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Conserved domains on  [gi|1800908425|ref|WP_160584927|]
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DNA-formamidopyrimidine glycosylase [Mesomycoplasma hyopneumoniae]

Protein Classification

Fpg/Nei family DNA glycosylase( domain architecture ID 11479425)

Fpg/Nei family DNA glycosylase similar to Escherichia coli DNA-formamidopyrimidine glycosylase (Fpg), a DNA repair enzyme that excises oxidized purines from damaged DNA

CATH:  3.20.190.10
EC:  3.2.2.23
Gene Ontology:  GO:0140078|GO:0003684|GO:0008534|GO:0008270|GO:0006284
PubMed:  21486746|14607836
SCOP:  4000303

Graphical summary

 Zoom to residue level

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Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-272 4.52e-126

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


:

Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 359.40  E-value: 4.52e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   1 MPELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKEInFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGK 80
Cdd:PRK01103    1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPV-PEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425  81 YFTYKSPQ-WGKYDYISFVFSDNSVLNYNDSRKFGTFMIRDVELLFKTKPLKDLAPEPFFI--KVDDFYQKIRKSTRSIK 157
Cdd:PRK01103   80 LRLLPEDTpPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSDafDGEYLAAKLRKKKTAIK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 158 AILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQESIKLGGSSISSYTSLNAKEGKFQNFLK 237
Cdd:PRK01103  160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1800908425 238 VHTKQNFPCSNCQTKILKTVIAGRGTYFCPFCQKL 272
Cdd:PRK01103  240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQKR 274
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-272 4.52e-126

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 359.40  E-value: 4.52e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   1 MPELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKEInFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGK 80
Cdd:PRK01103    1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPV-PEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425  81 YFTYKSPQ-WGKYDYISFVFSDNSVLNYNDSRKFGTFMIRDVELLFKTKPLKDLAPEPFFI--KVDDFYQKIRKSTRSIK 157
Cdd:PRK01103   80 LRLLPEDTpPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSDafDGEYLAAKLRKKKTAIK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 158 AILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQESIKLGGSSISSYTSLNAKEGKFQNFLK 237
Cdd:PRK01103  160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1800908425 238 VHTKQNFPCSNCQTKILKTVIAGRGTYFCPFCQKL 272
Cdd:PRK01103  240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQKR 274
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-270 3.38e-97

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: 286.12  E-value: 3.38e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   2 PELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKE-INFFDFQKSIVNATIIDIQNRAKHILIFLDNrKVILSHLRMNGK 80
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVLRpAGSEDLQKRLLGQTILSIQRRGKYLLFELDD-GALVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425  81 YFTYKSP-QWGKYDYISFVFSDNSVLNYNDSRKFGTFMIRDVELLFKTKPLKDLAPEPF---FiKVDDFYQKIRKSTRSI 156
Cdd:TIGR00577  80 YRLEAVPdAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQVENIPLLAKLGPEPLsedF-TAEYLFEKLAKSKRKI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 157 KAILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQESIKLGGSSISSYTSLNAKEGKFQNFL 236
Cdd:TIGR00577 159 KTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQSDGHNGYFQQEL 238

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1800908425 237 KVHTKQNFPCSNCQTKILKTVIAGRGTYFCPFCQ 270
Cdd:TIGR00577 239 QVYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-271 4.18e-92

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 273.15  E-value: 4.18e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   2 PELPEVVTVVNALKTEVIGKKIKNVLARDSNfIKEINFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGKY 81
Cdd:COG0266     1 PELPEVETVRRGLAPALVGRTITRVEVRSPR-LRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425  82 FTYKSPQ-WGKYDYISFVFSDNSVLNYNDSRKFGTFMIRDVELLFKTKPLKDLAPEPF---FiKVDDFYQKIRKSTRSIK 157
Cdd:COG0266    80 RVVPPGEpPEKHDHVRLVLDDGTELRFADPRRFGALELLTPDELEVHPLLARLGPEPLdpdF-DPEYLAARLRRRRRPIK 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 158 AILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQESIKLGGSSISSYTSLNAKEGKFQNFLK 237
Cdd:COG0266   159 ALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADGEPGYFQQRLY 238

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1800908425 238 VHTKQNFPCSNCQTKILKTVIAGRGTYFCPFCQK 271
Cdd:COG0266   239 VYGREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-120 9.03e-44

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: 144.56  E-value: 9.03e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   2 PELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKEINFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGKY 81
Cdd:cd08966     1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1800908425  82 FTYKSPQ-WGKYDYISFVFSDNSVLNYNDSRKFGTFMIRD 120
Cdd:cd08966    81 LVVPPDEpPEKHDHVIFELDDGRELRFNDPRRFGTLLLVP 120
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-116 9.51e-37

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: 126.47  E-value: 9.51e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   1 MPELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKEINFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGK 80
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1800908425  81 YFtYKSPQWG-KYDYISFVFSDNSVLNYNDSRKFGTF 116
Cdd:pfam01149  81 LL-IKTEEWPpKHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-116 6.27e-34

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: 119.21  E-value: 6.27e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425    2 PELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKeiNFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGKY 81
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQLR--FPDEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSL 78

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1800908425   82 FTYKSPQW-GKYDYISFVFSDNSVLNYNDSRKFGTF 116
Cdd:smart00898  79 RVVPAGTPpPKHDHVRLVLDDGTELRFNDPRRFGAV 114
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-272 4.52e-126

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 359.40  E-value: 4.52e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   1 MPELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKEInFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGK 80
Cdd:PRK01103    1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPV-PEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425  81 YFTYKSPQ-WGKYDYISFVFSDNSVLNYNDSRKFGTFMIRDVELLFKTKPLKDLAPEPFFI--KVDDFYQKIRKSTRSIK 157
Cdd:PRK01103   80 LRLLPEDTpPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSDafDGEYLAAKLRKKKTAIK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 158 AILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQESIKLGGSSISSYTSLNAKEGKFQNFLK 237
Cdd:PRK01103  160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1800908425 238 VHTKQNFPCSNCQTKILKTVIAGRGTYFCPFCQKL 272
Cdd:PRK01103  240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQKR 274
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-270 3.38e-97

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: 286.12  E-value: 3.38e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   2 PELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKE-INFFDFQKSIVNATIIDIQNRAKHILIFLDNrKVILSHLRMNGK 80
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVLRpAGSEDLQKRLLGQTILSIQRRGKYLLFELDD-GALVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425  81 YFTYKSP-QWGKYDYISFVFSDNSVLNYNDSRKFGTFMIRDVELLFKTKPLKDLAPEPF---FiKVDDFYQKIRKSTRSI 156
Cdd:TIGR00577  80 YRLEAVPdAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQVENIPLLAKLGPEPLsedF-TAEYLFEKLAKSKRKI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 157 KAILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQESIKLGGSSISSYTSLNAKEGKFQNFL 236
Cdd:TIGR00577 159 KTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQSDGHNGYFQQEL 238

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1800908425 237 KVHTKQNFPCSNCQTKILKTVIAGRGTYFCPFCQ 270
Cdd:TIGR00577 239 QVYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-271 4.18e-92

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 273.15  E-value: 4.18e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   2 PELPEVVTVVNALKTEVIGKKIKNVLARDSNfIKEINFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGKY 81
Cdd:COG0266     1 PELPEVETVRRGLAPALVGRTITRVEVRSPR-LRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425  82 FTYKSPQ-WGKYDYISFVFSDNSVLNYNDSRKFGTFMIRDVELLFKTKPLKDLAPEPF---FiKVDDFYQKIRKSTRSIK 157
Cdd:COG0266    80 RVVPPGEpPEKHDHVRLVLDDGTELRFADPRRFGALELLTPDELEVHPLLARLGPEPLdpdF-DPEYLAARLRRRRRPIK 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 158 AILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQESIKLGGSSISSYTSLNAKEGKFQNFLK 237
Cdd:COG0266   159 ALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADGEPGYFQQRLY 238

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1800908425 238 VHTKQNFPCSNCQTKILKTVIAGRGTYFCPFCQK 271
Cdd:COG0266   239 VYGREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-271 3.27e-52

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 171.63  E-value: 3.27e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   1 MPELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKEINFFDFQKSIVNATIIDIQNRAKHILIFLDN----RKVILSHLR 76
Cdd:PRK14810    1 MPELPEVETVARGLAPRAAGRRIATAEFRNLRIPRKGDPDLMAARLAGRKILSVKRVGKHIVADLEGpgepRGQWIIHLG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425  77 MNGK--YFTYKSPQwGKYDYISFVFSDNSVLNYNDSRKFGTFMIRDVellfKTKPLKDLAPEPFFIKVDDFYQKIRKSTR 154
Cdd:PRK14810   81 MTGKllLGGPDTPS-PKHTHAVLTLSSGKELRFVDSRQFGCIEYSEA----FPKRFARPGPEPLEISFEDFAALFRGRKT 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 155 SIKAILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQESIKLGGSSISSYTSLNAKEGKFQN 234
Cdd:PRK14810  156 RIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAIELGGSSVSDYVDAEGRSGFFQL 235

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1800908425 235 FLKVHTKQNFPCSNCQTKILKTVIAGRGTYFCPFCQK 271
Cdd:PRK14810  236 SHRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHCQK 272
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 1-271 3.57e-52

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 171.65  E-value: 3.57e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   1 MPELPEVVTVVNALKTEVIGKKIKNV---LARD--SNFIKEinffDFQKSIVNATIIDIQNRAKHILIFLD-----NRKV 70
Cdd:PRK13945    1 MPELPEVETVRRGLEQLLLNFIIKGVevlLERTiaSPGGVE----EFIKGLKGSLIGQWQRRGKYLLASLKkegseNAGW 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425  71 ILSHLRMNGkYFTY----KSPQwgKYDYISFVFSDNSVLNYNDSRKFGT--FMIRDVELLFKTKPLKDLAPEPF---FiK 141
Cdd:PRK13945   77 LGVHLRMTG-QFLWveqsTPPC--KHTRVRLFFEKNQELRFVDIRSFGQmwWVPPGVSPESIITGLQKLGPEPFspeF-S 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 142 VDDFYQKIRKSTRSIKAILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQESIKLGGSSISS 221
Cdd:PRK13945  153 VEYLKKKLKKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLKTSIGAGGTTFSD 232

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1800908425 222 YTSLNAKEGKFQNFLKVHTKQNFPCSNCQTKILKTVIAGRGTYFCPFCQK 271
Cdd:PRK13945  233 FRDLEGVNGNYGGQAWVYRRTGKPCRKCGTPIERIKLAGRSTHWCPNCQK 282
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-120 9.03e-44

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: 144.56  E-value: 9.03e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   2 PELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKEINFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGKY 81
Cdd:cd08966     1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1800908425  82 FTYKSPQ-WGKYDYISFVFSDNSVLNYNDSRKFGTFMIRD 120
Cdd:cd08966    81 LVVPPDEpPEKHDHVIFELDDGRELRFNDPRRFGTLLLVP 120
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-272 1.12e-41

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 144.17  E-value: 1.12e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   1 MPELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKEINFFDFQKsivnatIIDIQNRAKHILIFLDNRKVILSHLRMNGK 80
Cdd:PRK14811    1 MPELPEVETTRRKLEPLLLGQTIQQVVHDDPARYRNTELAEGRR------VLGLSRRGKYLLLHLPHDLELIVHLGMTGG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425  81 yFTYKSpqwGKYDYISFVFsDNSVLNYNDSRKFGT-FMIRDVEllFKTKP-LKDLAPEPFfikVDDF----YQKIRKSTR 154
Cdd:PRK14811   75 -FRLEP---GPHTRVTLEL-PGRTLYFTDPRRFGKwWVVRAGD--YREIPlLARMGPEPL---SDDFtepeFVRALATAR 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 155 SIKAILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQESIKLGGSSIS--SYTSLNAKEGKF 232
Cdd:PRK14811  145 PVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEAVEAGGSTLSdgSYRQPDGEPGGF 224

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1800908425 233 QNFLKVHTKQNFPCSNCQTKILKTVIAGRGTYFCPFCQKL 272
Cdd:PRK14811  225 QFQHAVYGREGQPCPRCGTPIEKIVVGGRGTHFCPQCQPL 264
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-116 9.51e-37

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: 126.47  E-value: 9.51e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   1 MPELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKEINFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGK 80
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1800908425  81 YFtYKSPQWG-KYDYISFVFSDNSVLNYNDSRKFGTF 116
Cdd:pfam01149  81 LL-IKTEEWPpKHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-116 6.27e-34

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: 119.21  E-value: 6.27e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425    2 PELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKeiNFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGKY 81
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQLR--FPDEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSL 78

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1800908425   82 FTYKSPQW-GKYDYISFVFSDNSVLNYNDSRKFGTF 116
Cdd:smart00898  79 RVVPAGTPpPKHDHVRLVLDDGTELRFNDPRRFGAV 114
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 133-219 8.73e-27

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: 99.67  E-value: 8.73e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 133 LAPEPFF--IKVDDFYQKIRKSTRSIKAILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQE 210
Cdd:pfam06831   1 LGPEPLSedFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVLQE 80


                  ....*....
gi 1800908425 211 SIKLGGSSI 219
Cdd:pfam06831  81 AIEMGGGGI 89
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-271 1.02e-20

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 88.55  E-value: 1.02e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   1 MPELPEVVTVVNALKTEVIGKKIknvlaRDSNF----IKEinffdFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLR 76
Cdd:PRK10445    1 MPEGPEIRRAADNLEAAIKGKPL-----TDVWFafpqLKP-----YESQLIGQRVTHIETRGKALLTHFSNGLTLYSHNQ 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425  77 MNGKYF---TYKSPQWGKYDYISFVFSDNSVLNYNDSrkfgtfmirDVELLfktkPLKDLAPEPFFIKV----------- 142
Cdd:PRK10445   71 LYGVWRvvdTGEEPQTTRVLRVRLQTADKTILLYSAS---------DIEML----TPEQLTTHPFLQRVgpdvldpnltp 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 143 DDFYQKI---RKSTRSIKAILLDQKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKILQESIKLGGSsi 219
Cdd:PRK10445  138 EQVKERLlspRFRNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRGQ-- 215

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1800908425 220 ssyTSLNAKEGKFQNFlKVHTKQNFPCSNCQTKILKTVIAGRGTYFCPFCQK 271
Cdd:PRK10445  216 ---VDENKHHGALFRF-KVFHRDGEACERCGGIIEKTTLSSRPFYWCPGCQK 263
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-116 1.87e-18

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: 78.94  E-value: 1.87e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   2 PELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKEiNFFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGKY 81
Cdd:cd08773     1 PELPEVELLRRKLRRALKGKRVTRVEVSDPRRLFT-PAAELAAALIGRRVRGAERRGKYLLLELSGGPWLVIHLGMTGRL 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1800908425  82 FTYKSPQW-GKYDYISFVFSDNSVLNYNDSRKFGTF 116
Cdd:cd08773    80 RVCPEGEPpPKHDRLVLRLANGSQLRFTDPRKFGRV 115
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-114 6.83e-13

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: 64.25  E-value: 6.83e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   1 MPELPEVVTVVNALKTEVIGKKIKNVLAR-DSNFIKEINFFDFQKSIVNATIIDIQNRAKHILIFLDNR-KVILSHLRMN 78
Cdd:cd08972     1 MPELPEVERARRLLEEHCLGKKITKVDAQdDDKVFGGVTPGAFQKALLGRTITSAHRKGKYFWLTLDGDaPVPVMHFGMT 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1800908425  79 G----------KYFTYKSP-----QW-GKYDYISFVFSDNSVLNYNDSRKFG 114
Cdd:cd08972    81 GaisikgvktiYYKMLRPPkeedqTWpPRFYKFVLTLEDGTELAFTDPRRLG 132
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-114 1.01e-09

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: 55.05  E-value: 1.01e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   2 PELPEVVTVVNALKTEVIGKKIKNVLARDSNFIKEINfFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRMNGKY 81
Cdd:cd08976     1 PELPEVEVQKQYLERTSLHRKIVEVEVGDDKILGEPK-ATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTGKL 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1800908425  82 FTYKSPQ-WGKYDYISFVFSDNSVLNYNDSRKFG 114
Cdd:cd08976    80 DYYPDDEdPPKHARLLLHFEDGFRLAFECPRKFG 113
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-102 2.88e-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: 51.10  E-value: 2.88e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   1 MPELPEVVTVVNALKTEVIGKKIKNV-LARdsnfiKEIN--FFDFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLrM 77
Cdd:cd08973     1 MPELPEVEVYAENLERRLTGKTITRVeLAS-----KSLLvtPDPPLEALEGRTVTGVRRHGKRLDFEFDNGLHLVLHL-M 74

                          90       100
                  ....*....|....*....|....*...
gi 1800908425  78 NGKYFTYKSPQ---WGKYDYISFVFSDN 102
Cdd:cd08973    75 LAGWLYWTEAGallPGKKGPIALRFEDY 102
zf-FPG_IleRS pfam06827
Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of ...
 245-270 2.23e-06

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: 43.35  E-value: 2.23e-06
                          10        20
                  ....*....|....*....|....*.
gi 1800908425 245 PCSNCQTKILKTVIAGRGTYFCPFCQ 270
Cdd:pfam06827   3 KCPRCWTYIEKVGVGGRSTYFCPRCQ 28
EcNei-like_N cd08965
N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases; This ...
 2-88 5.37e-04

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: 38.88  E-value: 5.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   2 PELPEVVTVVNALKTEVIGKKIKNVlardsNF----IKEinffdFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHLRM 77
Cdd:cd08965     1 PEGPEIRRAADRIEAAIKGRPLEEV-----WFafphLKE-----YEAQLKGQNVTRVETRGKALLTHFDNGLSIYSHNQL 70

                          90
                  ....*....|....
gi 1800908425  78 NGKYF---TYKSPQ 88
Cdd:cd08965    71 YGVWRvrkRGNYPK 84
RqcH COG1293
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) ...
 129-210 8.25e-04

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: 40.59  E-value: 8.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425 129 PLKDLAPEPFFIKVDDFYQKIRKSTRSIKAILLdqKIISGLGNIYADEVCFAIKIFPGKAAKLISRKEAELIIDFSKKIL 208
Cdd:COG1293   164 PPSQDKLNPLELSEEEFAELLSESDGDLVRTLA--TNFLGLSPLLAEEICYRAGLDKDTPTDELSEEDLEALYEALQELL 241


                  ..
gi 1800908425 209 QE 210
Cdd:COG1293   242 EE 243
BaFpgNei_N_3 cd08975
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 3-107 1.02e-03

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: 38.07  E-value: 1.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800908425   3 ELPEVVTVVNALKTEVIGKKIKNVLARDSnFIKEINFF----DFQKSIVNATIIDIQNRAKHILIFLDNRKVILSHlRMN 78
Cdd:cd08975     2 ELPESATLSKQLNETLKGKRITDVFPATS-PHKFTWYNgdpnEYDELLVGKRITSAEGFGGFVEIIFEDKRLLFND-GVN 79

                          90       100
                  ....*....|....*....|....*....
gi 1800908425  79 GKYFTYKSPQWGKYDYIsFVFSDNSVLNY 107
Cdd:cd08975    80 VRYYYGGEKIPKKYQLL-IEFDDDSFLVF 107
 
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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