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Conserved domains on  [gi|1359985904|gb|PRX48185|]
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formamidopyrimidine-DNA glycosylase [Salegentibacter salegens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-117 2.20e-57

Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_4 domain, most enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


:

Pssm-ID: 176810  Cd Length: 117  Bit Score: 178.70  E-value: 2.20e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   2 PELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKLE 81
Cdd:cd08976     1 PELPEVEVQKQYLERTSLHRKIVEVEVGDDKILGEPKATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTGKLD 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1359985904  82 YYQH-EETPKYAQLTLTFEDHSRVSFTCPRKFGKLYL 117
Cdd:cd08976    81 YYPDdEDPPKHARLLLHFEDGFRLAFECPRKFGRVRL 117
H2TH super family cl38215
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 130-207 1.59e-19

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.


The actual alignment was detected with superfamily member pfam06831:

Pssm-ID: 399664 [Multi-domain]  Cd Length: 89  Bit Score: 80.41  E-value: 1.59e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904 130 LGVDAL--ALKEEEFFKILKTRTGTIKALLMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLEV 207
Cdd:pfam06831   1 LGPEPLseDFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVLQE 80
 
Name Accession Description Interval E-value
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-117 2.20e-57

Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_4 domain, most enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176810  Cd Length: 117  Bit Score: 178.70  E-value: 2.20e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   2 PELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKLE 81
Cdd:cd08976     1 PELPEVEVQKQYLERTSLHRKIVEVEVGDDKILGEPKATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTGKLD 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1359985904  82 YYQH-EETPKYAQLTLTFEDHSRVSFTCPRKFGKLYL 117
Cdd:cd08976    81 YYPDdEDPPKHARLLLHFEDGFRLAFECPRKFGRVRL 117
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-206 2.12e-54

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 176.47  E-value: 2.12e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   2 PELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKLE 81
Cdd:COG0266     1 PELPEVETVRRGLAPALVGRTITRVEVRSPRLRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904  82 YYQHEETP-KYAQLTLTFEDHSRVSFTCPRKFGKLYL--TKSLAEFQKENNLGVDAL--ALKEEEFFKILKTRTGTIKAL 156
Cdd:COG0266    81 VVPPGEPPeKHDHVRLVLDDGTELRFADPRRFGALELltPDELEVHPLLARLGPEPLdpDFDPEYLAARLRRRRRPIKAL 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1359985904 157 LMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLE 206
Cdd:COG0266   161 LLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLR 210
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-223 3.74e-50

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 165.64  E-value: 3.74e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   1 MPELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKL 80
Cdd:PRK01103    1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904  81 EYYQHEETP-KYAQLTLTFEDHSRVSFTCPRKFGKLYLTKSLAEFQKE--NNLGVDAL--ALKEEEFFKILKTRTGTIKA 155
Cdd:PRK01103   81 RLLPEDTPPeKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPllAHLGPEPLsdAFDGEYLAAKLRKKKTAIKP 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904 156 LLMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLEvvkEArIE--GSKLpKSYL 223
Cdd:PRK01103  161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLA---EA-IEqgGTTL-RDYV 225
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-206 2.34e-42

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: 145.52  E-value: 2.34e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   2 PELPEVAYQKKYADATILHKKIVKIETGD--KKIYQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKqGVLVVHFGMTGK 79
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLrnPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDD-GALVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904  80 LEYY-QHEETPKYAQLTLTFEDHSRVSFTCPRKFGKLYLTKSLAEFQKE--NNLGVDAL--ALKEEEFFKILKTRTGTIK 154
Cdd:TIGR00577  80 YRLEaVPDAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQVENIPllAKLGPEPLseDFTAEYLFEKLAKSKRKIK 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1359985904 155 ALLMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLE 206
Cdd:TIGR00577 160 TALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLR 211
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-115 2.88e-32

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: 114.53  E-value: 2.88e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   1 MPELPEVAYQKKYADATILHKKIVKIETGDKKI--YQSAKSiFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTG 78
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNlrGPSPEE-FAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTG 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1359985904  79 KLEYYQHEETPKYAQLTLTFEDHSRVSFTCPRKFGKL 115
Cdd:pfam01149  80 WLLIKTEEWPPKHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-116 6.72e-25

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: 95.33  E-value: 6.72e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904    2 PELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAkSIFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKLE 81
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQLRFP-DEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSLR 79

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1359985904   82 YYQHEETP-KYAQLTLTFEDHSRVSFTCPRKFGKLY 116
Cdd:smart00898  80 VVPAGTPPpKHDHVRLVLDDGTELRFNDPRRFGAVR 115
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 130-207 1.59e-19

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: 80.41  E-value: 1.59e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904 130 LGVDAL--ALKEEEFFKILKTRTGTIKALLMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLEV 207
Cdd:pfam06831   1 LGPEPLseDFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVLQE 80
RqcH COG1293
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) ...
 132-215 7.70e-08

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


Pssm-ID: 440904 [Multi-domain]  Cd Length: 578  Bit Score: 52.53  E-value: 7.70e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904 132 VDALALKEEEFFKILKTRTGTIKALLMNQklIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLEVVKEA 211
Cdd:COG1293   170 LNPLELSEEEFAELLSESDGDLVRTLATN--FLGLSPLLAEEICYRAGLDKDTPTDELSEEDLEALYEALQELLEELENG 247


                  ....
gi 1359985904 212 RIEG 215
Cdd:COG1293   248 EFKP 251
PRK10445 PRK10445
endonuclease VIII; Provisional
 155-224 6.30e-06

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 46.18  E-value: 6.30e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904 155 ALLMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEkteifkeieevLEVVKEARIEGSKLpkSYLT 224
Cdd:PRK10445  156 GLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQ-----------LDALAHALLDIPRL--SYAT 212
 
Name Accession Description Interval E-value
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-117 2.20e-57

Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_4 domain, most enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176810  Cd Length: 117  Bit Score: 178.70  E-value: 2.20e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   2 PELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKLE 81
Cdd:cd08976     1 PELPEVEVQKQYLERTSLHRKIVEVEVGDDKILGEPKATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTGKLD 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1359985904  82 YYQH-EETPKYAQLTLTFEDHSRVSFTCPRKFGKLYL 117
Cdd:cd08976    81 YYPDdEDPPKHARLLLHFEDGFRLAFECPRKFGRVRL 117
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-206 2.12e-54

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 176.47  E-value: 2.12e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   2 PELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKLE 81
Cdd:COG0266     1 PELPEVETVRRGLAPALVGRTITRVEVRSPRLRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904  82 YYQHEETP-KYAQLTLTFEDHSRVSFTCPRKFGKLYL--TKSLAEFQKENNLGVDAL--ALKEEEFFKILKTRTGTIKAL 156
Cdd:COG0266    81 VVPPGEPPeKHDHVRLVLDDGTELRFADPRRFGALELltPDELEVHPLLARLGPEPLdpDFDPEYLAARLRRRRRPIKAL 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1359985904 157 LMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLE 206
Cdd:COG0266   161 LLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLR 210
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-223 3.74e-50

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 165.64  E-value: 3.74e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   1 MPELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKL 80
Cdd:PRK01103    1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904  81 EYYQHEETP-KYAQLTLTFEDHSRVSFTCPRKFGKLYLTKSLAEFQKE--NNLGVDAL--ALKEEEFFKILKTRTGTIKA 155
Cdd:PRK01103   81 RLLPEDTPPeKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPllAHLGPEPLsdAFDGEYLAAKLRKKKTAIKP 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904 156 LLMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLEvvkEArIE--GSKLpKSYL 223
Cdd:PRK01103  161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLA---EA-IEqgGTTL-RDYV 225
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-206 2.34e-42

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: 145.52  E-value: 2.34e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   2 PELPEVAYQKKYADATILHKKIVKIETGD--KKIYQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKqGVLVVHFGMTGK 79
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLrnPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDD-GALVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904  80 LEYY-QHEETPKYAQLTLTFEDHSRVSFTCPRKFGKLYLTKSLAEFQKE--NNLGVDAL--ALKEEEFFKILKTRTGTIK 154
Cdd:TIGR00577  80 YRLEaVPDAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQVENIPllAKLGPEPLseDFTAEYLFEKLAKSKRKIK 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1359985904 155 ALLMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLE 206
Cdd:TIGR00577 160 TALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLR 211
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-218 1.36e-34

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 125.29  E-value: 1.36e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   1 MPELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAksifeETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKl 80
Cdd:PRK14811    1 MPELPEVETTRRKLEPLLLGQTIQQVVHDDPARYRNT-----ELAEGRRVLGLSRRGKYLLLHLPHDLELIVHLGMTGG- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904  81 eyYQHEETPkYAQLTLTFeDHSRVSFTCPRKFGKLYLTKS--LAEFQKENNLGVDAL--ALKEEEFFKILKTRtGTIKAL 156
Cdd:PRK14811   75 --FRLEPGP-HTRVTLEL-PGRTLYFTDPRRFGKWWVVRAgdYREIPLLARMGPEPLsdDFTEPEFVRALATA-RPVKPW 149

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1359985904 157 LMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLEVVKEAriEGSKL 218
Cdd:PRK14811  150 LLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEAVEA--GGSTL 209
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-115 2.88e-32

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: 114.53  E-value: 2.88e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   1 MPELPEVAYQKKYADATILHKKIVKIETGDKKI--YQSAKSiFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTG 78
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNlrGPSPEE-FAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTG 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1359985904  79 KLEYYQHEETPKYAQLTLTFEDHSRVSFTCPRKFGKL 115
Cdd:pfam01149  80 WLLIKTEEWPPKHDHVRLELDDGRELRFTDPRRFGRV 116
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 1-206 1.04e-31

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 117.72  E-value: 1.04e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   1 MPELPEVAYQKKYADATILHKKIVKIET-GDKKI-YQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKQ-----GVLVVH 73
Cdd:PRK13945    1 MPELPEVETVRRGLEQLLLNFIIKGVEVlLERTIaSPGGVEEFIKGLKGSLIGQWQRRGKYLLASLKKEgsenaGWLGVH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904  74 FGMTGKLEYYQHEETP-KYAQLTLTFEDHSRVSFTCPRKFGKLY-------LTKSLAEFQKennLGVDAL--ALKEEEFF 143
Cdd:PRK13945   81 LRMTGQFLWVEQSTPPcKHTRVRLFFEKNQELRFVDIRSFGQMWwvppgvsPESIITGLQK---LGPEPFspEFSVEYLK 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1359985904 144 KILKTRTGTIKALLMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLE 206
Cdd:PRK13945  158 KKLKKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLK 220
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-211 2.63e-31

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 116.54  E-value: 2.63e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   1 MPELPEVAYQKKYADATILHKKIVKIETGDKKI-YQSAKSIFEETLKDNQFTGSERLGKYLFLKLEK----QGVLVVHFG 75
Cdd:PRK14810    1 MPELPEVETVARGLAPRAAGRRIATAEFRNLRIpRKGDPDLMAARLAGRKILSVKRVGKHIVADLEGpgepRGQWIIHLG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904  76 MTGKLEYYQHEE-TPKYAQLTLTFEDHSRVSFTCPRKFGKLYLTKSLAefQKENNLGVDALALKEEEFFKILKTRTGTIK 154
Cdd:PRK14810   81 MTGKLLLGGPDTpSPKHTHAVLTLSSGKELRFVDSRQFGCIEYSEAFP--KRFARPGPEPLEISFEDFAALFRGRKTRIK 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1359985904 155 ALLMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLEVVKEA 211
Cdd:PRK14810  159 SALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAIEL 215
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-117 2.84e-27

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: 101.67  E-value: 2.84e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   2 PELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKLE 81
Cdd:cd08773     1 PELPEVELLRRKLRRALKGKRVTRVEVSDPRRLFTPAAELAAALIGRRVRGAERRGKYLLLELSGGPWLVIHLGMTGRLR 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1359985904  82 YY-QHEETPKYAQLTLTFEDHSRVSFTCPRKFGKLYL 117
Cdd:cd08773    81 VCpEGEPPPKHDRLVLRLANGSQLRFTDPRKFGRVEL 117
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-116 6.72e-25

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: 95.33  E-value: 6.72e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904    2 PELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAkSIFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKLE 81
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQLRFP-DEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSLR 79

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1359985904   82 YYQHEETP-KYAQLTLTFEDHSRVSFTCPRKFGKLY 116
Cdd:smart00898  80 VVPAGTPPpKHDHVRLVLDDGTELRFNDPRRFGAVR 115
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-117 3.82e-24

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: 93.33  E-value: 3.82e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   2 PELPEVAYQKKYADATILHKKIVKIETGDKK-IYQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKL 80
Cdd:cd08966     1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKlRRPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1359985904  81 EYY-QHEETPKYAQLTLTFEDHSRVSFTCPRKFGKLYL 117
Cdd:cd08966    81 LVVpPDEPPEKHDHVIFELDDGRELRFNDPRRFGTLLL 118
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-117 1.18e-20

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: 84.67  E-value: 1.18e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   1 MPELPEVAYQKKYADATILHKKIVKIET-GDKKIYQSAK-SIFEETLKDNQFTGSERLGKYLFLKLEKQG-VLVVHFGMT 77
Cdd:cd08972     1 MPELPEVERARRLLEEHCLGKKITKVDAqDDDKVFGGVTpGAFQKALLGRTITSAHRKGKYFWLTLDGDApVPVMHFGMT 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1359985904  78 GKLE-------YY---------QHEETPKYAQLTLTFEDHSRVSFTCPRKFGKLYL 117
Cdd:cd08972    81 GAISikgvktiYYkmlrppkeeDQTWPPRFYKFVLTLEDGTELAFTDPRRLGRVRL 136
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 130-207 1.59e-19

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: 80.41  E-value: 1.59e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904 130 LGVDAL--ALKEEEFFKILKTRTGTIKALLMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLEV 207
Cdd:pfam06831   1 LGPEPLseDFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVLQE 80
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-118 3.30e-12

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: 61.88  E-value: 3.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   1 MPELPEVAYQKKYADATILHKKIVKIETGDKKIYQSAKSiFEETLKDNQFTGSERLGKYLFLKLEKQGVLVVHFGMTGKL 80
Cdd:cd08973     1 MPELPEVEVYAENLERRLTGKTITRVELASKSLLVTPDP-PLEALEGRTVTGVRRHGKRLDFEFDNGLHLVLHLMLAGWL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1359985904  81 EYYQHEE--TPKYAQLTLTFEDHsrvsftcprkFGKLYLT 118
Cdd:cd08973    80 YWTEAGAllPGKKGPIALRFEDY----------GGGLDLT 109
RqcH COG1293
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) ...
 132-215 7.70e-08

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


Pssm-ID: 440904 [Multi-domain]  Cd Length: 578  Bit Score: 52.53  E-value: 7.70e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904 132 VDALALKEEEFFKILKTRTGTIKALLMNQklIAGIGNLYADEILFQVKIHPTTKVDQLSEKEKTEIFKEIEEVLEVVKEA 211
Cdd:COG1293   170 LNPLELSEEEFAELLSESDGDLVRTLATN--FLGLSPLLAEEICYRAGLDKDTPTDELSEEDLEALYEALQELLEELENG 247


                  ....
gi 1359985904 212 RIEG 215
Cdd:COG1293   248 EFKP 251
PRK10445 PRK10445
endonuclease VIII; Provisional
 155-224 6.30e-06

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 46.18  E-value: 6.30e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904 155 ALLMNQKLIAGIGNLYADEILFQVKIHPTTKVDQLSEKEkteifkeieevLEVVKEARIEGSKLpkSYLT 224
Cdd:PRK10445  156 GLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQ-----------LDALAHALLDIPRL--SYAT 212
BaFpgNei_N_3 cd08975
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 3-107 6.73e-05

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. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In this family the N-terminal proline is replaced by an isoleucine or valine. 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_3 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176809  Cd Length: 117  Bit Score: 41.16  E-value: 6.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359985904   3 ELPEVAYQKKYADATILHKKI--VKIETGDKKI--YQSAKSIFEETLKDNQFTGSERLGKYLFLKLEKQgVLVVHFGMTG 78
Cdd:cd08975     2 ELPESATLSKQLNETLKGKRItdVFPATSPHKFtwYNGDPNEYDELLVGKRITSAEGFGGFVEIIFEDK-RLLFNDGVNV 80

                          90       100
                  ....*....|....*....|....*....
gi 1359985904  79 KLeYYQHEETPKYAQLTLTFEDHSRVSFT 107
Cdd:cd08975    81 RY-YYGGEKIPKKYQLLIEFDDDSFLVFT 108
MeNeil1_N cd08967
N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the ...
 70-114 1.22e-03

N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the N-terminal domain of metazoan NEIL1. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL1 recognizes the oxidized pyrimidines 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino- 5-formamidopyrimidine (FapyA), thymine glycol (Tg) and 5-hydroxyuracil (5-OHU). However, even though it has weak activity on 8-oxo-7,8-dihydroguanine (8-oxoG), it does show strong preference for the products of its further oxidation: spiroiminodihydantoin and guanidinohydantoin. In addition to this MeNeil1_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zincless finger motif. This characteristic "zincless finger" motif, is a structural equivalent of the zinc finger common to other members of the Fpg/Nei family. Neil1 is one of three homologs found in eukaryotes and its lineage extends back as far as early metazoans.


Pssm-ID: 176801  Cd Length: 131  Bit Score: 38.21  E-value: 1.22e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1359985904  70 LVVHFGMTGKLEYYQHEETPKYAQLTL-TFEDHSRV-SFTCPRKFGK 114
Cdd:cd08967    80 IVFRFGMSGSFQFTPVDEIPKHAHLRFyTKEEPKRVlSFVDIRRFGT 126
MeNeil3_N cd08969
N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the ...
 38-87 5.93e-03

N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the N-terminal domain of the Metazoan Neil3. 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. In contrast, mouse NEIL3 (MmuNEIL3) forms a Schiff base intermediate via its N-terminal valine. The latter is a functional DNA glycosylase in vitro and in vivo. MmuNEIL3 prefers lesions in single-stranded DNA and in bubble structures. In duplex DNA, it recognizes the oxidized purines spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino-5-formamidopyrimidine (FapyA), but not 8-oxo-7,8-dihydroguanine (8-oxoG). Since the expression of the MmuNeil3 glycosylase domain (MmuNeil3delta324) reduces both the high spontaneous mutation frequency and the FapyG level in a Escherichia coli mutant lacking Fpg, Nei and MutY glycosylase activites, NEIL3 may play a role in repairing FapyG in vivo. In addition to this MeNeil3_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc finger motif, plus a characteristic C-terminal extension that contains additional zinc fingers. Neil3 is one of three homologs found in eukaryotes.


Pssm-ID: 176803  Cd Length: 140  Bit Score: 36.24  E-value: 5.93e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1359985904  38 KSIFEETLKDNQFTGSERLGKYLFLKLEkQGVLVVHFGMTGKLEYYQHEE 87
Cdd:cd08969    50 RSHVLDSLTGQVYTGVETLGKELFMYFG-DKALRIHFGMNGSMRINPLES 98
 
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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