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Conserved domains on  [gi|15241478|ref|NP_199252|]
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FAD-binding Berberine family protein [Arabidopsis thaliana]

Protein Classification

FAD-dependent oxidoreductase( domain architecture ID 10481387)

FAD-dependent oxidoreductase is an FAD/FMN-binding enzyme that catalyzes the transfer of electrons from one molecule, the electron donor or reductant, to another molecule, the electron acceptor or oxidant; also contains BBE (Berberine and berberine like) domain

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
FAD_binding_4 pfam01565
FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most ...
 86-225 4.99e-28

FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidizes the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan.


:

Pssm-ID: 426326 [Multi-domain]  Cd Length: 139  Bit Score: 108.83  E-value: 4.99e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241478    86 PGFIFKPVHESHVQASVICSKKLEIHFRVRSGGHDYEGVSYVSQIekpfVLIDLSKLRQI-NVDIKDTSAWVEAGATVGE 164
Cdd:pfam01565   1 PAAVVLPESEEEVAAIVRLANENGLPVLPRGGGSSLLGGAVQTGG----IVLDLSRLNGIlEIDPEDGTATVEAGVTLGD 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15241478   165 LYYRIAEKSKFHGFPAGVYPSLGIGGHITGGAYGSLMRKYGLAADNVLDAKIVDANGKLLD 225
Cdd:pfam01565  77 LVRALAAKGLLLGLDPGSGIPGTVGGAIATNAGGYGSEKYGLTRDNVLGLEVVLADGEVVR 137
BBE pfam08031
Berberine and berberine like; This domain is found in the berberine bridge and berberine ...
 480-538 4.40e-19

Berberine and berberine like; This domain is found in the berberine bridge and berberine bridge- like enzymes which are involved in the biosynthesis of numerous isoquinoline alkaloids. They catalyze the transformation of the N-methyl group of (S)-reticuline into the C-8 berberine bridge carbon of (S)-scoulerine.


:

Pssm-ID: 369658 [Multi-domain]  Cd Length: 45  Bit Score: 80.68  E-value: 4.40e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15241478   480 AYVNYRDLDLGqnkdnsksnfieakIWGANYFKDNFNRLVRIKSKVDPDNFFRHEQSIP 538
Cdd:pfam08031   1 AYVNYPDLDLG--------------DWGERYFGSNFERLVEVKAKYDPDNVFRNEQSIP 45
 
Name Accession Description Interval E-value
FAD_binding_4 pfam01565
FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most ...
 86-225 4.99e-28

FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidizes the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan.


Pssm-ID: 426326 [Multi-domain]  Cd Length: 139  Bit Score: 108.83  E-value: 4.99e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241478    86 PGFIFKPVHESHVQASVICSKKLEIHFRVRSGGHDYEGVSYVSQIekpfVLIDLSKLRQI-NVDIKDTSAWVEAGATVGE 164
Cdd:pfam01565   1 PAAVVLPESEEEVAAIVRLANENGLPVLPRGGGSSLLGGAVQTGG----IVLDLSRLNGIlEIDPEDGTATVEAGVTLGD 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15241478   165 LYYRIAEKSKFHGFPAGVYPSLGIGGHITGGAYGSLMRKYGLAADNVLDAKIVDANGKLLD 225
Cdd:pfam01565  77 LVRALAAKGLLLGLDPGSGIPGTVGGAIATNAGGYGSEKYGLTRDNVLGLEVVLADGEVVR 137
GlcD COG0277
FAD/FMN-containing lactate dehydrogenase/glycolate oxidase [Energy production and conversion];
67-268 8.75e-24

FAD/FMN-containing lactate dehydrogenase/glycolate oxidase [Energy production and conversion];


Pssm-ID: 440046 [Multi-domain]  Cd Length: 462  Bit Score: 104.21  E-value: 8.75e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241478  67 EVLESTAQNQRYLTKTMP----KPGFIFKPVHESHVQASVICSKKLEIHFRVRSGGHDYEGVSYVSQIEkpfVLIDLSKL 142
Cdd:COG0277  17 RVLTDPADRAAYARDGNSlyrgRPDAVVRPRSTEDVAAVVRLAAEHGVPVVPRGGGTGLAGGAVPLDGG---VVLDLSRM 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241478 143 RQIN-VDIKDTSAWVEAGATVGELYyRIAEKskfHGFPAGVYPSL----GIGGHITGGAYGSLMRKYGLAADNVLDAKIV 217
Cdd:COG0277  94 NRILeVDPEDRTATVEAGVTLADLN-AALAP---HGLFFPPDPSSqgtaTIGGNIATNAGGPRSLKYGLTRDNVLGLEVV 169

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15241478 218 DANGKLLD------RASMGEDLFWAIRGgsggsfgiilSW---------KIKLVPVPETLTVFTVT 268
Cdd:COG0277 170 LADGEVVRtggrvpKNVTGYDLFWLLVG----------SEgtlgviteaTLRLHPLPEAVATALVA 225
BBE pfam08031
Berberine and berberine like; This domain is found in the berberine bridge and berberine ...
 480-538 4.40e-19

Berberine and berberine like; This domain is found in the berberine bridge and berberine bridge- like enzymes which are involved in the biosynthesis of numerous isoquinoline alkaloids. They catalyze the transformation of the N-methyl group of (S)-reticuline into the C-8 berberine bridge carbon of (S)-scoulerine.


Pssm-ID: 369658 [Multi-domain]  Cd Length: 45  Bit Score: 80.68  E-value: 4.40e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15241478   480 AYVNYRDLDLGqnkdnsksnfieakIWGANYFKDNFNRLVRIKSKVDPDNFFRHEQSIP 538
Cdd:pfam08031   1 AYVNYPDLDLG--------------DWGERYFGSNFERLVEVKAKYDPDNVFRNEQSIP 45
PLN02805 PLN02805
D-lactate dehydrogenase [cytochrome]
 76-228 1.47e-05

D-lactate dehydrogenase [cytochrome]


Pssm-ID: 178402 [Multi-domain]  Cd Length: 555  Bit Score: 47.70  E-value: 1.47e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241478   76 QRYLTKTMPKPGFIFKPVHESHVQASVICSKKLEIHFRVRSGGHDYEGVSYVSqieKPFVLIDLSKLRQIN-VDIKDTSA 154
Cdd:PLN02805 124 QNSFHKAVNIPDVVVFPRSEEEVSKIVKSCNKYKVPIVPYGGATSIEGHTLAP---HGGVCIDMSLMKSVKaLHVEDMDV 200

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15241478  155 WVEAGATVGELYYRIAEKSKFhgFPAGVYPSLGIGGHITGGAYGSLMRKYGLAADNVLDAKIVDANGKLLDRAS 228
Cdd:PLN02805 201 VVEPGIGWLELNEYLEPYGLF--FPLDPGPGATIGGMCATRCSGSLAVRYGTMRDNVISLKVVLPNGDVVKTAS 272
 
Name Accession Description Interval E-value
FAD_binding_4 pfam01565
FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most ...
 86-225 4.99e-28

FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidizes the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan.


Pssm-ID: 426326 [Multi-domain]  Cd Length: 139  Bit Score: 108.83  E-value: 4.99e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241478    86 PGFIFKPVHESHVQASVICSKKLEIHFRVRSGGHDYEGVSYVSQIekpfVLIDLSKLRQI-NVDIKDTSAWVEAGATVGE 164
Cdd:pfam01565   1 PAAVVLPESEEEVAAIVRLANENGLPVLPRGGGSSLLGGAVQTGG----IVLDLSRLNGIlEIDPEDGTATVEAGVTLGD 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15241478   165 LYYRIAEKSKFHGFPAGVYPSLGIGGHITGGAYGSLMRKYGLAADNVLDAKIVDANGKLLD 225
Cdd:pfam01565  77 LVRALAAKGLLLGLDPGSGIPGTVGGAIATNAGGYGSEKYGLTRDNVLGLEVVLADGEVVR 137
GlcD COG0277
FAD/FMN-containing lactate dehydrogenase/glycolate oxidase [Energy production and conversion];
67-268 8.75e-24

FAD/FMN-containing lactate dehydrogenase/glycolate oxidase [Energy production and conversion];


Pssm-ID: 440046 [Multi-domain]  Cd Length: 462  Bit Score: 104.21  E-value: 8.75e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241478  67 EVLESTAQNQRYLTKTMP----KPGFIFKPVHESHVQASVICSKKLEIHFRVRSGGHDYEGVSYVSQIEkpfVLIDLSKL 142
Cdd:COG0277  17 RVLTDPADRAAYARDGNSlyrgRPDAVVRPRSTEDVAAVVRLAAEHGVPVVPRGGGTGLAGGAVPLDGG---VVLDLSRM 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241478 143 RQIN-VDIKDTSAWVEAGATVGELYyRIAEKskfHGFPAGVYPSL----GIGGHITGGAYGSLMRKYGLAADNVLDAKIV 217
Cdd:COG0277  94 NRILeVDPEDRTATVEAGVTLADLN-AALAP---HGLFFPPDPSSqgtaTIGGNIATNAGGPRSLKYGLTRDNVLGLEVV 169

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15241478 218 DANGKLLD------RASMGEDLFWAIRGgsggsfgiilSW---------KIKLVPVPETLTVFTVT 268
Cdd:COG0277 170 LADGEVVRtggrvpKNVTGYDLFWLLVG----------SEgtlgviteaTLRLHPLPEAVATALVA 225
BBE pfam08031
Berberine and berberine like; This domain is found in the berberine bridge and berberine ...
 480-538 4.40e-19

Berberine and berberine like; This domain is found in the berberine bridge and berberine bridge- like enzymes which are involved in the biosynthesis of numerous isoquinoline alkaloids. They catalyze the transformation of the N-methyl group of (S)-reticuline into the C-8 berberine bridge carbon of (S)-scoulerine.


Pssm-ID: 369658 [Multi-domain]  Cd Length: 45  Bit Score: 80.68  E-value: 4.40e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15241478   480 AYVNYRDLDLGqnkdnsksnfieakIWGANYFKDNFNRLVRIKSKVDPDNFFRHEQSIP 538
Cdd:pfam08031   1 AYVNYPDLDLG--------------DWGERYFGSNFERLVEVKAKYDPDNVFRNEQSIP 45
PLN02805 PLN02805
D-lactate dehydrogenase [cytochrome]
 76-228 1.47e-05

D-lactate dehydrogenase [cytochrome]


Pssm-ID: 178402 [Multi-domain]  Cd Length: 555  Bit Score: 47.70  E-value: 1.47e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241478   76 QRYLTKTMPKPGFIFKPVHESHVQASVICSKKLEIHFRVRSGGHDYEGVSYVSqieKPFVLIDLSKLRQIN-VDIKDTSA 154
Cdd:PLN02805 124 QNSFHKAVNIPDVVVFPRSEEEVSKIVKSCNKYKVPIVPYGGATSIEGHTLAP---HGGVCIDMSLMKSVKaLHVEDMDV 200

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15241478  155 WVEAGATVGELYYRIAEKSKFhgFPAGVYPSLGIGGHITGGAYGSLMRKYGLAADNVLDAKIVDANGKLLDRAS 228
Cdd:PLN02805 201 VVEPGIGWLELNEYLEPYGLF--FPLDPGPGATIGGMCATRCSGSLAVRYGTMRDNVISLKVVLPNGDVVKTAS 272
 
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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