePRGQWIIHL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345  70 QLYGVWRVVEADEQ--PQTTRVLRvrlqtadkailLYSASDIEMLTPEQL----LTHPFLQRV-GPDVLDMRLTASDVKA 142
Cdd:PRK14810  80 GMTGKLLLGGPDTPspKHTHAVLT-----------LSSGKELRFVDSRQFgcieYSEAFPKRFaRPGPEPLEISFEDFAA 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345 143 RLlspKFRNRQFSGLFLDQAFLAGLGNYLRVEILWEVGLAPQHKASQLSDEQLEALSHALLDIPRLSYNTRGVA-----D 217
Cdd:PRK14810 149 LF---RGRKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAIELGGSSvsdyvD 225

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 697052345 218 ENTHHGAL-FRFKVFHQAGKKCERCGGIIDRIMLSSRPFYWCPHCQK 263
Cdd:PRK14810 226 AEGRSGFFqLSHRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHCQK 272
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 127-205 3.37e-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: 58.07  E-value: 3.37e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 697052345  127 GPDVLDMRLTASDVKARLlspKFRNRQFSGLFLDQAFLAGLGNYLRVEILWEVGLAPQHKASQLSDEQLEALSHALLDI 205
Cdd:pfam06831   2 GPEPLSEDFTVDYFAERL---AKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAV 77
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-104 2.71e-10

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: 56.35  E-value: 2.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   2 PEGPE---IRRaadSLEAAIKGKPLTDVWFAFPQL------KPFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLY 72
Cdd:cd08966    1 PELPEvetVRR---GLAPHLVGRRIEDVEVRRPKLrrppdpEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMT 77

                         90       100       110
                 ....*....|....*....|....*....|..
gi 697052345  73 GVWRVVEADEQPQttRVLRVRLQTADKAILLY 104
Cdd:cd08966   78 GRLLVVPPDEPPE--KHDHVIFELDDGRELRF 107
AcNei1_N cd08970
N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases; This family contains ...
 1-112 1.40e-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: 54.18  E-value: 1.40e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPEIRRAADSLEAAIKGKPLTdvwFAFPQLKpF---ESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYGVWRV 77
Cdd:cd08970    1 MPEGHVIHRLARDLNAAFAGQPVR---VSSPQGR-FadgAALLDGRVLADAEAHGKHLFLGFEGDRILHVHLGLYGKFRF 76

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 697052345  78 VEADEQPQTTRVlRVRLQTADKAILLYSASDIEML 112
Cdd:cd08970   77 GGDPPPPPRGQV-RLRLVGDTHAADLRGPTVCELL 110
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-121 8.70e-08

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: 49.55  E-value: 8.70e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPEIRRAADSLEAAIKGKPLTDVWFAFPQL----KPFESQLVGQTVTHIETRGKALLTHFSHNLTLYSHNQLYG--V 74
Cdd:cd08973    1 MPELPEVEVYAENLERRLTGKTITRVELASKSLlvtpDPPLEALEGRTVTGVRRHGKRLDFEFDNGLHLVLHLMLAGwlY 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 697052345  75 WRVVEADEQPQTTrVLRVRLQTADKAILLYsasdiEMLTPEQLLTHP 121
Cdd:cd08973   81 WTEAGALLPGKKG-PIALRFEDYGGGLDLT-----EAGTKKRAALHL 121
zf-FPG_IleRS pfam06827
Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of ...
 235-262 8.40e-07

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: 44.50  E-value: 8.40e-07
                          10        20
                  ....*....|....*....|....*...
gi 697052345  235 GKKCERCGGIIDRIMLSSRPFYWCPHCQ 262
Cdd:pfam06827   1 GEKCPRCWTYIEKVGVGGRSTYFCPRCQ 28
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-53 2.11e-06

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: 46.15  E-value: 2.11e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPEIRRAADSLEAAIKGKPLTDVWFA-----FPQLKP--FESQLVGQTVTHIETRGK 53
Cdd:cd08972    1 MPELPEVERARRLLEEHCLGKKITKVDAQdddkvFGGVTPgaFQKALLGRTITSAHRKGK 60
BaFpgNei_N_2 cd08974
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-107 2.19e-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: 45.01  E-value: 2.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697052345   1 MPEGPEI---RRAAdsleAAIKGKPLTDVWFAFPQLKpfeSQLVGQTVTHIETRGKALLTHFShNLTLYSHNQLYGVWRV 77
Cdd:cd08974    1 MPEGPSIvilREAA----AAFKGQTVIRASGNAKIDK---DRLAGQKVLAIRSWGKHFLLEFE-DFTVRIHLLLFGSYRI 72

                         90       100       110
                 ....*....|....*....|....*....|
gi 697052345  78 veaDEQPQTTrvLRVRLQTADKAILLYSAS 107
Cdd:cd08974   73 ---NERKDAP--PRLSLGFDNGELNFYTCS 97
 
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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