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Conserved domains on  [gi|4235006|gb|AAD13063|]
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naphthalene dioxygenase, partial [uncultured bacterium U4c]

Protein Classification

aromatic ring-hydroxylating dioxygenase subunit alpha( domain architecture ID 11468605)

aromatic ring-hydroxylating dioxygenase subunit alpha is the catalytic component of a complex that catalyzes the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds

CATH:  3.90.380.10|2.102.10.10
EC:  1.14.13.-
Gene Ontology:  GO:0051537|GO:0016491
PubMed:  11849939
SCOP:  4001667

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HcaE COG4638
Phenylpropionate dioxygenase or related ring-hydroxylating dioxygenase, large terminal subunit ...
 4-140 4.94e-47

Phenylpropionate dioxygenase or related ring-hydroxylating dioxygenase, large terminal subunit [Inorganic ion transport and metabolism, General function prediction only];


:

Pssm-ID: 443676 [Multi-domain]  Cd Length: 298  Bit Score: 153.99  E-value: 4.94e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    4 IPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVnAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKElyGDA 83
Cdd:COG4638  36 LPEPGDYLTRTILGEPVVLVRDKDGEVRAFHNVCPHRGAPLS-EGRGNGGRLVCPYHGWTYDLDGRLVGIPHMEG--FPD 112

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 4235006   84 IKKKCLGLKEVPrVESFHGFIYGCFDAEAPPLMDYLGDAAWYLEPIfkHSGGLELVG 140
Cdd:COG4638 113 FDPARAGLRSVP-VEEWGGLIFVWLGPDAPPLAEYLGPLAEYLDPY--DFGELKVAG 166
 
Name Accession Description Interval E-value
HcaE COG4638
Phenylpropionate dioxygenase or related ring-hydroxylating dioxygenase, large terminal subunit ...
 4-140 4.94e-47

Phenylpropionate dioxygenase or related ring-hydroxylating dioxygenase, large terminal subunit [Inorganic ion transport and metabolism, General function prediction only];


Pssm-ID: 443676 [Multi-domain]  Cd Length: 298  Bit Score: 153.99  E-value: 4.94e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    4 IPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVnAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKElyGDA 83
Cdd:COG4638  36 LPEPGDYLTRTILGEPVVLVRDKDGEVRAFHNVCPHRGAPLS-EGRGNGGRLVCPYHGWTYDLDGRLVGIPHMEG--FPD 112

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 4235006   84 IKKKCLGLKEVPrVESFHGFIYGCFDAEAPPLMDYLGDAAWYLEPIfkHSGGLELVG 140
Cdd:COG4638 113 FDPARAGLRSVP-VEEWGGLIFVWLGPDAPPLAEYLGPLAEYLDPY--DFGELKVAG 166
Rieske_RO_Alpha_NDO cd03535
Rieske non-heme iron oxygenase (RO) family, Nathphalene 1,2-dioxygenase (NDO) subfamily, ...
 1-115 7.92e-47

Rieske non-heme iron oxygenase (RO) family, Nathphalene 1,2-dioxygenase (NDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. NDO is a three-component RO system consisting of a reductase, a ferredoxin, and a hetero-hexameric alpha-beta subunit oxygenase component. NDO catalyzes the oxidation of naphthalene to cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene (naphthalene cis-dihydrodiol) with the consumption of O2 and NAD(P)H. NDO has a relaxed substrate specificity and can oxidize almost 100 substrates. Included in its varied activities are the enantiospecific cis-dihydroxylation of polycyclic aromatic hydrocarbons and benzocycloalkenes, benzylic hydroxylation, N- and O-dealkylation, sulfoxidation and desaturation reactions.


Pssm-ID: 239609 [Multi-domain]  Cd Length: 123  Bit Score: 147.96  E-value: 7.92e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    1 DSLIPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKELY 80
Cdd:cd03535   9 ESEIPNAGDYVVRYIGDDSFIVCRDEDGEIRAMFNSCRHRGMQVCRAEMGNTSHFRCPYHGWTYRNTGRLVGVPAQQEAY 88

                        90       100       110
                ....*....|....*....|....*....|....*
gi 4235006   81 GDAIKKKCLGLKEVPRVESFHGFIYGCFDAEAPPL 115
Cdd:cd03535  89 GGGFDKSQWGLRPAPNLDSYNGLIFGSLDPKAPSL 123
Rieske pfam00355
Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines ...
 6-79 1.41e-14

Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilizes the protein.


Pssm-ID: 425632 [Multi-domain]  Cd Length: 89  Bit Score: 64.68  E-value: 1.41e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4235006      6 SPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKEL 79
Cdd:pfam00355  12 PEGEPKVVEVGGEPLVVFRDEDGELYALEDRCPHRGAPLSEGKVNGGGRLECPYHGWRFDGTGKVVKVPAPRPL 85
PLN02518 PLN02518
pheophorbide a oxygenase
 1-74 4.37e-05

pheophorbide a oxygenase


Pssm-ID: 215283 [Multi-domain]  Cd Length: 539  Bit Score: 42.16  E-value: 4.37e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4235006     1 DSLIPSPGDYvtakMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVP 74
Cdd:PLN02518 101 DPSVPTPFQL----LGRDLVLWKDPNQGEWVAFDDKCPHRLAPLSEGRIDENGHLQCSYHGWSFDGCGSCTRIP 170
 
Name Accession Description Interval E-value
HcaE COG4638
Phenylpropionate dioxygenase or related ring-hydroxylating dioxygenase, large terminal subunit ...
 4-140 4.94e-47

Phenylpropionate dioxygenase or related ring-hydroxylating dioxygenase, large terminal subunit [Inorganic ion transport and metabolism, General function prediction only];


Pssm-ID: 443676 [Multi-domain]  Cd Length: 298  Bit Score: 153.99  E-value: 4.94e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    4 IPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVnAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKElyGDA 83
Cdd:COG4638  36 LPEPGDYLTRTILGEPVVLVRDKDGEVRAFHNVCPHRGAPLS-EGRGNGGRLVCPYHGWTYDLDGRLVGIPHMEG--FPD 112

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 4235006   84 IKKKCLGLKEVPrVESFHGFIYGCFDAEAPPLMDYLGDAAWYLEPIfkHSGGLELVG 140
Cdd:COG4638 113 FDPARAGLRSVP-VEEWGGLIFVWLGPDAPPLAEYLGPLAEYLDPY--DFGELKVAG 166
Rieske_RO_Alpha_NDO cd03535
Rieske non-heme iron oxygenase (RO) family, Nathphalene 1,2-dioxygenase (NDO) subfamily, ...
 1-115 7.92e-47

Rieske non-heme iron oxygenase (RO) family, Nathphalene 1,2-dioxygenase (NDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. NDO is a three-component RO system consisting of a reductase, a ferredoxin, and a hetero-hexameric alpha-beta subunit oxygenase component. NDO catalyzes the oxidation of naphthalene to cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene (naphthalene cis-dihydrodiol) with the consumption of O2 and NAD(P)H. NDO has a relaxed substrate specificity and can oxidize almost 100 substrates. Included in its varied activities are the enantiospecific cis-dihydroxylation of polycyclic aromatic hydrocarbons and benzocycloalkenes, benzylic hydroxylation, N- and O-dealkylation, sulfoxidation and desaturation reactions.


Pssm-ID: 239609 [Multi-domain]  Cd Length: 123  Bit Score: 147.96  E-value: 7.92e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    1 DSLIPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKELY 80
Cdd:cd03535   9 ESEIPNAGDYVVRYIGDDSFIVCRDEDGEIRAMFNSCRHRGMQVCRAEMGNTSHFRCPYHGWTYRNTGRLVGVPAQQEAY 88

                        90       100       110
                ....*....|....*....|....*....|....*
gi 4235006   81 GDAIKKKCLGLKEVPRVESFHGFIYGCFDAEAPPL 115
Cdd:cd03535  89 GGGFDKSQWGLRPAPNLDSYNGLIFGSLDPKAPSL 123
Rieske_RO_Alpha_N cd03469
Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha ...
 2-115 1.83e-45

Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the initial source of two electrons for dioxygen activation.


Pssm-ID: 239551 [Multi-domain]  Cd Length: 118  Bit Score: 144.27  E-value: 1.83e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    2 SLIPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKELYG 81
Cdd:cd03469   8 SELPEPGDYVTLELGGEPLVLVRDRDGEVRAFHNVCPHRGARLCEGRGGNAGRLVCPYHGWTYDLDGKLVGVPREEGFPG 87

                        90       100       110
                ....*....|....*....|....*....|....
gi 4235006   82 daIKKKCLGLKEVPrVESFHGFIYGCFDAEAPPL 115
Cdd:cd03469  88 --FDKEKLGLRTVP-VEEWGGLIFVNLDPDAPPL 118
Rieske_RO_Alpha_BPDO_like cd03472
Rieske non-heme iron oxygenase (RO) family, Biphenyl dioxygenase (BPDO)-like subfamily, ...
 1-115 4.91e-40

Rieske non-heme iron oxygenase (RO) family, Biphenyl dioxygenase (BPDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of BPDO and similar proteins including cumene dioxygenase (CumDO), nitrobenzene dioxygenase (NBDO), alkylbenzene dioxygenase (AkbDO) and dibenzofuran 4,4a-dioxygenase (DFDO). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. BPDO degrades biphenyls and polychlorinated biphenyls (PCB's) while CumDO degrades cumene (isopropylbenzene), an aromatic hydrocarbon that is intermediate in size between ethylbenzene and biphenyl. NBDO catalyzes the initial reaction in nitrobenzene degradation, oxidizing the aromatic rings of mono- and dinitrotoluenes to form catechol and nitrite. NBDO belongs to the naphthalene subfamily of ROs. AkbDO is involved in alkylbenzene catabolism, converting o-xylene to 2,3- and 3,4-dimethylphenol and ethylbenzene to cis-dihydrodiol. DFDO is involved in dibenzofuran degradation.


Pssm-ID: 239554 [Multi-domain]  Cd Length: 128  Bit Score: 131.12  E-value: 4.91e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    1 DSLIPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKELY 80
Cdd:cd03472  15 ETHIPKAGDYLTTYMGEDPVIVVRQKDGSIRVFLNQCRHRGMRICRSDAGNAKAFTCTYHGWAYDTAGNLVNVPFEKEAF 94

                        90       100       110
                ....*....|....*....|....*....|....*
gi 4235006   81 GDAIKKKCLGLKEVpRVESFHGFIYGCFDAEAPPL 115
Cdd:cd03472  95 CDGLDKADWGPLQA-RVETYKGLIFANWDAEAPDL 128
Rieske_RO_Alpha_HBDO cd03542
Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, ...
 1-115 5.79e-28

Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. HBDO catalyzes the double hydroxylation of 2-halobenzoates with concomitant release of halogenide and carbon dioxide, yielding catechol.


Pssm-ID: 239615 [Multi-domain]  Cd Length: 123  Bit Score: 100.21  E-value: 5.79e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    1 DSLIPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKEL- 79
Cdd:cd03542   7 ESQIPNNNDYFTTTIGRQPVVITRDKDGELNAFINACSHRGAMLCRRKQGNKGTFTCPFHGWTFSNTGKLLKVKDPKTAg 86

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 4235006   80 YGDAIkkKCLG---LKEVPRVESFHGFIYGCFDAEAPPL 115
Cdd:cd03542  87 YPEGF--NCDGshdLTKVARFESYRGFLFGSLNADVAPL 123
Rieske_RO_Alpha_DTDO cd03536
This alignment model represents the N-terminal rieske domain of the oxygenase alpha subunit ...
 1-117 1.43e-27

This alignment model represents the N-terminal rieske domain of the oxygenase alpha subunit (DitA) of diterpenoid dioxygenase (DTDO). DTDO is a novel aromatic-ring-hydroxylating dioxygenase found in Pseudomonas and other proteobacteria that degrades dehydroabietic acid (DhA). Specifically, DitA hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8, 13-abietadien acid. The ditA1 and ditA2 genes encode the alpha and beta subunits of the oxygenase component of DTDO while the ditA3 gene encodes the ferredoxin component of DTDO. The organization of the genes encoding the various diterpenoid dioxygenase components, the phylogenetic distinctiveness of both the alpha subunit and the ferredoxin component, and the unusual iron-sulfur cluster of the ferredoxin all suggest that this enzyme belongs to a new class of aromatic ring-hydroxylating dioxygenases.


Pssm-ID: 239610 [Multi-domain]  Cd Length: 123  Bit Score: 99.24  E-value: 1.43e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    1 DSLIPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKE-L 79
Cdd:cd03536   7 ESEIPNKGDFMVRDMGSDSVIVARDKDGEIHVSLNVCPHRGMRISTTDGGNTQIHVCIYHGWAFRPNGDFIGAPVEKEcM 86

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 4235006   80 YGDAIKKKCLGLKEVpRVESFHGFIYGCFDAEAPPLMD 117
Cdd:cd03536  87 HGKMRTKAELGLHKA-RVTLYGGLIFATWNIDGPSFED 123
Rieske_RO_Alpha_OHBDO_like cd03545
Rieske non-heme iron oxygenase (RO) family, Ortho-halobenzoate-1,2-dioxygenase (OHBDO)-like ...
 4-115 4.44e-25

Rieske non-heme iron oxygenase (RO) family, Ortho-halobenzoate-1,2-dioxygenase (OHBDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of OHBDO, salicylate 5-hydroxylase (S5H), terephthalate 1,2-dioxygenase system (TERDOS) and similar proteins. ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OHBDO converts 2-chlorobenzoate (2-CBA) to catechol as well as 2,4-dCBA and 2,5-dCBA to 4-chlorocatechol, as part of the chlorobenzoate degradation pathway. Although ortho-substituted chlorobenzoates appear to be particularly recalcitrant to biodegradation, several strains utilize 2-CBA and the dCBA derivatives as a sole carbon and energy source. S5H converts salicylate (2-hydroxybenzoate), a metabolic intermediate of phenanthrene, to gentisate (2,5-dihydroxybenzoate) as part of an alternate pathway for naphthalene catabolism. S5H is a multicomponent enzyme made up of NagGH (the oxygenase components), NagAa (the ferredoxin reductase component), and NagAb (the ferredoxin component). The oxygenase component is made up of alpha (NagG) and beta (NagH) subunits. TERDOS is present in gram-positive bacteria and proteobacteria where it converts terephthalate (1,4-dicarboxybenzene) to protocatechuate as part of the terephthalate degradation pathway. The oxygenase component of TERDOS, called TerZ, is a hetero-hexamer with 3 alpha (TerZalpha) and 3 beta (TerZbeta) subunits.


Pssm-ID: 239616 [Multi-domain]  Cd Length: 150  Bit Score: 93.66  E-value: 4.44e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    4 IPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKELYGDA 83
Cdd:cd03545  35 IPNAGDFKSTFVGDTPVVVTRAEDGSLHAWVNRCAHRGALVCRERRGNDGSLTCVYHQWAYDLKGNLKGVPFRRGLKGQG 114

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 4235006   84 -----IKKKCLGLKEVpRVESFHGFIYGCFDAEAPPL 115
Cdd:cd03545 115 gmpkdFDMKQHGLEKL-RVETVGGLVFASFSDEVEPL 150
Rieske_RO_Alpha_AntDO cd03538
Rieske non-heme iron oxygenase (RO) family, Anthranilate 1,2-dioxygenase (AntDO) subfamily, ...
 1-115 7.19e-23

Rieske non-heme iron oxygenase (RO) family, Anthranilate 1,2-dioxygenase (AntDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. AntDO converts anthranilate to catechol, a naturally occurring compound formed through tryptophan degradation and an important intermediate in the metabolism of many N-heterocyclic compounds such as indole, o-nitrobenzoate, carbazole, and quinaldine.


Pssm-ID: 239612 [Multi-domain]  Cd Length: 146  Bit Score: 87.52  E-value: 7.19e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    1 DSLIPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGN-AKGFVCSYHGWGFGSNGELQSVPFEKEL 79
Cdd:cd03538  29 ESQVPNPGDYITTRIGDQPVVMVRHTDGSVHVLYNRCPHKGTKIVSDGCGNtGKFFRCPYHAWSFKTDGSLLAIPLKKGY 108

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 4235006   80 YGDAI--KKKCLGLKEVPRVESFHGFIYGCFDAEAPPL 115
Cdd:cd03538 109 EGTGFdpSHADKGMQRVGAVDIYRGFVFARLSPSGPDF 146
Rieske_RO_Alpha_S5H cd03539
This alignment model represents the N-terminal rieske iron-sulfur domain of the oxygenase ...
 4-115 1.43e-20

This alignment model represents the N-terminal rieske iron-sulfur domain of the oxygenase alpha subunit (NagG) of salicylate 5-hydroxylase (S5H). S5H converts salicylate (2-hydroxybenzoate), a metabolic intermediate of phenanthrene, to gentisate (2,5-dihydroxybenzoate) as part of an alternate pathway for naphthalene catabolism. S5H is a multicomponent enzyme made up of NagGH (the oxygenase components), NagAa (the ferredoxin reductase component), and NagAb (the ferredoxin component). The oxygenase component is made up of alpha (NagG) and beta (NagH) subunits.


Pssm-ID: 239613 [Multi-domain]  Cd Length: 129  Bit Score: 81.51  E-value: 1.43e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    4 IPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKELYGDA 83
Cdd:cd03539  10 IPNPGDFKRTLIGERSVIMTRDPDGGINVVENVCAHRGMRFCRERNGNAKDFVCPYHQWNYSLKGDLQGVPFRRGVKKDG 89

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 4235006   84 ---------IKKKCLGLKEVpRVESFHGFIYGCFDAEAPPL 115
Cdd:cd03539  90 kvnggmpkdFKTKDHGLTKL-KVATRGGVVFASFDHDVESF 129
Rieske pfam00355
Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines ...
 6-79 1.41e-14

Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilizes the protein.


Pssm-ID: 425632 [Multi-domain]  Cd Length: 89  Bit Score: 64.68  E-value: 1.41e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4235006      6 SPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKEL 79
Cdd:pfam00355  12 PEGEPKVVEVGGEPLVVFRDEDGELYALEDRCPHRGAPLSEGKVNGGGRLECPYHGWRFDGTGKVVKVPAPRPL 85
Rieske_RO_Alpha_CMO cd03541
Rieske non-heme iron oxygenase (RO) family, Choline monooxygenase (CMO) subfamily, N-terminal ...
 4-70 3.12e-14

Rieske non-heme iron oxygenase (RO) family, Choline monooxygenase (CMO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. CMO is a novel RO found in certain plants which catalyzes the first step in betaine synthesis. CMO is not found in animals or bacteria. In these organisms, the first step in betaine synthesis is catalyzed by either the membrane-bound choline dehydrogenase (CDH) or the soluble choline oxidase (COX).


Pssm-ID: 239614 [Multi-domain]  Cd Length: 118  Bit Score: 64.49  E-value: 3.12e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4235006    4 IPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAeAGNAKGFVCSYHGWGFGSNGEL 70
Cdd:cd03541  11 VKEKNQYFTGRLGNVEYVVCRDGNGKLHAFHNVCTHRASILACG-SGKKSCFVCPYHGWVYGLDGSL 76
Rieske cd03467
Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron ...
 7-76 1.12e-11

Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis.


Pssm-ID: 239550 [Multi-domain]  Cd Length: 98  Bit Score: 57.50  E-value: 1.12e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 4235006    7 PGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEaGNAKGFVCSYHGWGFG-SNGELQSVPFE 76
Cdd:cd03467  12 PGGGRVVVVGGGPVVVVRREGGEVYALSNRCTHQGCPLSEGE-GEDGCIVCPCHGSRFDlRTGEVVSGPAP 81
PobA COG5749
Chlorophyllide a oxygenase/letal leaf spot protein [Coenzyme transport and metabolism];
24-124 7.90e-09

Chlorophyllide a oxygenase/letal leaf spot protein [Coenzyme transport and metabolism];


Pssm-ID: 444459 [Multi-domain]  Cd Length: 349  Bit Score: 52.70  E-value: 7.90e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006   24 RQNDGSVRAFLNVCRHRGKTLvnaeagnAKG------FVCSYHGWGFGSNGELQSVPFEKElyGDAIKKKClGLKEVPRV 97
Cdd:COG5749  48 RDSDGKVVALEDRCPHRGAPL-------SEGrveggnLRCPYHGWQFDGDGKCVHIPQLPE--NQPIPKNA-KVKSYPVQ 117

                        90       100       110
                ....*....|....*....|....*....|...
gi 4235006   98 ESfHGFIYGCFDAEA------PPLMDYLGDAAW 124
Cdd:COG5749 118 ER-YGLIWVWLGDPPqadetpIPDIPELDDPEW 149
Rieske_RO_Alpha_PaO cd03480
Rieske non-heme iron oxygenase (RO) family, Pheophorbide a oxygenase (PaO) subfamily, ...
 15-74 2.82e-07

Rieske non-heme iron oxygenase (RO) family, Pheophorbide a oxygenase (PaO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of a small subfamily of enzymes found in plants as well as oxygenic cyanobacterial photosynthesizers including LLS1 (lethal leaf spot 1, also known as PaO) and ACD1 (accelerated cell death 1). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. PaO expression increases upon physical wounding of plant leaves and is thought to catalyze a key step in chlorophyll degradation. The Arabidopsis-accelerated cell death gene ACD1 is involved in oxygenation of PaO.


Pssm-ID: 239562 [Multi-domain]  Cd Length: 138  Bit Score: 46.93  E-value: 2.82e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4235006   15 MGVDEVIVSRQNDGSVRAFLNVCRHRgktLVNAEAG--NAKGFV-CSYHGWGFGSNGELQSVP 74
Cdd:cd03480  38 LGRDLVIWWDRNSQQWRAFDDQCPHR---LAPLSEGriDEEGCLeCPYHGWSFDGSGSCQRIP 97
Rieske_RO_Alpha_VanA_DdmC cd03532
Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and ...
 20-83 4.27e-06

Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Vanillate-O-demethylase is a heterodimeric enzyme consisting of a terminal oxygenase (VanA) and reductase (VanB) components. This enzyme reductively catalyzes the conversion of vanillate into protocatechuate and formaldehyde. Protocatechuate and vanillate are important intermediate metabolites in the degradation pathway of lignin-derived compounds such as ferulic acid and vanillin by soil microbes. DDmC is the oxygenase component of a three-component dicamba O-demethylase found in Pseudomonas maltophila, that catalyzes the conversion of a widely used herbicide called herbicide dicamba (2-methoxy-3,6-dichlorobenzoic acid) to DCSA (3,6-dichlorosalicylic acid).


Pssm-ID: 239608 [Multi-domain]  Cd Length: 116  Bit Score: 43.12  E-value: 4.27e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4235006   20 VIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAkGFVCSYHGWGFGSNGELQSVPFEKELYGDA 83
Cdd:cd03532  29 VVLYRTQDGRVAALEDRCPHRSAPLSKGSVEGG-GLVCGYHGLEFDSDGRCVHMPGQERVPAKA 91
PLN02518 PLN02518
pheophorbide a oxygenase
 1-74 4.37e-05

pheophorbide a oxygenase


Pssm-ID: 215283 [Multi-domain]  Cd Length: 539  Bit Score: 42.16  E-value: 4.37e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4235006     1 DSLIPSPGDYvtakMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFVCSYHGWGFGSNGELQSVP 74
Cdd:PLN02518 101 DPSVPTPFQL----LGRDLVLWKDPNQGEWVAFDDKCPHRLAPLSEGRIDENGHLQCSYHGWSFDGCGSCTRIP 170
Rieske_RO_Alpha_Tic55 cd04338
Tic55 is a 55kDa LLS1-related non-heme iron oxygenase associated with protein transport ...
 18-74 7.73e-05

Tic55 is a 55kDa LLS1-related non-heme iron oxygenase associated with protein transport through the plant inner chloroplast membrane. This domain represents the N-terminal Rieske domain of the Tic55 oxygenase alpha subunit. Tic55 is closely related to the oxygenase alpha subunits of a small subfamily of enzymes found in plants as well as oxygenic cyanobacterial photosynthesizers including LLS1 (lethal leaf spot 1, also known as PaO), Ptc52, and ACD1 (accelerated cell death 1). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis.


Pssm-ID: 239830 [Multi-domain]  Cd Length: 134  Bit Score: 40.20  E-value: 7.73e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 4235006   18 DEVIV-SRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKgFVCSYHGWGFGSNGELQSVP 74
Cdd:cd04338  39 DEPFVlFRDQNGQLRCLEDRCPHRLAKLSEGQLIDGK-LECLYHGWQFGGEGKCVKIP 95
Rieske_RO_Alpha_OMO_CARDO cd03548
Rieske non-heme iron oxygenase (RO) family, 2-Oxoquinoline 8-monooxygenase (OMO) and Carbazole ...
 19-115 3.75e-04

Rieske non-heme iron oxygenase (RO) family, 2-Oxoquinoline 8-monooxygenase (OMO) and Carbazole 1,9a-dioxygenase (CARDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OMO catalyzes the NADH-dependent oxidation of the N-heterocyclic aromatic compound 2-oxoquinoline to 8-hydroxy-2-oxoquinoline, the second step in the bacterial degradation of quinoline. OMO consists of a reductase component (OMR) and an oxygenase component (OMO) that together function to shuttle electrons from the reduced pyridine nucleotide to the active site of OMO, where O2 activation and 2-oxoquinoline hydroxylation occurs. CARDO, which contains oxygenase (CARDO-O), ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R) components, catalyzes the dihydroxylation at the C1 and C9a positions of carbazole. The oxygenase component of OMO and CARDO contain only alpha subunits arranged in a trimeric structure.


Pssm-ID: 239617 [Multi-domain]  Cd Length: 136  Bit Score: 38.17  E-value: 3.75e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006   19 EVIVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGFV-CSYHGWGFG-SNGELQSV---PfEKELYGDAikkkclGLKE 93
Cdd:cd03548  37 EPILLRRVDGKVYALKDRCLHRGVPLSKKPECFTKGTItCWYHGWTYRlDDGKLVTIlanP-DDPLIGRT------GLKT 109

                        90       100
                ....*....|....*....|....*.
gi 4235006   94 VPrVESFHG--FIYGCFD--AEAPPL 115
Cdd:cd03548 110 YP-VEEAKGmiFVFVGDGdyADPPPL 134
Rieske_RO_Alpha_KSH cd03531
The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase ...
 19-77 3.94e-04

The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase component of 3-ketosteroid 9-alpha-hydroxylase (KSH). The terminal oxygenase component of KSH is a key enzyme in the microbial steroid degradation pathway, catalyzing the 9 alpha-hydroxylation of 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD). KSH is a two-component class IA monooxygenase, with terminal oxygenase (KshA) and oxygenase reductase (KshB) components. KSH activity has been found in many actino- and proteo- bacterial genera including Rhodococcus, Nocardia, Arthrobacter, Mycobacterium, and Burkholderia.


Pssm-ID: 239607 [Multi-domain]  Cd Length: 115  Bit Score: 37.78  E-value: 3.94e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 4235006   19 EVIVSRQNDGSVRAFLNVCRHRGKTLVNaeaGNAKG--FVCSYHGWGFGSNGELQSVPFEK 77
Cdd:cd03531  25 KLVVFADSDGALNVLDAYCRHMGGDLSQ---GTVKGdeIACPFHDWRWGGDGRCKAIPYAR 82
Rieske_RO_Alpha_PhDO_like cd03479
Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, ...
 4-87 8.12e-04

Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3,4-dioxygenase (CBDO), phenoxybenzoate dioxygenase (POB-dioxygenase) and 3-nitrobenzoate oxygenase (MnbA). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. PhDO and CBDO are two-component RO systems, containing oxygenase and reductase components. PhDO catalyzes the dihydroxylation of phthalate to form the 4,5-dihydro-cis-dihydrodiol of phthalate (DHD). CBDO, together with CbaC dehydrogenase, converts the environmental pollutant 3CBA to protocatechuate (PCA) and 5-Cl-PCA, which are then metabolized by the chromosomal PCA meta (extradiol) ring fission pathway. POB-dioxygenase catalyzes the initial catabolic step in the angular dioxygenation of phenoxybenzoate, converting mono- and dichlorinated phenoxybenzoates to protocatechuate and chlorophenols. These phenoxybenzoates are metabolic products formed during the degradation of pyrethroid insecticides.


Pssm-ID: 239561 [Multi-domain]  Cd Length: 144  Bit Score: 37.23  E-value: 8.12e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4235006    4 IPSPGDYVTAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLV---NAEAGnakgFVCSYHGWGFGSNGELQSVPFEKEly 80
Cdd:cd03479  31 LTEDGQPVRVRLLGEDLVAFRDTSGRVGLLDEHCPHRGASLVfgrVEECG----LRCCYHGWKFDVDGQCLEMPSEPP-- 104


                ....*..
gi 4235006   81 GDAIKKK 87
Cdd:cd03479 105 DSQLKQK 111
NirD COG2146
Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion ...
 7-64 1.25e-03

Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 441749 [Multi-domain]  Cd Length: 103  Bit Score: 36.36  E-value: 1.25e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4235006    7 PGDYVTAKMGVDEVIVSRqNDGSVRAFLNVCRHRGKTLvnaeagnAKGFV------CSYHGWGF 64
Cdd:COG2146  14 EGGGVVVEVGGKQIAVFR-TDGEVYAYDNRCPHQGAPL-------SEGIVdggvvtCPLHGARF 69
PLN02281 PLN02281
chlorophyllide a oxygenase
 21-79 2.25e-03

chlorophyllide a oxygenase


Pssm-ID: 177920 [Multi-domain]  Cd Length: 536  Bit Score: 37.02  E-value: 2.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 4235006    21 IVSRQNDGSVRAFLNVCRHRGKTLvNAEAGNAKGFVCSYHGWGFGSNGELQSVPFEKEL 79
Cdd:PLN02281 246 VIFRGEDGKPGCVRNTCAHRACPL-DLGTVNEGRIQCPYHGWEYSTDGECKKMPSTKLL 303
PLN00095 PLN00095
chlorophyllide a oxygenase; Provisional
 21-85 2.43e-03

chlorophyllide a oxygenase; Provisional


Pssm-ID: 165668 [Multi-domain]  Cd Length: 394  Bit Score: 36.97  E-value: 2.43e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4235006    21 IVSRQNDGSVRAFLNVCRHRGKTLVNAEAGNAKGfVCSYHGWGFGSNGELQSVP----FEKELYGDAIK 85
Cdd:PLN00095  99 VLFRDADGEAGCIKDECAHRACPLSLGKLVDGKA-QCPYHGWEYETGGECAKMPsckkFLKGVFADAAP 166
 
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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