flavin biosynthesis I

MetaCyc:RIBOSYN2-PWY

Flavin biosynthesis I converts GTP into 5-amino-6-(5-phospho-D-ribitylamino)uracil, dephosphorylates that intermediate, condenses it with the D-ribulose 5-phosphate-derived precursor (2S)-2-hydroxy-3-oxobutyl phosphate to form 6,7-dimethyl-8-(1-D-ribityl)lumazine, and then forms riboflavin, FMN, and FAD.

Pathway type

cofactor biosynthesis

Organism scope

Escherichia coli NCBITaxon:562

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Pathway network

52 nodes · 84 asserted directed edges

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Escherichia coli `NCBITaxon:562`	taxon
GTP cyclohydrolase II `EC:3.5.4.25`	molecular activity
diaminohydroxyphosphoribosylaminopyrimidine deaminase `EC:3.5.4.26`	molecular activity
5-amino-6-(5-phosphoribosylamino)uracil reductase `EC:1.1.1.193`	molecular activity
3,4-dihydroxy-2-butanone 4-phosphate synthase `EC:4.1.99.12`	molecular activity
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase `EC:3.1.3.104`	molecular activity
6,7-dimethyl-8-ribityllumazine synthase `EC:2.5.1.78`	molecular activity
riboflavin synthase `EC:2.5.1.9`	molecular activity
riboflavin kinase `EC:2.7.1.26`	molecular activity
FAD synthase `EC:2.7.7.2`	molecular activity
GTP `CHEBI:37565`	small molecule
H2O `CHEBI:15377`	small molecule
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine `CHEBI:58614`	small molecule
formate `CHEBI:15740`	small molecule
phosphate `CHEBI:43474`	small molecule
H(+) `CHEBI:15378`	small molecule
5-amino-6-(5-phospho-D-ribosylamino)uracil `CHEBI:58453`	small molecule
NH4(+) `CHEBI:28938`	small molecule
5-amino-6-(5-phospho-D-ribitylamino)uracil `CHEBI:58421`	small molecule
NADPH `CHEBI:57783`	small molecule
NADP(+) `CHEBI:58349`	small molecule
D-ribulose 5-phosphate `CHEBI:58121`	small molecule
(2S)-2-hydroxy-3-oxobutyl phosphate `CHEBI:58830`	small molecule
5-amino-6-(D-ribitylamino)uracil `CHEBI:15934`	small molecule
6,7-dimethyl-8-(1-D-ribityl)lumazine `CHEBI:58201`	small molecule
riboflavin `CHEBI:57986`	small molecule
ATP `CHEBI:30616`	small molecule
FMN `CHEBI:58210`	small molecule
ADP `CHEBI:456216`	small molecule
FAD `CHEBI:57692`	small molecule
diphosphate `CHEBI:33019`	small molecule
GTP cyclohydrolase-2 `UniProtKB:P0A7I7`	protein
zinc(2+) `CHEBI:29105`	cofactor
3,4-dihydroxy-2-butanone 4-phosphate synthase `UniProtKB:P0A7J0`	protein
plasma membrane `GO:0005886`	cellular component
magnesium(2+) `CHEBI:18420`	cofactor
manganese(2+) `CHEBI:29035`	cofactor
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB `UniProtKB:P0ADP0`	protein
cobalt(2+) `CHEBI:48828`	cofactor
Riboflavin synthase `UniProtKB:P0AFU8`	protein
Bifunctional riboflavin kinase/FMN adenylyltransferase `UniProtKB:P0AG40`	protein
Riboflavin biosynthesis protein RibD `UniProtKB:P25539`	protein
6,7-dimethyl-8-ribityllumazine synthase `UniProtKB:P61714`	protein
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI `UniProtKB:P75809`	protein
GTP cyclohydrolase II reaction `RHEA:23705`	reaction	left to right
diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction `RHEA:21869`	reaction	left to right
5-amino-6-(5-phosphoribosylamino)uracil reductase reaction `RHEA:17847`	reaction	right to left
3,4-dihydroxy-2-butanone 4-phosphate synthase reaction `RHEA:18458`	reaction	left to right
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction `RHEA:25198`	reaction	left to right
6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	reaction	left to right
riboflavin synthase reaction `RHEA:20773`	reaction	left to right
riboflavin kinase reaction `RHEA:14358`	reaction	left to right
FAD synthase reaction `RHEA:17238`	reaction	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
H2O `CHEBI:15377`	consumes	GTP cyclohydrolase II reaction `RHEA:23705`	RHEA:23705 Source assertion: Rhea lists CHEBI:15377 on the substrates side of RHEA:23705 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/23705']/rh:substrates; rh:contains/rh:compound/rh:accession`
GTP `CHEBI:37565`	consumes	GTP cyclohydrolase II reaction `RHEA:23705`	RHEA:23705 Source assertion: Rhea lists CHEBI:37565 on the substrates side of RHEA:23705 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/23705']/rh:substrates; rh:contains/rh:compound/rh:accession`
GTP cyclohydrolase II reaction `RHEA:23705`	produces	H(+) `CHEBI:15378`	RHEA:23705 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:23705 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/23705']/rh:products; rh:contains/rh:compound/rh:accession`
GTP cyclohydrolase II reaction `RHEA:23705`	produces	formate `CHEBI:15740`	RHEA:23705 Source assertion: Rhea lists CHEBI:15740 on the products side of RHEA:23705 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/23705']/rh:products; rh:contains/rh:compound/rh:accession`
GTP cyclohydrolase II reaction `RHEA:23705`	produces	phosphate `CHEBI:43474`	RHEA:23705 Source assertion: Rhea lists CHEBI:43474 on the products side of RHEA:23705 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/23705']/rh:products; rh:contains/rh:compound/rh:accession`
GTP cyclohydrolase II reaction `RHEA:23705`	produces	2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine `CHEBI:58614`	RHEA:23705 Source assertion: Rhea lists CHEBI:58614 on the products side of RHEA:23705 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/23705']/rh:products; rh:contains/rh:compound/rh:accession`
H2O `CHEBI:15377`	consumes	diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction `RHEA:21869`	RHEA:21869 Source assertion: Rhea lists CHEBI:15377 on the substrates side of RHEA:21869 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21869']/rh:substrates; rh:contains/rh:compound/rh:accession`
H(+) `CHEBI:15378`	consumes	diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction `RHEA:21869`	RHEA:21869 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:21869 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21869']/rh:substrates; rh:contains/rh:compound/rh:accession`
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine `CHEBI:58614`	consumes	diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction `RHEA:21869`	RHEA:21869 Source assertion: Rhea lists CHEBI:58614 on the substrates side of RHEA:21869 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21869']/rh:substrates; rh:contains/rh:compound/rh:accession`
diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction `RHEA:21869`	produces	NH4(+) `CHEBI:28938`	RHEA:21869 Source assertion: Rhea lists CHEBI:28938 on the products side of RHEA:21869 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21869']/rh:products; rh:contains/rh:compound/rh:accession`
diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction `RHEA:21869`	produces	5-amino-6-(5-phospho-D-ribosylamino)uracil `CHEBI:58453`	RHEA:21869 Source assertion: Rhea lists CHEBI:58453 on the products side of RHEA:21869 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21869']/rh:products; rh:contains/rh:compound/rh:accession`
H(+) `CHEBI:15378`	consumes	5-amino-6-(5-phosphoribosylamino)uracil reductase reaction `RHEA:17847`	RHEA:17847 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:17847 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17847']/rh:substrates; rh:contains/rh:compound/rh:accession`
NADPH `CHEBI:57783`	consumes	5-amino-6-(5-phosphoribosylamino)uracil reductase reaction `RHEA:17847`	RHEA:17847 Source assertion: Rhea lists CHEBI:57783 on the substrates side of RHEA:17847 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17847']/rh:substrates; rh:contains/rh:compound/rh:accession`
5-amino-6-(5-phospho-D-ribosylamino)uracil `CHEBI:58453`	consumes	5-amino-6-(5-phosphoribosylamino)uracil reductase reaction `RHEA:17847`	RHEA:17847 Source assertion: Rhea lists CHEBI:58453 on the substrates side of RHEA:17847 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17847']/rh:substrates; rh:contains/rh:compound/rh:accession`
5-amino-6-(5-phosphoribosylamino)uracil reductase reaction `RHEA:17847`	produces	NADP(+) `CHEBI:58349`	RHEA:17847 Source assertion: Rhea lists CHEBI:58349 on the products side of RHEA:17847 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17847']/rh:products; rh:contains/rh:compound/rh:accession`
5-amino-6-(5-phosphoribosylamino)uracil reductase reaction `RHEA:17847`	produces	5-amino-6-(5-phospho-D-ribitylamino)uracil `CHEBI:58421`	RHEA:17847 Source assertion: Rhea lists CHEBI:58421 on the products side of RHEA:17847 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17847']/rh:products; rh:contains/rh:compound/rh:accession`
D-ribulose 5-phosphate `CHEBI:58121`	consumes	3,4-dihydroxy-2-butanone 4-phosphate synthase reaction `RHEA:18458`	RHEA:18458 Source assertion: Rhea lists CHEBI:58121 on the substrates side of RHEA:18458 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18458']/rh:substrates; rh:contains/rh:compound/rh:accession`
3,4-dihydroxy-2-butanone 4-phosphate synthase reaction `RHEA:18458`	produces	H(+) `CHEBI:15378`	RHEA:18458 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:18458 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18458']/rh:products; rh:contains/rh:compound/rh:accession`
3,4-dihydroxy-2-butanone 4-phosphate synthase reaction `RHEA:18458`	produces	formate `CHEBI:15740`	RHEA:18458 Source assertion: Rhea lists CHEBI:15740 on the products side of RHEA:18458 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18458']/rh:products; rh:contains/rh:compound/rh:accession`
3,4-dihydroxy-2-butanone 4-phosphate synthase reaction `RHEA:18458`	produces	(2S)-2-hydroxy-3-oxobutyl phosphate `CHEBI:58830`	RHEA:18458 Source assertion: Rhea lists CHEBI:58830 on the products side of RHEA:18458 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18458']/rh:products; rh:contains/rh:compound/rh:accession`
H2O `CHEBI:15377`	consumes	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction `RHEA:25198`	RHEA:25198 Source assertion: Rhea lists CHEBI:15377 on the substrates side of RHEA:25198 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/25198']/rh:substrates; rh:contains/rh:compound/rh:accession`
5-amino-6-(5-phospho-D-ribitylamino)uracil `CHEBI:58421`	consumes	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction `RHEA:25198`	RHEA:25198 Source assertion: Rhea lists CHEBI:58421 on the substrates side of RHEA:25198 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/25198']/rh:substrates; rh:contains/rh:compound/rh:accession`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction `RHEA:25198`	produces	5-amino-6-(D-ribitylamino)uracil `CHEBI:15934`	RHEA:25198 Source assertion: Rhea lists CHEBI:15934 on the products side of RHEA:25198 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/25198']/rh:products; rh:contains/rh:compound/rh:accession`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction `RHEA:25198`	produces	phosphate `CHEBI:43474`	RHEA:25198 Source assertion: Rhea lists CHEBI:43474 on the products side of RHEA:25198 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/25198']/rh:products; rh:contains/rh:compound/rh:accession`
5-amino-6-(D-ribitylamino)uracil `CHEBI:15934`	consumes	6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	RHEA:26153 Source assertion: Rhea lists CHEBI:15934 on the substrates side of RHEA:26153 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/26153']/rh:substrates; rh:contains/rh:compound/rh:accession`
(2S)-2-hydroxy-3-oxobutyl phosphate `CHEBI:58830`	consumes	6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	RHEA:26153 Source assertion: Rhea lists CHEBI:58830 on the substrates side of RHEA:26153 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/26153']/rh:substrates; rh:contains/rh:compound/rh:accession`
6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	produces	H2O `CHEBI:15377`	RHEA:26153 Source assertion: Rhea lists CHEBI:15377 on the products side of RHEA:26153 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/26153']/rh:products; rh:contains/rh:compound/rh:accession`
6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	produces	H(+) `CHEBI:15378`	RHEA:26153 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:26153 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/26153']/rh:products; rh:contains/rh:compound/rh:accession`
6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	produces	phosphate `CHEBI:43474`	RHEA:26153 Source assertion: Rhea lists CHEBI:43474 on the products side of RHEA:26153 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/26153']/rh:products; rh:contains/rh:compound/rh:accession`
6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	produces	6,7-dimethyl-8-(1-D-ribityl)lumazine `CHEBI:58201`	RHEA:26153 Source assertion: Rhea lists CHEBI:58201 on the products side of RHEA:26153 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/26153']/rh:products; rh:contains/rh:compound/rh:accession`
H(+) `CHEBI:15378`	consumes	riboflavin synthase reaction `RHEA:20773`	RHEA:20773 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:20773 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/20773']/rh:substrates; rh:contains/rh:compound/rh:accession`
6,7-dimethyl-8-(1-D-ribityl)lumazine `CHEBI:58201`	consumes	riboflavin synthase reaction `RHEA:20773`	RHEA:20773 Source assertion: Rhea lists CHEBI:58201 on the substrates side of RHEA:20773 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/20773']/rh:substrates; rh:contains/rh:compound/rh:accession`
riboflavin synthase reaction `RHEA:20773`	produces	5-amino-6-(D-ribitylamino)uracil `CHEBI:15934`	RHEA:20773 Source assertion: Rhea lists CHEBI:15934 on the products side of RHEA:20773 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/20773']/rh:products; rh:contains/rh:compound/rh:accession`
riboflavin synthase reaction `RHEA:20773`	produces	riboflavin `CHEBI:57986`	RHEA:20773 Source assertion: Rhea lists CHEBI:57986 on the products side of RHEA:20773 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/20773']/rh:products; rh:contains/rh:compound/rh:accession`
ATP `CHEBI:30616`	consumes	riboflavin kinase reaction `RHEA:14358`	RHEA:14358 Source assertion: Rhea lists CHEBI:30616 on the substrates side of RHEA:14358 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/14358']/rh:substrates; rh:contains/rh:compound/rh:accession`
riboflavin `CHEBI:57986`	consumes	riboflavin kinase reaction `RHEA:14358`	RHEA:14358 Source assertion: Rhea lists CHEBI:57986 on the substrates side of RHEA:14358 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/14358']/rh:substrates; rh:contains/rh:compound/rh:accession`
riboflavin kinase reaction `RHEA:14358`	produces	H(+) `CHEBI:15378`	RHEA:14358 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:14358 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/14358']/rh:products; rh:contains/rh:compound/rh:accession`
riboflavin kinase reaction `RHEA:14358`	produces	ADP `CHEBI:456216`	RHEA:14358 Source assertion: Rhea lists CHEBI:456216 on the products side of RHEA:14358 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/14358']/rh:products; rh:contains/rh:compound/rh:accession`
riboflavin kinase reaction `RHEA:14358`	produces	FMN `CHEBI:58210`	RHEA:14358 Source assertion: Rhea lists CHEBI:58210 on the products side of RHEA:14358 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/14358']/rh:products; rh:contains/rh:compound/rh:accession`
H(+) `CHEBI:15378`	consumes	FAD synthase reaction `RHEA:17238`	RHEA:17238 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:17238 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17238']/rh:substrates; rh:contains/rh:compound/rh:accession`
ATP `CHEBI:30616`	consumes	FAD synthase reaction `RHEA:17238`	RHEA:17238 Source assertion: Rhea lists CHEBI:30616 on the substrates side of RHEA:17238 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17238']/rh:substrates; rh:contains/rh:compound/rh:accession`
FMN `CHEBI:58210`	consumes	FAD synthase reaction `RHEA:17238`	RHEA:17238 Source assertion: Rhea lists CHEBI:58210 on the substrates side of RHEA:17238 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17238']/rh:substrates; rh:contains/rh:compound/rh:accession`
FAD synthase reaction `RHEA:17238`	produces	diphosphate `CHEBI:33019`	RHEA:17238 Source assertion: Rhea lists CHEBI:33019 on the products side of RHEA:17238 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17238']/rh:products; rh:contains/rh:compound/rh:accession`
FAD synthase reaction `RHEA:17238`	produces	FAD `CHEBI:57692`	RHEA:17238 Source assertion: Rhea lists CHEBI:57692 on the products side of RHEA:17238 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17238']/rh:products; rh:contains/rh:compound/rh:accession`
GTP cyclohydrolase II `EC:3.5.4.25`	catalyzes	GTP cyclohydrolase II reaction `RHEA:23705`	RHEA:23704 Source assertion: Rhea associates EC:3.5.4.25 with the reaction family containing RHEA:23705. Source location `rh:ec`
diaminohydroxyphosphoribosylaminopyrimidine deaminase `EC:3.5.4.26`	catalyzes	diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction `RHEA:21869`	RHEA:21868 Source assertion: Rhea associates EC:3.5.4.26 with the reaction family containing RHEA:21869. Source location `rh:ec`
5-amino-6-(5-phosphoribosylamino)uracil reductase `EC:1.1.1.193`	catalyzes	5-amino-6-(5-phosphoribosylamino)uracil reductase reaction `RHEA:17847`	RHEA:17845 Source assertion: Rhea associates EC:1.1.1.193 with the reaction family containing RHEA:17847. Source location `rh:ec`
3,4-dihydroxy-2-butanone 4-phosphate synthase `EC:4.1.99.12`	catalyzes	3,4-dihydroxy-2-butanone 4-phosphate synthase reaction `RHEA:18458`	RHEA:18457 Source assertion: Rhea associates EC:4.1.99.12 with the reaction family containing RHEA:18458. Source location `rh:ec`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase `EC:3.1.3.104`	catalyzes	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction `RHEA:25198`	RHEA:25197 Source assertion: Rhea associates EC:3.1.3.104 with the reaction family containing RHEA:25198. Source location `rh:ec`
6,7-dimethyl-8-ribityllumazine synthase `EC:2.5.1.78`	catalyzes	6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	RHEA:26152 Source assertion: Rhea associates EC:2.5.1.78 with the reaction family containing RHEA:26153. Source location `rh:ec`
riboflavin synthase `EC:2.5.1.9`	catalyzes	riboflavin synthase reaction `RHEA:20773`	RHEA:20772 Source assertion: Rhea associates EC:2.5.1.9 with the reaction family containing RHEA:20773. Source location `rh:ec`
riboflavin kinase `EC:2.7.1.26`	catalyzes	riboflavin kinase reaction `RHEA:14358`	RHEA:14357 Source assertion: Rhea associates EC:2.7.1.26 with the reaction family containing RHEA:14358. Source location `rh:ec`
FAD synthase `EC:2.7.7.2`	catalyzes	FAD synthase reaction `RHEA:17238`	RHEA:17237 Source assertion: Rhea associates EC:2.7.7.2 with the reaction family containing RHEA:17238. Source location `rh:ec`
riboflavin kinase reaction `RHEA:14358`	precedes	FAD synthase reaction `RHEA:17238`	MetaCyc:RIBOSYN2-PWY Source assertion: MetaCyc pathway ordering places RHEA:14358 before RHEA:17238 in this pathway. Shared intermediate: CHEBI:58210. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
5-amino-6-(5-phosphoribosylamino)uracil reductase reaction `RHEA:17847`	precedes	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction `RHEA:25198`	MetaCyc:RIBOSYN2-PWY Source assertion: MetaCyc pathway ordering places RHEA:17847 before RHEA:25198 in this pathway. Shared intermediate: CHEBI:58421. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
3,4-dihydroxy-2-butanone 4-phosphate synthase reaction `RHEA:18458`	precedes	6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	MetaCyc:RIBOSYN2-PWY Source assertion: MetaCyc pathway ordering places RHEA:18458 before RHEA:26153 in this pathway. Shared intermediate: CHEBI:58830. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
riboflavin synthase reaction `RHEA:20773`	precedes	riboflavin kinase reaction `RHEA:14358`	MetaCyc:RIBOSYN2-PWY Source assertion: MetaCyc pathway ordering places RHEA:20773 before RHEA:14358 in this pathway. Shared intermediate: CHEBI:57986. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction `RHEA:21869`	precedes	5-amino-6-(5-phosphoribosylamino)uracil reductase reaction `RHEA:17847`	MetaCyc:RIBOSYN2-PWY Source assertion: MetaCyc pathway ordering places RHEA:21869 before RHEA:17847 in this pathway. Shared intermediate: CHEBI:58453. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
GTP cyclohydrolase II reaction `RHEA:23705`	precedes	diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction `RHEA:21869`	MetaCyc:RIBOSYN2-PWY Source assertion: MetaCyc pathway ordering places RHEA:23705 before RHEA:21869 in this pathway. Shared intermediate: CHEBI:58614. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction `RHEA:25198`	precedes	6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	MetaCyc:RIBOSYN2-PWY Source assertion: MetaCyc pathway ordering places RHEA:25198 before RHEA:26153 in this pathway. Shared intermediate: CHEBI:15934. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	precedes	riboflavin synthase reaction `RHEA:20773`	MetaCyc:RIBOSYN2-PWY Source assertion: MetaCyc pathway ordering places RHEA:26153 before RHEA:20773 in this pathway. Shared intermediate: CHEBI:58201. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
GTP cyclohydrolase-2 `UniProtKB:P0A7I7`	enables	GTP cyclohydrolase II reaction `RHEA:23705`	UniProtKB:P0A7I7 Source assertion: UniProt annotates UniProtKB:P0A7I7 with catalytic activity for the reaction family of RHEA:23705. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
GTP cyclohydrolase-2 `UniProtKB:P0A7I7`	has_cofactor	zinc(2+) `CHEBI:29105`	UniProtKB:P0A7I7 Source assertion: UniProt lists CHEBI:29105 as a cofactor of UniProtKB:P0A7I7 (evidence: ECO:0000269). Binds 1 zinc ion per subunit. Source location `comments[commentType='COFACTOR'].cofactors and note`
3,4-dihydroxy-2-butanone 4-phosphate synthase `UniProtKB:P0A7J0`	enables	3,4-dihydroxy-2-butanone 4-phosphate synthase reaction `RHEA:18458`	UniProtKB:P0A7J0 Source assertion: UniProt annotates UniProtKB:P0A7J0 with catalytic activity for the reaction family of RHEA:18458. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
3,4-dihydroxy-2-butanone 4-phosphate synthase `UniProtKB:P0A7J0`	located_in	plasma membrane `GO:0005886`	UniProtKB:P0A7J0 Source assertion: UniProt locates UniProtKB:P0A7J0 in Cell membrane (SL-0039, mapped by UniProt to GO:0005886). Annotation evidence: ECO:0000305. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
3,4-dihydroxy-2-butanone 4-phosphate synthase `UniProtKB:P0A7J0`	has_cofactor	magnesium(2+) `CHEBI:18420`	UniProtKB:P0A7J0 Source assertion: UniProt lists CHEBI:18420 as a cofactor of UniProtKB:P0A7J0 (evidence: ECO:0000269). Binds 2 divalent metal cations per subunit. Magnesium or manganese. Source location `comments[commentType='COFACTOR'].cofactors and note`
3,4-dihydroxy-2-butanone 4-phosphate synthase `UniProtKB:P0A7J0`	has_cofactor	manganese(2+) `CHEBI:29035`	UniProtKB:P0A7J0 Source assertion: UniProt lists CHEBI:29035 as a cofactor of UniProtKB:P0A7J0 (evidence: ECO:0000255). Binds 2 divalent metal cations per subunit. Magnesium or manganese. Source location `comments[commentType='COFACTOR'].cofactors and note`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB `UniProtKB:P0ADP0`	enables	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction `RHEA:25198`	UniProtKB:P0ADP0 Source assertion: UniProt annotates UniProtKB:P0ADP0 with catalytic activity for the reaction family of RHEA:25198. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB `UniProtKB:P0ADP0`	has_cofactor	magnesium(2+) `CHEBI:18420`	UniProtKB:P0ADP0 Source assertion: UniProt lists CHEBI:18420 as a cofactor of UniProtKB:P0ADP0 (evidence: ECO:0000269). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc. Source location `comments[commentType='COFACTOR'].cofactors and note`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB `UniProtKB:P0ADP0`	has_cofactor	manganese(2+) `CHEBI:29035`	UniProtKB:P0ADP0 Source assertion: UniProt lists CHEBI:29035 as a cofactor of UniProtKB:P0ADP0 (evidence: ECO:0000269). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc. Source location `comments[commentType='COFACTOR'].cofactors and note`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB `UniProtKB:P0ADP0`	has_cofactor	cobalt(2+) `CHEBI:48828`	UniProtKB:P0ADP0 Source assertion: UniProt lists CHEBI:48828 as a cofactor of UniProtKB:P0ADP0 (evidence: ECO:0000269). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc. Source location `comments[commentType='COFACTOR'].cofactors and note`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB `UniProtKB:P0ADP0`	has_cofactor	zinc(2+) `CHEBI:29105`	UniProtKB:P0ADP0 Source assertion: UniProt lists CHEBI:29105 as a cofactor of UniProtKB:P0ADP0 (evidence: ECO:0000269). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc. Source location `comments[commentType='COFACTOR'].cofactors and note`
Riboflavin synthase `UniProtKB:P0AFU8`	enables	riboflavin synthase reaction `RHEA:20773`	UniProtKB:P0AFU8 Source assertion: UniProt annotates UniProtKB:P0AFU8 with catalytic activity for the reaction family of RHEA:20773. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Bifunctional riboflavin kinase/FMN adenylyltransferase `UniProtKB:P0AG40`	enables	riboflavin kinase reaction `RHEA:14358`	UniProtKB:P0AG40 Source assertion: UniProt annotates UniProtKB:P0AG40 with catalytic activity for the reaction family of RHEA:14358. Annotation evidence: ECO:0000250; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Bifunctional riboflavin kinase/FMN adenylyltransferase `UniProtKB:P0AG40`	enables	FAD synthase reaction `RHEA:17238`	UniProtKB:P0AG40 Source assertion: UniProt annotates UniProtKB:P0AG40 with catalytic activity for the reaction family of RHEA:17238. Annotation evidence: ECO:0000250; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Riboflavin biosynthesis protein RibD `UniProtKB:P25539`	enables	diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction `RHEA:21869`	UniProtKB:P25539 Source assertion: UniProt annotates UniProtKB:P25539 with catalytic activity for the reaction family of RHEA:21869. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Riboflavin biosynthesis protein RibD `UniProtKB:P25539`	enables	5-amino-6-(5-phosphoribosylamino)uracil reductase reaction `RHEA:17847`	UniProtKB:P25539 Source assertion: UniProt annotates UniProtKB:P25539 with catalytic activity for the reaction family of RHEA:17847. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Riboflavin biosynthesis protein RibD `UniProtKB:P25539`	has_cofactor	zinc(2+) `CHEBI:29105`	UniProtKB:P25539 Source assertion: UniProt lists CHEBI:29105 as a cofactor of UniProtKB:P25539 (evidence: ECO:0000250). Binds 1 zinc ion. Source location `comments[commentType='COFACTOR'].cofactors and note`
6,7-dimethyl-8-ribityllumazine synthase `UniProtKB:P61714`	enables	6,7-dimethyl-8-ribityllumazine synthase reaction `RHEA:26153`	UniProtKB:P61714 Source assertion: UniProt annotates UniProtKB:P61714 with catalytic activity for the reaction family of RHEA:26153. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI `UniProtKB:P75809`	enables	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction `RHEA:25198`	UniProtKB:P75809 Source assertion: UniProt annotates UniProtKB:P75809 with catalytic activity for the reaction family of RHEA:25198. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI `UniProtKB:P75809`	has_cofactor	magnesium(2+) `CHEBI:18420`	UniProtKB:P75809 Source assertion: UniProt lists CHEBI:18420 as a cofactor of UniProtKB:P75809 (evidence: ECO:0000269). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc. Source location `comments[commentType='COFACTOR'].cofactors and note`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI `UniProtKB:P75809`	has_cofactor	manganese(2+) `CHEBI:29035`	UniProtKB:P75809 Source assertion: UniProt lists CHEBI:29035 as a cofactor of UniProtKB:P75809 (evidence: ECO:0000269). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc. Source location `comments[commentType='COFACTOR'].cofactors and note`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI `UniProtKB:P75809`	has_cofactor	cobalt(2+) `CHEBI:48828`	UniProtKB:P75809 Source assertion: UniProt lists CHEBI:48828 as a cofactor of UniProtKB:P75809 (evidence: ECO:0000269). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc. Source location `comments[commentType='COFACTOR'].cofactors and note`
5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI `UniProtKB:P75809`	has_cofactor	zinc(2+) `CHEBI:29105`	UniProtKB:P75809 Source assertion: UniProt lists CHEBI:29105 as a cofactor of UniProtKB:P75809 (evidence: ECO:0000269). Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc. Source location `comments[commentType='COFACTOR'].cofactors and note`

References

MetaCyc:RIBOSYN2-PWY MetaCyc flavin biosynthesis I pathway (source version: 22.5)
RHEA:23704 Rhea GTP cyclohydrolase II reaction (source version: 139)
RHEA:23705 Rhea 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine-forming direction (source version: 139)
RHEA:21868 Rhea diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction (source version: 139)
RHEA:21869 Rhea 5-amino-6-(5-phospho-D-ribosylamino)uracil-forming direction (source version: 139)
RHEA:17845 Rhea 5-amino-6-(5-phosphoribosylamino)uracil reductase reaction (source version: 139)
RHEA:17847 Rhea 5-amino-6-(5-phospho-D-ribitylamino)uracil-forming direction (source version: 139)
RHEA:18457 Rhea 3,4-dihydroxy-2-butanone 4-phosphate synthase reaction (source version: 139)
RHEA:18458 Rhea (2S)-2-hydroxy-3-oxobutyl phosphate-forming direction (source version: 139)
RHEA:25197 Rhea 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction (source version: 139)
RHEA:25198 Rhea 5-amino-6-(D-ribitylamino)uracil-forming direction (source version: 139)
RHEA:26152 Rhea 6,7-dimethyl-8-ribityllumazine synthase reaction (source version: 139)
RHEA:26153 Rhea 6,7-dimethyl-8-(1-D-ribityl)lumazine-forming direction (source version: 139)
RHEA:20772 Rhea riboflavin synthase reaction (source version: 139)
RHEA:20773 Rhea riboflavin-forming direction (source version: 139)
RHEA:14357 Rhea riboflavin kinase reaction (source version: 139)
RHEA:14358 Rhea FMN-forming direction (source version: 139)
RHEA:17237 Rhea FAD synthase reaction (source version: 139)
RHEA:17238 Rhea FAD-forming direction (source version: 139)
UniProtKB:P0A7I7 UniProtKB:P0A7I7 authority record (source version: 2026_03)
UniProtKB:P0A7J0 UniProtKB:P0A7J0 authority record (source version: 2026_03)
UniProtKB:P0ADP0 UniProtKB:P0ADP0 authority record (source version: 2026_03)
UniProtKB:P0AFU8 UniProtKB:P0AFU8 authority record (source version: 2026_03)
UniProtKB:P0AG40 UniProtKB:P0AG40 authority record (source version: 2026_03)
UniProtKB:P25539 UniProtKB:P25539 authority record (source version: 2026_03)
UniProtKB:P61714 UniProtKB:P61714 authority record (source version: 2026_03)
UniProtKB:P75809 UniProtKB:P75809 authority record (source version: 2026_03)

Curation history

2026-10-05T06:25:52Z codex
- EDIT — Review causal chemistry and add sourced molecular context
  Reviewed the entire record against MetaCyc 22.5 native pathway XML (including nested pathways), Rhea 139 explicit sides and directions, ENZYME 02-Sep-2026, PubMed records, and reviewed UniProt 2026_03 annotations within the record's taxon scope. Replaced generated structured-source quotations with source_assertion and source_locator. Typed molecular activities and participants. Reaction count 9 to 9; 0 directed-ID corrections; 8 protein annotations, 12 cofactor annotations and 1 sourced locations. All Rhea reaction substrate/product sets checked against independent Rhea authority; native pathway leaf coverage and source exceptions recorded in reports/causal_graph_review/metacyc-review.json. Full source URLs, versions and byte hashes are in metacyc-sources.json. All 50 MetaCyc records passed native schema validation; six targeted chemistry/evidence regression tests passed. Missing protein or cofactor annotations are not treated as biological absence; qualifications and exclusions are preserved in the ledger.
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