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Conserved domains on  [gi|30695252|ref|NP_849798|]
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MUTM homolog-1 [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
fpg super family cl36691
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-256 3.36e-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]


The actual alignment was detected with superfamily member TIGR00577:

Pssm-ID: 273150 [Multi-domain]  Cd Length: 272  Bit Score: 286.12  E-value: 3.36e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252     2 PELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGISPSDFQTSILGKTIISARRKGKNLWLELDSppfpsfqfgmaGA 81
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDD-----------GA 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252    82 IYIKGVAVTKYKRSAVKDSeewPSKYSKFFVELDDGLELSFTDKRRFAKVRLLANPT--SVSPISELGPDALLEPMTVDE 159
Cdd:TIGR00577  70 LVSHLRMEGKYRLEAVPDA---PDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQveNIPLLAKLGPEPLSEDFTAEY 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   160 FAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIQHAVQVNADSKEFPVE 239
Cdd:TIGR00577 147 LFEKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQ 226

                         250
                  ....*....|....*..
gi 30695252   240 WLFHFRWGKKAGKVNGK 256
Cdd:TIGR00577 227 SDGHNGYFQQELQVYGR 243
 
Name Accession Description Interval E-value
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-256 3.36e-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: 3.36e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252     2 PELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGISPSDFQTSILGKTIISARRKGKNLWLELDSppfpsfqfgmaGA 81
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDD-----------GA 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252    82 IYIKGVAVTKYKRSAVKDSeewPSKYSKFFVELDDGLELSFTDKRRFAKVRLLANPT--SVSPISELGPDALLEPMTVDE 159
Cdd:TIGR00577  70 LVSHLRMEGKYRLEAVPDA---PDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQveNIPLLAKLGPEPLSEDFTAEY 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   160 FAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIQHAVQVNADSKEFPVE 239
Cdd:TIGR00577 147 LFEKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQ 226

                         250
                  ....*....|....*..
gi 30695252   240 WLFHFRWGKKAGKVNGK 256
Cdd:TIGR00577 227 SDGHNGYFQQELQVYGR 243
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-134 6.13e-71

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: 214.48  E-value: 6.13e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   1 MPELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGISPSDFQTSILGKTIISARRKGKNLWLELDS-PPFPSFQFGMA 79
Cdd:cd08972   1 MPELPEVERARRLLEEHCLGKKITKVDAQDDDKVFGGVTPGAFQKALLGRTITSAHRKGKYFWLTLDGdAPVPVMHFGMT 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 30695252  80 GAIYIKGVAVTKYK--RSAVKDSEEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLL 134
Cdd:cd08972  81 GAISIKGVKTIYYKmlRPPKEEDQTWPPRFYKFVLTLEDGTELAFTDPRRLGRVRLV 137
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-228 1.21e-61

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 195.73  E-value: 1.21e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   2 PELPEVEAARRAIEENCLGKKIKRVIIADDNkvIHGISPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQFGMAGA 81
Cdd:COG0266   1 PELPEVETVRRGLAPALVGRTITRVEVRSPR--LRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGR 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252  82 IYikgvavtkykrsaVKDSEEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLL--ANPTSVSPISELGPDALLEPMTVDE 159
Cdd:COG0266  79 LR-------------VVPPGEPPEKHDHVRLVLDDGTELRFADPRRFGALELLtpDELEVHPLLARLGPEPLDPDFDPEY 145

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30695252 160 FAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIQHAVQ 228
Cdd:COG0266 146 LAARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIE 214
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-227 2.53e-59

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 189.52  E-value: 2.53e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252    1 MPELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGisPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQFGMAG 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPV--PEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   81 aiyikgvavtKYKrsaVKDSEEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLA--NPTSVSPISELGPDALLEPMTVD 158
Cdd:PRK01103  79 ----------SLR---LLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPkgDLEAHPLLAHLGPEPLSDAFDGE 145

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30695252  159 EFAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIQHAV 227
Cdd:PRK01103 146 YLAAKLRKKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAI 214
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-131 2.72e-41

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: 138.02  E-value: 2.72e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252     1 MPELPEVEAARRAIEENCLGKKIKRVIIADDnKVIHGISPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQFGMAG 80
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDD-KNLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTG 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 30695252    81 AIYIKgvavtkykrsavkdSEEWPSKYSKFFVELDDGLELSFTDKRRFAKV 131
Cdd:pfam01149  80 WLLIK--------------TEEWPPKHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-132 7.91e-31

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: 111.12  E-value: 7.91e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252      2 PELPEVEAARRAIEENCLGKKIKRVIIADDNKvihGISPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQFGMAGA 81
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQ---LRFPDEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGS 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 30695252     82 IYIkgvavtkykrsavKDSEEWPSKYSKFFVELDDGLELSFTDKRRFAKVR 132
Cdd:smart00898  78 LRV-------------VPAGTPPPKHDHVRLVLDDGTELRFNDPRRFGAVR 115
 
Name Accession Description Interval E-value
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-256 3.36e-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: 3.36e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252     2 PELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGISPSDFQTSILGKTIISARRKGKNLWLELDSppfpsfqfgmaGA 81
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDD-----------GA 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252    82 IYIKGVAVTKYKRSAVKDSeewPSKYSKFFVELDDGLELSFTDKRRFAKVRLLANPT--SVSPISELGPDALLEPMTVDE 159
Cdd:TIGR00577  70 LVSHLRMEGKYRLEAVPDA---PDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQveNIPLLAKLGPEPLSEDFTAEY 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   160 FAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIQHAVQVNADSKEFPVE 239
Cdd:TIGR00577 147 LFEKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQ 226

                         250
                  ....*....|....*..
gi 30695252   240 WLFHFRWGKKAGKVNGK 256
Cdd:TIGR00577 227 SDGHNGYFQQELQVYGR 243
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-134 6.13e-71

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: 214.48  E-value: 6.13e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   1 MPELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGISPSDFQTSILGKTIISARRKGKNLWLELDS-PPFPSFQFGMA 79
Cdd:cd08972   1 MPELPEVERARRLLEEHCLGKKITKVDAQDDDKVFGGVTPGAFQKALLGRTITSAHRKGKYFWLTLDGdAPVPVMHFGMT 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 30695252  80 GAIYIKGVAVTKYK--RSAVKDSEEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLL 134
Cdd:cd08972  81 GAISIKGVKTIYYKmlRPPKEEDQTWPPRFYKFVLTLEDGTELAFTDPRRLGRVRLV 137
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-228 1.21e-61

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 195.73  E-value: 1.21e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   2 PELPEVEAARRAIEENCLGKKIKRVIIADDNkvIHGISPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQFGMAGA 81
Cdd:COG0266   1 PELPEVETVRRGLAPALVGRTITRVEVRSPR--LRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGR 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252  82 IYikgvavtkykrsaVKDSEEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLL--ANPTSVSPISELGPDALLEPMTVDE 159
Cdd:COG0266  79 LR-------------VVPPGEPPEKHDHVRLVLDDGTELRFADPRRFGALELLtpDELEVHPLLARLGPEPLDPDFDPEY 145

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30695252 160 FAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIQHAVQ 228
Cdd:COG0266 146 LAARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIE 214
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-227 2.53e-59

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 189.52  E-value: 2.53e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252    1 MPELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGisPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQFGMAG 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPV--PEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   81 aiyikgvavtKYKrsaVKDSEEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLA--NPTSVSPISELGPDALLEPMTVD 158
Cdd:PRK01103  79 ----------SLR---LLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPkgDLEAHPLLAHLGPEPLSDAFDGE 145

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30695252  159 EFAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIQHAV 227
Cdd:PRK01103 146 YLAAKLRKKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAI 214
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-131 2.72e-41

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: 138.02  E-value: 2.72e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252     1 MPELPEVEAARRAIEENCLGKKIKRVIIADDnKVIHGISPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQFGMAG 80
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDD-KNLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTG 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 30695252    81 AIYIKgvavtkykrsavkdSEEWPSKYSKFFVELDDGLELSFTDKRRFAKV 131
Cdd:pfam01149  80 WLLIK--------------TEEWPPKHDHVRLELDDGRELRFTDPRRFGRV 116
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 146-233 4.98e-39

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: 131.26  E-value: 4.98e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   146 LGPDALLEPMTVDEFAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIQH 225
Cdd:pfam06831   1 LGPEPLSEDFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVLQE 80


                  ....*...
gi 30695252   226 AVQVNADS 233
Cdd:pfam06831  81 AIEMGGGG 88
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 1-224 1.27e-33

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 123.50  E-value: 1.27e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252    1 MPELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGISPSDFQTSILGKTIISARRKGKNLWLELDSPPFPS------- 73
Cdd:PRK13945   1 MPELPEVETVRRGLEQLLLNFIIKGVEVLLERTIASPGGVEEFIKGLKGSLIGQWQRRGKYLLASLKKEGSENagwlgvh 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   74 ------FQFgmagaiyikgvavtkykrsaVKDSEEwPSKYSKFFVELDDGLELSFTDKRRFAKVRLLANPTSVSPI---- 143
Cdd:PRK13945  81 lrmtgqFLW--------------------VEQSTP-PCKHTRVRLFFEKNQELRFVDIRSFGQMWWVPPGVSPESIitgl 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252  144 SELGPDALLEPMTVDEFAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVI 223
Cdd:PRK13945 140 QKLGPEPFSPEFSVEYLKKKLKKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVL 219


                 .
gi 30695252  224 Q 224
Cdd:PRK13945 220 K 220
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-233 1.37e-33

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 123.09  E-value: 1.37e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252    1 MPELPEVEAARRAIEENCLGKKIKRVIIADdNKVIHGISPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQF---- 76
Cdd:PRK14810   1 MPELPEVETVARGLAPRAAGRRIATAEFRN-LRIPRKGDPDLMAARLAGRKILSVKRVGKHIVADLEGPGEPRGQWiihl 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   77 GMAGAIYIKGVAVtkykrsavkdseewPS-KYSKFFVELDDGLELSFTDKRRFAKVRLlaNPTSVSPISELGPdallEPM 155
Cdd:PRK14810  80 GMTGKLLLGGPDT--------------PSpKHTHAVLTLSSGKELRFVDSRQFGCIEY--SEAFPKRFARPGP----EPL 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252  156 TV--DEFAESLAKKKITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIQHAVQVNADS 233
Cdd:PRK14810 140 EIsfEDFAALFRGRKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAIELGGSS 219
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-228 1.24e-32

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 120.67  E-value: 1.24e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252    1 MPELPEVEAARRAIEENCLGKKIKRVIIADdnkvihgisPSDFQTSIL--GKTIISARRKGKNLWLELDSPPFPSFQFGM 78
Cdd:PRK14811   1 MPELPEVETTRRKLEPLLLGQTIQQVVHDD---------PARYRNTELaeGRRVLGLSRRGKYLLLHLPHDLELIVHLGM 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   79 AGAIYIKgvavtkykrsavkdseewPSKYSKFFVELDdGLELSFTDKRRFAKVRLLA--NPTSVSPISELGPDALLEPMT 156
Cdd:PRK14811  72 TGGFRLE------------------PGPHTRVTLELP-GRTLYFTDPRRFGKWWVVRagDYREIPLLARMGPEPLSDDFT 132

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30695252  157 VDEFAESLAKKKiTIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIQHAVQ 228
Cdd:PRK14811 133 EPEFVRALATAR-PVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEAVE 203
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-132 7.91e-31

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: 111.12  E-value: 7.91e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252      2 PELPEVEAARRAIEENCLGKKIKRVIIADDNKvihGISPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQFGMAGA 81
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQ---LRFPDEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGS 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 30695252     82 IYIkgvavtkykrsavKDSEEWPSKYSKFFVELDDGLELSFTDKRRFAKVR 132
Cdd:smart00898  78 LRV-------------VPAGTPPPKHDHVRLVLDDGTELRFNDPRRFGAVR 115
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-135 1.59e-28

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: 105.27  E-value: 1.59e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   2 PELPEVEAARRAIEENCLGKKIKRVIIaDDNKVIHGISPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQFGMAGA 81
Cdd:cd08966   1 PELPEVETVRRGLAPHLVGRRIEDVEV-RRPKLRRPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGR 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 30695252  82 IYikgvavtkykrsaVKDSEEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLA 135
Cdd:cd08966  80 LL-------------VVPPDEPPEKHDHVIFELDDGRELRFNDPRRFGTLLLVP 120
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-133 9.84e-26

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: 97.82  E-value: 9.84e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   2 PELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGisPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQFGMAGA 81
Cdd:cd08773   1 PELPEVELLRRKLRRALKGKRVTRVEVSDPRRLFTP--AAELAAALIGRRVRGAERRGKYLLLELSGGPWLVIHLGMTGR 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 30695252  82 IYIkgvavtkykrsavKDSEEWPSKYSKFFVELDDGLELSFTDKRRFAKVRL 133
Cdd:cd08773  79 LRV-------------CPEGEPPPKHDRLVLRLANGSQLRFTDPRKFGRVEL 117
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-133 1.05e-23

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: 92.80  E-value: 1.05e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   2 PELPEVEAARRAIEENCLGKKIKRVIIADDnkVIHGISPSDFQTSILGKTIISARRKGKNLWLELDSPPFPSFQFGMAGa 81
Cdd:cd08976   1 PELPEVEVQKQYLERTSLHRKIVEVEVGDD--KILGEPKATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTG- 77

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 30695252  82 iyikgvavtkyKRSAVKDSEEWPsKYSKFFVELDDGLELSFTDKRRFAKVRL 133
Cdd:cd08976  78 -----------KLDYYPDDEDPP-KHARLLLHFEDGFRLAFECPRKFGRVRL 117
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-224 5.49e-14

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 70.06  E-value: 5.49e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252    1 MPELPEVEAARRAIEENCLGKKIKRVIIAddnkvihgiSPS--DFQTSILGKTIISARRKGKNLWLEldsppfpsFQFGM 78
Cdd:PRK10445   1 MPEGPEIRRAADNLEAAIKGKPLTDVWFA---------FPQlkPYESQLIGQRVTHIETRGKALLTH--------FSNGL 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   79 AgaIYIKGvavTKYKRSAVKDSEEWPSKYSKFFVELDDG----LELSFTDKRRFAKVRLLANPTsvspISELGPDALLEP 154
Cdd:PRK10445  64 T--LYSHN---QLYGVWRVVDTGEEPQTTRVLRVRLQTAdktiLLYSASDIEMLTPEQLTTHPF----LQRVGPDVLDPN 134

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30695252  155 MTVDEFAESLAKKKITIKP---LLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIQ 224
Cdd:PRK10445 135 LTPEQVKERLLSPRFRNRQfsgLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPR 207
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-68 6.04e-10

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: 55.72  E-value: 6.04e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695252   1 MPELPEVEAARRAIEENCLGKKIKRVIIADD--NKvihgiSPSDFQTSILGKTIISARRKGKNLWLELDS 68
Cdd:cd08973   1 MPELPEVEVYAENLERRLTGKTITRVELASKslLV-----TPDPPLEALEGRTVTGVRRHGKRLDFEFDN 65
 
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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