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Conserved domains on  [gi|42572967|ref|NP_974580|]
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FAD-binding Berberine family protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
BBE pfam08031
Berberine and berberine like; This domain is found in the berberine bridge and berberine ...
 477-534 5.71e-18

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: 77.21  E-value: 5.71e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 42572967   477 SYFNYRDVDIGVndhgansykegevYGRKYFGENFDRLVKIKTAVDPGNFFRNEQSIP 534
Cdd:pfam08031   1 AYVNYPDLDLGD-------------WGERYFGSNFERLVEVKAKYDPDNVFRNEQSIP 45
FAD_binding_4 super family cl47204
FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most ...
 87-224 6.21e-14

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.


The actual alignment was detected with superfamily member pfam01565:

Pssm-ID: 426326 [Multi-domain]  Cd Length: 139  Bit Score: 68.77  E-value: 6.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572967    87 PTIIITPRSESHVSAAVTCSKTLNFLLKIRSGGHDYDGLSYISDkpFFILDMSNIRDV-SVDIASNSAWISAGATLGEVY 165
Cdd:pfam01565   1 PAAVVLPESEEEVAAIVRLANENGLPVLPRGGGSSLLGGAVQTG--GIVLDLSRLNGIlEIDPEDGTATVEAGVTLGDLV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 42572967   166 YRIWEKSRVHGFPAGVCPTVGVGGHLSGGGYGNMVRKFGLSVDYVEDAKIVDVNGRVLD 224
Cdd:pfam01565  79 RALAAKGLLLGLDPGSGIPGTVGGAIATNAGGYGSEKYGLTRDNVLGLEVVLADGEVVR 137
 
Name Accession Description Interval E-value
BBE pfam08031
Berberine and berberine like; This domain is found in the berberine bridge and berberine ...
 477-534 5.71e-18

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: 77.21  E-value: 5.71e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 42572967   477 SYFNYRDVDIGVndhgansykegevYGRKYFGENFDRLVKIKTAVDPGNFFRNEQSIP 534
Cdd:pfam08031   1 AYVNYPDLDLGD-------------WGERYFGSNFERLVEVKAKYDPDNVFRNEQSIP 45
FAD_binding_4 pfam01565
FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most ...
 87-224 6.21e-14

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: 68.77  E-value: 6.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572967    87 PTIIITPRSESHVSAAVTCSKTLNFLLKIRSGGHDYDGLSYISDkpFFILDMSNIRDV-SVDIASNSAWISAGATLGEVY 165
Cdd:pfam01565   1 PAAVVLPESEEEVAAIVRLANENGLPVLPRGGGSSLLGGAVQTG--GIVLDLSRLNGIlEIDPEDGTATVEAGVTLGDLV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 42572967   166 YRIWEKSRVHGFPAGVCPTVGVGGHLSGGGYGNMVRKFGLSVDYVEDAKIVDVNGRVLD 224
Cdd:pfam01565  79 RALAAKGLLLGLDPGSGIPGTVGGAIATNAGGYGSEKYGLTRDNVLGLEVVLADGEVVR 137
GlcD COG0277
FAD/FMN-containing lactate dehydrogenase/glycolate oxidase [Energy production and conversion];
51-266 3.32e-09

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


Pssm-ID: 440046 [Multi-domain]  Cd Length: 462  Bit Score: 59.14  E-value: 3.32e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572967  51 QSQITDNVFsqTNPAfssVLRAYIRnaRFNTSSTLKPTIIITPRSESHVSAAVTCSKTLNFLLKIRSGGHDYDGLSyISD 130
Cdd:COG0277  11 RAILAGRVL--TDPA---DRAAYAR--DGNSLYRGRPDAVVRPRSTEDVAAVVRLAAEHGVPVVPRGGGTGLAGGA-VPL 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572967 131 KPFFILDMSNIRDV-SVDIASNSAWISAGATLGEVYyriwEKSRVHGF-----PA----------------GVCptvgvg 188
Cdd:COG0277  83 DGGVVLDLSRMNRIlEVDPEDRTATVEAGVTLADLN----AALAPHGLffppdPSsqgtatiggniatnagGPR------ 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572967 189 ghlsgggygnmVRKFGLSVDYVEDAKIVDVNGRVLD------RKAMGEDLFWA----------ITgggggsygvvlGYKV 252
Cdd:COG0277 153 -----------SLKYGLTRDNVLGLEVVLADGEVVRtggrvpKNVTGYDLFWLlvgsegtlgvIT-----------EATL 210

                       250
                ....*....|....
gi 42572967 253 KLVPVPSVVTVFRV 266
Cdd:COG0277 211 RLHPLPEAVATALV 224
 
Name Accession Description Interval E-value
BBE pfam08031
Berberine and berberine like; This domain is found in the berberine bridge and berberine ...
 477-534 5.71e-18

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: 77.21  E-value: 5.71e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 42572967   477 SYFNYRDVDIGVndhgansykegevYGRKYFGENFDRLVKIKTAVDPGNFFRNEQSIP 534
Cdd:pfam08031   1 AYVNYPDLDLGD-------------WGERYFGSNFERLVEVKAKYDPDNVFRNEQSIP 45
FAD_binding_4 pfam01565
FAD binding domain; This family consists of various enzymes that use FAD as a co-factor, most ...
 87-224 6.21e-14

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: 68.77  E-value: 6.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572967    87 PTIIITPRSESHVSAAVTCSKTLNFLLKIRSGGHDYDGLSYISDkpFFILDMSNIRDV-SVDIASNSAWISAGATLGEVY 165
Cdd:pfam01565   1 PAAVVLPESEEEVAAIVRLANENGLPVLPRGGGSSLLGGAVQTG--GIVLDLSRLNGIlEIDPEDGTATVEAGVTLGDLV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 42572967   166 YRIWEKSRVHGFPAGVCPTVGVGGHLSGGGYGNMVRKFGLSVDYVEDAKIVDVNGRVLD 224
Cdd:pfam01565  79 RALAAKGLLLGLDPGSGIPGTVGGAIATNAGGYGSEKYGLTRDNVLGLEVVLADGEVVR 137
GlcD COG0277
FAD/FMN-containing lactate dehydrogenase/glycolate oxidase [Energy production and conversion];
51-266 3.32e-09

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


Pssm-ID: 440046 [Multi-domain]  Cd Length: 462  Bit Score: 59.14  E-value: 3.32e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572967  51 QSQITDNVFsqTNPAfssVLRAYIRnaRFNTSSTLKPTIIITPRSESHVSAAVTCSKTLNFLLKIRSGGHDYDGLSyISD 130
Cdd:COG0277  11 RAILAGRVL--TDPA---DRAAYAR--DGNSLYRGRPDAVVRPRSTEDVAAVVRLAAEHGVPVVPRGGGTGLAGGA-VPL 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572967 131 KPFFILDMSNIRDV-SVDIASNSAWISAGATLGEVYyriwEKSRVHGF-----PA----------------GVCptvgvg 188
Cdd:COG0277  83 DGGVVLDLSRMNRIlEVDPEDRTATVEAGVTLADLN----AALAPHGLffppdPSsqgtatiggniatnagGPR------ 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572967 189 ghlsgggygnmVRKFGLSVDYVEDAKIVDVNGRVLD------RKAMGEDLFWA----------ITgggggsygvvlGYKV 252
Cdd:COG0277 153 -----------SLKYGLTRDNVLGLEVVLADGEVVRtggrvpKNVTGYDLFWLlvgsegtlgvIT-----------EATL 210

                       250
                ....*....|....
gi 42572967 253 KLVPVPSVVTVFRV 266
Cdd:COG0277 211 RLHPLPEAVATALV 224
 
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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