uracil degradation III

MetaCyc:PWY0-1471

The complete Rut chemical route converts uracil to two ammonium ions, carbon dioxide and 3-hydroxypropionate, with FMN recycling. This E. coli K-12 reconstruction updates the older MetaCyc peracid model using measured RutA/RutF, RutB, RutC and YdfG activities. RutA is represented by the current net reaction, including spontaneous NADH reduction of its flavin-N5-oxide product; enzyme-bound intermediates are not separate pathway metabolites. RutC is a homotrimer that accelerates 3-aminoacrylate deamination, which also occurs spontaneously. Carbamate decay is spontaneous; the proposed RutD contribution remains unmeasured. YdfG provides directly demonstrated terminal reduction, while the alternative RutE assignment and its FMN cofactor remain qualified predictions. NCM3722 and derivative experiments establish nitrogen utilization near room temperature, not unrestricted growth at 37°C or carbon assimilation. The 2021 polarity controls show that RutC and RutD are not essential under the tested conditions. Upstream transport and nucleoside cleavage, thymine catabolism and regulatory circuitry are outside this uracil-route boundary.

Pathway type

uracil catabolism rut pathway

Organism scope

Escherichia coli K-12 NCBITaxon:83333

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Pathway network

31 nodes · 53 asserted directed edges

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Reaction / activity
Chemical / cofactor
Protein / complex
Pathway
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Dashed arrow: membership, location or cofactor relation

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Escherichia coli K-12 `NCBITaxon:83333`	taxon
FMN(3-) `CHEBI:58210`	cofactor
NADH(2-) `CHEBI:57945`	cofactor
hydron `CHEBI:15378`	small molecule
FMNH2(2-) `CHEBI:57618`	cofactor
NAD(1-) `CHEBI:57540`	cofactor
uracil `CHEBI:17568`	small molecule
dioxygen `CHEBI:15379`	small molecule
ureidoacrylate `CHEBI:59891`	small molecule
water `CHEBI:15377`	small molecule
(Z)-3-aminoacrylate `CHEBI:59894`	small molecule
carbamate `CHEBI:13941`	small molecule
ammonium `CHEBI:28938`	small molecule
carbon dioxide `CHEBI:16526`	small molecule
3-oxopropanoate `CHEBI:33190`	small molecule
NADPH(4-) `CHEBI:57783`	cofactor
3-hydroxypropionate `CHEBI:16510`	small molecule
NADP(3-) `CHEBI:58349`	cofactor
FMN reductase (NADH) RutF `UniProtKB:P75893`	protein
Pyrimidine monooxygenase RutA `UniProtKB:P75898`	protein
Ureidoacrylate amidohydrolase RutB `UniProtKB:P75897`	protein
3-aminoacrylate deaminase RutC `UniProtKB:P0AFQ5`	protein
NADP-dependent 3-hydroxy acid dehydrogenase YdfG `UniProtKB:P39831`	protein
Probable malonic semialdehyde reductase RutE `UniProtKB:P75894`	protein
3-hydroxy acid dehydrogenase `MetaCyc:CPLX0-1962`	complex
FMN + NADH + 2 H(+) => FMNH2 + NAD(+) `RHEA:21622`	molecular activity	right to left
uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	molecular activity	left to right
(Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) `RHEA:31604`	molecular activity	left to right
carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	reaction	left to right
(Z)-3-aminoacrylate + H2O + H(+) => 3-oxopropanoate + NH4(+) `RHEA:34948`	molecular activity	left to right
3-oxopropanoate + NADPH + H(+) => 3-hydroxypropanoate + NADP(+) `RHEA:26440`	molecular activity	right to left

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
FMN(3-) `CHEBI:58210`	consumes	FMN + NADH + 2 H(+) => FMNH2 + NAD(+) `RHEA:21622`	RHEA:21622 Source assertion: Rhea RHEA:21622 places CHEBI:58210 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/21622 rh:substrates http://rdf.rhea-db.org/21620_R; http://rdf.rhea-db.org/21620_R rh:contains1 http://rdf.rhea-db.org/Participant_21620_compound_2613; http://rdf.rhea-db.org/Participant_21620_compound_2613 rh:compound http://rdf.rhea-db.org/Compound_2613; http://rdf.rhea-db.org/Compound_2613 rh:chebi`
NADH(2-) `CHEBI:57945`	consumes	FMN + NADH + 2 H(+) => FMNH2 + NAD(+) `RHEA:21622`	RHEA:21622 Source assertion: Rhea RHEA:21622 places CHEBI:57945 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/21622 rh:substrates http://rdf.rhea-db.org/21620_R; http://rdf.rhea-db.org/21620_R rh:contains1 http://rdf.rhea-db.org/Participant_21620_compound_1650; http://rdf.rhea-db.org/Participant_21620_compound_1650 rh:compound http://rdf.rhea-db.org/Compound_1650; http://rdf.rhea-db.org/Compound_1650 rh:chebi`
hydron `CHEBI:15378`	consumes	FMN + NADH + 2 H(+) => FMNH2 + NAD(+) `RHEA:21622`	RHEA:21622 Source assertion: Rhea RHEA:21622 places CHEBI:15378 on its substrates side with stoichiometric coefficient 2. Source location `http://rdf.rhea-db.org/21622 rh:substrates http://rdf.rhea-db.org/21620_R; http://rdf.rhea-db.org/21620_R rh:contains2 http://rdf.rhea-db.org/Participant_21620_compound_3249; http://rdf.rhea-db.org/Participant_21620_compound_3249 rh:compound http://rdf.rhea-db.org/Compound_3249; http://rdf.rhea-db.org/Compound_3249 rh:chebi`
FMN + NADH + 2 H(+) => FMNH2 + NAD(+) `RHEA:21622`	produces	FMNH2(2-) `CHEBI:57618`	RHEA:21622 Source assertion: Rhea RHEA:21622 places CHEBI:57618 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/21622 rh:products http://rdf.rhea-db.org/21620_L; http://rdf.rhea-db.org/21620_L rh:contains1 http://rdf.rhea-db.org/Participant_21620_compound_1829; http://rdf.rhea-db.org/Participant_21620_compound_1829 rh:compound http://rdf.rhea-db.org/Compound_1829; http://rdf.rhea-db.org/Compound_1829 rh:chebi`
FMN + NADH + 2 H(+) => FMNH2 + NAD(+) `RHEA:21622`	produces	NAD(1-) `CHEBI:57540`	RHEA:21622 Source assertion: Rhea RHEA:21622 places CHEBI:57540 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/21622 rh:products http://rdf.rhea-db.org/21620_L; http://rdf.rhea-db.org/21620_L rh:contains1 http://rdf.rhea-db.org/Participant_21620_compound_3484; http://rdf.rhea-db.org/Participant_21620_compound_3484 rh:compound http://rdf.rhea-db.org/Compound_3484; http://rdf.rhea-db.org/Compound_3484 rh:chebi`
uracil `CHEBI:17568`	consumes	uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	RHEA:31588 Source assertion: Rhea RHEA:31588 places CHEBI:17568 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31588 rh:substrates http://rdf.rhea-db.org/31587_L; http://rdf.rhea-db.org/31587_L rh:contains1 http://rdf.rhea-db.org/Participant_31587_compound_4063; http://rdf.rhea-db.org/Participant_31587_compound_4063 rh:compound http://rdf.rhea-db.org/Compound_4063; http://rdf.rhea-db.org/Compound_4063 rh:chebi`
FMNH2(2-) `CHEBI:57618`	consumes	uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	RHEA:31588 Source assertion: Rhea RHEA:31588 places CHEBI:57618 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31588 rh:substrates http://rdf.rhea-db.org/31587_L; http://rdf.rhea-db.org/31587_L rh:contains1 http://rdf.rhea-db.org/Participant_31587_compound_1829; http://rdf.rhea-db.org/Participant_31587_compound_1829 rh:compound http://rdf.rhea-db.org/Compound_1829; http://rdf.rhea-db.org/Compound_1829 rh:chebi`
NADH(2-) `CHEBI:57945`	consumes	uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	RHEA:31588 Source assertion: Rhea RHEA:31588 places CHEBI:57945 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31588 rh:substrates http://rdf.rhea-db.org/31587_L; http://rdf.rhea-db.org/31587_L rh:contains1 http://rdf.rhea-db.org/Participant_31587_compound_1650; http://rdf.rhea-db.org/Participant_31587_compound_1650 rh:compound http://rdf.rhea-db.org/Compound_1650; http://rdf.rhea-db.org/Compound_1650 rh:chebi`
dioxygen `CHEBI:15379`	consumes	uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	RHEA:31588 Source assertion: Rhea RHEA:31588 places CHEBI:15379 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31588 rh:substrates http://rdf.rhea-db.org/31587_L; http://rdf.rhea-db.org/31587_L rh:contains1 http://rdf.rhea-db.org/Participant_31587_compound_1198; http://rdf.rhea-db.org/Participant_31587_compound_1198 rh:compound http://rdf.rhea-db.org/Compound_1198; http://rdf.rhea-db.org/Compound_1198 rh:chebi`
uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	produces	ureidoacrylate `CHEBI:59891`	RHEA:31588 Source assertion: Rhea RHEA:31588 places CHEBI:59891 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31588 rh:products http://rdf.rhea-db.org/31587_R; http://rdf.rhea-db.org/31587_R rh:contains1 http://rdf.rhea-db.org/Participant_31587_compound_6882; http://rdf.rhea-db.org/Participant_31587_compound_6882 rh:compound http://rdf.rhea-db.org/Compound_6882; http://rdf.rhea-db.org/Compound_6882 rh:chebi`
uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	produces	FMN(3-) `CHEBI:58210`	RHEA:31588 Source assertion: Rhea RHEA:31588 places CHEBI:58210 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31588 rh:products http://rdf.rhea-db.org/31587_R; http://rdf.rhea-db.org/31587_R rh:contains1 http://rdf.rhea-db.org/Participant_31587_compound_2613; http://rdf.rhea-db.org/Participant_31587_compound_2613 rh:compound http://rdf.rhea-db.org/Compound_2613; http://rdf.rhea-db.org/Compound_2613 rh:chebi`
uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	produces	NAD(1-) `CHEBI:57540`	RHEA:31588 Source assertion: Rhea RHEA:31588 places CHEBI:57540 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31588 rh:products http://rdf.rhea-db.org/31587_R; http://rdf.rhea-db.org/31587_R rh:contains1 http://rdf.rhea-db.org/Participant_31587_compound_3484; http://rdf.rhea-db.org/Participant_31587_compound_3484 rh:compound http://rdf.rhea-db.org/Compound_3484; http://rdf.rhea-db.org/Compound_3484 rh:chebi`
uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	produces	water `CHEBI:15377`	RHEA:31588 Source assertion: Rhea RHEA:31588 places CHEBI:15377 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31588 rh:products http://rdf.rhea-db.org/31587_R; http://rdf.rhea-db.org/31587_R rh:contains1 http://rdf.rhea-db.org/Participant_31587_compound_1283; http://rdf.rhea-db.org/Participant_31587_compound_1283 rh:compound http://rdf.rhea-db.org/Compound_1283; http://rdf.rhea-db.org/Compound_1283 rh:chebi`
uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	produces	hydron `CHEBI:15378`	RHEA:31588 Source assertion: Rhea RHEA:31588 places CHEBI:15378 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31588 rh:products http://rdf.rhea-db.org/31587_R; http://rdf.rhea-db.org/31587_R rh:contains1 http://rdf.rhea-db.org/Participant_31587_compound_3249; http://rdf.rhea-db.org/Participant_31587_compound_3249 rh:compound http://rdf.rhea-db.org/Compound_3249; http://rdf.rhea-db.org/Compound_3249 rh:chebi`
ureidoacrylate `CHEBI:59891`	consumes	(Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) `RHEA:31604`	RHEA:31604 Source assertion: Rhea RHEA:31604 places CHEBI:59891 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31604 rh:substrates http://rdf.rhea-db.org/31603_L; http://rdf.rhea-db.org/31603_L rh:contains1 http://rdf.rhea-db.org/Participant_31603_compound_6882; http://rdf.rhea-db.org/Participant_31603_compound_6882 rh:compound http://rdf.rhea-db.org/Compound_6882; http://rdf.rhea-db.org/Compound_6882 rh:chebi`
water `CHEBI:15377`	consumes	(Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) `RHEA:31604`	RHEA:31604 Source assertion: Rhea RHEA:31604 places CHEBI:15377 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31604 rh:substrates http://rdf.rhea-db.org/31603_L; http://rdf.rhea-db.org/31603_L rh:contains1 http://rdf.rhea-db.org/Participant_31603_compound_1283; http://rdf.rhea-db.org/Participant_31603_compound_1283 rh:compound http://rdf.rhea-db.org/Compound_1283; http://rdf.rhea-db.org/Compound_1283 rh:chebi`
(Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) `RHEA:31604`	produces	(Z)-3-aminoacrylate `CHEBI:59894`	RHEA:31604 Source assertion: Rhea RHEA:31604 places CHEBI:59894 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31604 rh:products http://rdf.rhea-db.org/31603_R; http://rdf.rhea-db.org/31603_R rh:contains1 http://rdf.rhea-db.org/Participant_31603_compound_6886; http://rdf.rhea-db.org/Participant_31603_compound_6886 rh:compound http://rdf.rhea-db.org/Compound_6886; http://rdf.rhea-db.org/Compound_6886 rh:chebi`
(Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) `RHEA:31604`	produces	carbamate `CHEBI:13941`	RHEA:31604 Source assertion: Rhea RHEA:31604 places CHEBI:13941 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31604 rh:products http://rdf.rhea-db.org/31603_R; http://rdf.rhea-db.org/31603_R rh:contains1 http://rdf.rhea-db.org/Participant_31603_compound_4239; http://rdf.rhea-db.org/Participant_31603_compound_4239 rh:compound http://rdf.rhea-db.org/Compound_4239; http://rdf.rhea-db.org/Compound_4239 rh:chebi`
(Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) `RHEA:31604`	produces	hydron `CHEBI:15378`	RHEA:31604 Source assertion: Rhea RHEA:31604 places CHEBI:15378 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/31604 rh:products http://rdf.rhea-db.org/31603_R; http://rdf.rhea-db.org/31603_R rh:contains1 http://rdf.rhea-db.org/Participant_31603_compound_3249; http://rdf.rhea-db.org/Participant_31603_compound_3249 rh:compound http://rdf.rhea-db.org/Compound_3249; http://rdf.rhea-db.org/Compound_3249 rh:chebi`
carbamate `CHEBI:13941`	consumes	carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	RHEA:15650 Source assertion: Rhea RHEA:15650 places CHEBI:13941 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/15650 rh:substrates http://rdf.rhea-db.org/15649_L; http://rdf.rhea-db.org/15649_L rh:contains1 http://rdf.rhea-db.org/Participant_15649_compound_4239; http://rdf.rhea-db.org/Participant_15649_compound_4239 rh:compound http://rdf.rhea-db.org/Compound_4239; http://rdf.rhea-db.org/Compound_4239 rh:chebi` MetaCyc:RXN0-5222 Source assertion: The native reaction explicitly sets spontaneous=true for carbamate decomposition to ammonium and carbon dioxide. Source location `Reaction[@frameid='RXN0-5222']/spontaneous; left; right`
hydron `CHEBI:15378`	consumes	carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	RHEA:15650 Source assertion: Rhea RHEA:15650 places CHEBI:15378 on its substrates side with stoichiometric coefficient 2. Source location `http://rdf.rhea-db.org/15650 rh:substrates http://rdf.rhea-db.org/15649_L; http://rdf.rhea-db.org/15649_L rh:contains2 http://rdf.rhea-db.org/Participant_15649_compound_3249; http://rdf.rhea-db.org/Participant_15649_compound_3249 rh:compound http://rdf.rhea-db.org/Compound_3249; http://rdf.rhea-db.org/Compound_3249 rh:chebi` MetaCyc:RXN0-5222 Source assertion: The native reaction explicitly sets spontaneous=true for carbamate decomposition to ammonium and carbon dioxide. Source location `Reaction[@frameid='RXN0-5222']/spontaneous; left; right`
carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	produces	ammonium `CHEBI:28938`	RHEA:15650 Source assertion: Rhea RHEA:15650 places CHEBI:28938 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/15650 rh:products http://rdf.rhea-db.org/15649_R; http://rdf.rhea-db.org/15649_R rh:contains1 http://rdf.rhea-db.org/Participant_15649_compound_1012; http://rdf.rhea-db.org/Participant_15649_compound_1012 rh:compound http://rdf.rhea-db.org/Compound_1012; http://rdf.rhea-db.org/Compound_1012 rh:chebi` MetaCyc:RXN0-5222 Source assertion: The native reaction explicitly sets spontaneous=true for carbamate decomposition to ammonium and carbon dioxide. Source location `Reaction[@frameid='RXN0-5222']/spontaneous; left; right`
carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	produces	carbon dioxide `CHEBI:16526`	RHEA:15650 Source assertion: Rhea RHEA:15650 places CHEBI:16526 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/15650 rh:products http://rdf.rhea-db.org/15649_R; http://rdf.rhea-db.org/15649_R rh:contains1 http://rdf.rhea-db.org/Participant_15649_compound_4391; http://rdf.rhea-db.org/Participant_15649_compound_4391 rh:compound http://rdf.rhea-db.org/Compound_4391; http://rdf.rhea-db.org/Compound_4391 rh:chebi` MetaCyc:RXN0-5222 Source assertion: The native reaction explicitly sets spontaneous=true for carbamate decomposition to ammonium and carbon dioxide. Source location `Reaction[@frameid='RXN0-5222']/spontaneous; left; right`
(Z)-3-aminoacrylate `CHEBI:59894`	consumes	(Z)-3-aminoacrylate + H2O + H(+) => 3-oxopropanoate + NH4(+) `RHEA:34948`	RHEA:34948 Source assertion: Rhea RHEA:34948 places CHEBI:59894 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/34948 rh:substrates http://rdf.rhea-db.org/34947_L; http://rdf.rhea-db.org/34947_L rh:contains1 http://rdf.rhea-db.org/Participant_34947_compound_6886; http://rdf.rhea-db.org/Participant_34947_compound_6886 rh:compound http://rdf.rhea-db.org/Compound_6886; http://rdf.rhea-db.org/Compound_6886 rh:chebi`
water `CHEBI:15377`	consumes	(Z)-3-aminoacrylate + H2O + H(+) => 3-oxopropanoate + NH4(+) `RHEA:34948`	RHEA:34948 Source assertion: Rhea RHEA:34948 places CHEBI:15377 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/34948 rh:substrates http://rdf.rhea-db.org/34947_L; http://rdf.rhea-db.org/34947_L rh:contains1 http://rdf.rhea-db.org/Participant_34947_compound_1283; http://rdf.rhea-db.org/Participant_34947_compound_1283 rh:compound http://rdf.rhea-db.org/Compound_1283; http://rdf.rhea-db.org/Compound_1283 rh:chebi`
hydron `CHEBI:15378`	consumes	(Z)-3-aminoacrylate + H2O + H(+) => 3-oxopropanoate + NH4(+) `RHEA:34948`	RHEA:34948 Source assertion: Rhea RHEA:34948 places CHEBI:15378 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/34948 rh:substrates http://rdf.rhea-db.org/34947_L; http://rdf.rhea-db.org/34947_L rh:contains1 http://rdf.rhea-db.org/Participant_34947_compound_3249; http://rdf.rhea-db.org/Participant_34947_compound_3249 rh:compound http://rdf.rhea-db.org/Compound_3249; http://rdf.rhea-db.org/Compound_3249 rh:chebi`
(Z)-3-aminoacrylate + H2O + H(+) => 3-oxopropanoate + NH4(+) `RHEA:34948`	produces	3-oxopropanoate `CHEBI:33190`	RHEA:34948 Source assertion: Rhea RHEA:34948 places CHEBI:33190 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/34948 rh:products http://rdf.rhea-db.org/34947_R; http://rdf.rhea-db.org/34947_R rh:contains1 http://rdf.rhea-db.org/Participant_34947_compound_5274; http://rdf.rhea-db.org/Participant_34947_compound_5274 rh:compound http://rdf.rhea-db.org/Compound_5274; http://rdf.rhea-db.org/Compound_5274 rh:chebi`
(Z)-3-aminoacrylate + H2O + H(+) => 3-oxopropanoate + NH4(+) `RHEA:34948`	produces	ammonium `CHEBI:28938`	RHEA:34948 Source assertion: Rhea RHEA:34948 places CHEBI:28938 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/34948 rh:products http://rdf.rhea-db.org/34947_R; http://rdf.rhea-db.org/34947_R rh:contains1 http://rdf.rhea-db.org/Participant_34947_compound_1012; http://rdf.rhea-db.org/Participant_34947_compound_1012 rh:compound http://rdf.rhea-db.org/Compound_1012; http://rdf.rhea-db.org/Compound_1012 rh:chebi`
3-oxopropanoate `CHEBI:33190`	consumes	3-oxopropanoate + NADPH + H(+) => 3-hydroxypropanoate + NADP(+) `RHEA:26440`	RHEA:26440 Source assertion: Rhea RHEA:26440 places CHEBI:33190 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/26440 rh:substrates http://rdf.rhea-db.org/26438_R; http://rdf.rhea-db.org/26438_R rh:contains1 http://rdf.rhea-db.org/Participant_26438_compound_5274; http://rdf.rhea-db.org/Participant_26438_compound_5274 rh:compound http://rdf.rhea-db.org/Compound_5274; http://rdf.rhea-db.org/Compound_5274 rh:chebi`
NADPH(4-) `CHEBI:57783`	consumes	3-oxopropanoate + NADPH + H(+) => 3-hydroxypropanoate + NADP(+) `RHEA:26440`	RHEA:26440 Source assertion: Rhea RHEA:26440 places CHEBI:57783 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/26440 rh:substrates http://rdf.rhea-db.org/26438_R; http://rdf.rhea-db.org/26438_R rh:contains1 http://rdf.rhea-db.org/Participant_26438_compound_3438; http://rdf.rhea-db.org/Participant_26438_compound_3438 rh:compound http://rdf.rhea-db.org/Compound_3438; http://rdf.rhea-db.org/Compound_3438 rh:chebi`
hydron `CHEBI:15378`	consumes	3-oxopropanoate + NADPH + H(+) => 3-hydroxypropanoate + NADP(+) `RHEA:26440`	RHEA:26440 Source assertion: Rhea RHEA:26440 places CHEBI:15378 on its substrates side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/26440 rh:substrates http://rdf.rhea-db.org/26438_R; http://rdf.rhea-db.org/26438_R rh:contains1 http://rdf.rhea-db.org/Participant_26438_compound_3249; http://rdf.rhea-db.org/Participant_26438_compound_3249 rh:compound http://rdf.rhea-db.org/Compound_3249; http://rdf.rhea-db.org/Compound_3249 rh:chebi`
3-oxopropanoate + NADPH + H(+) => 3-hydroxypropanoate + NADP(+) `RHEA:26440`	produces	3-hydroxypropionate `CHEBI:16510`	RHEA:26440 Source assertion: Rhea RHEA:26440 places CHEBI:16510 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/26440 rh:products http://rdf.rhea-db.org/26438_L; http://rdf.rhea-db.org/26438_L rh:contains1 http://rdf.rhea-db.org/Participant_26438_compound_3378; http://rdf.rhea-db.org/Participant_26438_compound_3378 rh:compound http://rdf.rhea-db.org/Compound_3378; http://rdf.rhea-db.org/Compound_3378 rh:chebi`
3-oxopropanoate + NADPH + H(+) => 3-hydroxypropanoate + NADP(+) `RHEA:26440`	produces	NADP(3-) `CHEBI:58349`	RHEA:26440 Source assertion: Rhea RHEA:26440 places CHEBI:58349 on its products side with stoichiometric coefficient 1. Source location `http://rdf.rhea-db.org/26440 rh:products http://rdf.rhea-db.org/26438_L; http://rdf.rhea-db.org/26438_L rh:contains1 http://rdf.rhea-db.org/Participant_26438_compound_5188; http://rdf.rhea-db.org/Participant_26438_compound_5188 rh:compound http://rdf.rhea-db.org/Compound_5188; http://rdf.rhea-db.org/Compound_5188 rh:chebi`
FMN reductase (NADH) RutF `UniProtKB:P75893`	enables Functional protein/activity assertion; no monomeric assembly is inferred.	FMN + NADH + 2 H(+) => FMNH2 + NAD(+) `RHEA:21622`	UniProtKB:P75893 Source assertion: The reviewed entry assigns P75893 to master RHEA:21620 with ECO:0000269 experimental citations; the reaction entry is mapped separately to the selected directed member. Source location `/comments/1/reaction/reactionCrossReferences; /comments/1/reaction/evidences` RHEA:21622 Source assertion: Rhea master 21620 explicitly links directed member 21622; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/21620 rh:directionalReaction http://rdf.rhea-db.org/21622; http://rdf.rhea-db.org/21622 rh:substrates; rh:products; rh:equation` PMID:20369853 Source assertion: Partially purified RutF plus purified RutA, NADH and FMN yielded ureidoacrylate; homogeneous Fre substituted in vitro. RutF supplies reduced FMN. Source location `PMC2873085 paragraphs P1-P2; Figure 1; Scheme 1`
Pyrimidine monooxygenase RutA `UniProtKB:P75898`	enables Current net chemistry includes spontaneous NADH reduction of FMN-N5-oxide. The old free-peracid pathway layout is not carried forward; this is not a claim that RutA catalyzes every elementary net substep.	uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	UniProtKB:P75898 Source assertion: The reviewed entry assigns P75898 to master RHEA:31587 with ECO:0000269 experimental citations; the reaction entry is mapped separately to the selected directed member. Source location `/comments/1/reaction/reactionCrossReferences; /comments/1/reaction/evidences` RHEA:31588 Source assertion: Rhea master 31587 explicitly links directed member 31588; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/31587 rh:directionalReaction http://rdf.rhea-db.org/31588; http://rdf.rhea-db.org/31588 rh:substrates; rh:products; rh:equation` PMID:28661684 Source assertion: RutA assays without NADH accumulated FMN-N5-oxide, verified against a synthetic standard by chromatography, mass spectrometry and 18O2 labeling. Source location `PMC6040642 main text following Figure 3; Figure 4A-F`
Ureidoacrylate amidohydrolase RutB `UniProtKB:P75897`	enables The explicit intermediate reaction is selected; net RHEA:42624 is excluded to avoid counting carbamate decomposition twice.	(Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) `RHEA:31604`	UniProtKB:P75897 Source assertion: The reviewed entry assigns P75897 to master RHEA:31603 with ECO:0000269 experimental citations; the reaction entry is mapped separately to the selected directed member. Source location `/comments/2/reaction/reactionCrossReferences; /comments/2/reaction/evidences` RHEA:31604 Source assertion: Rhea master 31603 explicitly links directed member 31604; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/31603 rh:directionalReaction http://rdf.rhea-db.org/31604; http://rdf.rhea-db.org/31604 rh:substrates; rh:products; rh:equation` PMID:20400551 Source assertion: RutB hydrolyzed synthetic ureidoacrylate; coupled measurements supported aminoacrylate and carbamate intermediates, followed by spontaneous nitrogen release. Source location `PMC2916427 Results section sec18 The RutB reaction; Figure 5B; Table 4`
3-aminoacrylate deaminase RutC `UniProtKB:P0AFQ5`	enables Functional protein/activity assertion preserves the measured homotrimer without inventing an external complex identifier. The reaction also proceeds spontaneously; RutC is not essential in the tested whole-cell conditions.	(Z)-3-aminoacrylate + H2O + H(+) => 3-oxopropanoate + NH4(+) `RHEA:34948`	UniProtKB:P0AFQ5 Source assertion: The reviewed entry assigns P0AFQ5 to master RHEA:34947 with ECO:0000269 experimental citations; the reaction entry is mapped separately to the selected directed member. Source location `/comments/1/reaction/reactionCrossReferences; /comments/1/reaction/evidences` RHEA:34948 Source assertion: Rhea master 34947 explicitly links directed member 34948; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/34947 rh:directionalReaction http://rdf.rhea-db.org/34948; http://rdf.rhea-db.org/34948 rh:substrates; rh:products; rh:equation` PMID:33839153 Source assertion: At 23°C RutC accelerated 3-aminoacrylate deamination in the RutB/YdfG coupled assay; inactive R104A gave the spontaneous background rate. Source location `PMC8113886 Results: RutC is a 3-AA deaminase; Figure 2; Table 1; Assay for 3-AA deaminase activity` PMID:23143235 Source assertion: Gel filtration demonstrates a RutC trimer in solution; the crystal contains two trimers. The paper's proposed peracid-reductase function is superseded by the 2021 direct deaminase assays. Source location `PMC3515367 Results and discussion 3.1; Figure 2`
NADP-dependent 3-hydroxy acid dehydrogenase YdfG `UniProtKB:P39831`	part_of	3-hydroxy acid dehydrogenase `MetaCyc:CPLX0-1962`	MetaCyc:CPLX0-1962 Source assertion: The native YdfG complex contains four EG12345-MONOMER subunits and is annotated to MG1655. Source location `Protein[@frameid='CPLX0-1962']/component/Protein; component/coefficient; species` MetaCyc:EG12345-MONOMER Source assertion: Native EG12345-MONOMER carries the UniProt P39831 identity and component-of CPLX0-1962 relationship. Source location `Protein[@frameid='EG12345-MONOMER']/dblink; component-of` UniProtKB:P39831 Source assertion: The reviewed SUBUNIT annotation describes a homotetramer, a dimer of dimers, with experimental references 12535615 and 21349860. Source location `/comments/7/texts`
3-hydroxy acid dehydrogenase `MetaCyc:CPLX0-1962`	catalyzes Direct biochemical support is for YdfG reduction. Mutant growth defects support detoxification under specified conditions; they do not measure universal wild-type pathway flux.	3-oxopropanoate + NADPH + H(+) => 3-hydroxypropanoate + NADP(+) `RHEA:26440`	MetaCyc:CPLX0-1962 Source assertion: The native complex catalyzes ENZRXN0-7359 linked to RXN-8974, the malonic semialdehyde reductase reaction. Source location `Protein[@frameid='CPLX0-1962']/catalyzes/Enzymatic-Reaction[@frameid='ENZRXN0-7359']/reaction` UniProtKB:P39831 Source assertion: The reviewed YdfG reaction explicitly selects physiological RHEA:26440, right-to-left reduction of 3-oxopropanoate using NADPH, with experimental PMID20400551. Source location `/comments/5/reaction; /comments/5/physiologicalReactions` RHEA:26440 Source assertion: Rhea master 26438 explicitly links directed member 26440; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/26438 rh:directionalReaction http://rdf.rhea-db.org/26440; http://rdf.rhea-db.org/26440 rh:substrates; rh:products; rh:equation` PMID:20400551 Source assertion: RutB and YdfG together converted synthetic ureidoacrylate to approximately one equivalent of 3-hydroxypropionate while oxidizing NADPH; product was quantified by GC/MS. Source location `PMC2916427 Methods sec13; Results sec18; Table 4; Figure 5C`
Probable malonic semialdehyde reductase RutE `UniProtKB:P75894`	enables Qualified genetic/annotation inference, not a purified RutE assay or established NADPH specificity. YdfG directly grounds the displayed reduction chemistry.	3-oxopropanoate + NADPH + H(+) => 3-hydroxypropanoate + NADP(+) `RHEA:26440`	UniProtKB:P75894 Source assertion: The reviewed entry calls RutE a probable malonic semialdehyde reductase and supplies RHEA:26438 without an experimental reaction evidence code. FUNCTION says it may reduce the toxic intermediate. Source location `/proteinDescription/recommendedName; /comments/0/texts; /comments/1/reaction` RHEA:26440 Source assertion: Rhea master 26438 explicitly links directed member 26440; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/26438 rh:directionalReaction http://rdf.rhea-db.org/26440; http://rdf.rhea-db.org/26440 rh:substrates; rh:products; rh:equation` PMID:20400551 Source assertion: Shared suppression of rutE and ydfG defects by nemR lesions leads to the postulate that RutE also reduces malonic semialdehyde. The discussion explicitly calls for biochemical studies of RutE. Source location `PMC2916427 Results sec24; Discussion sec26` PMID:33839153 Source assertion: Figure 1 distinguishes YdfG reduction demonstrated in vitro from the predicted physiologically relevant RutE enzyme. Source location `PMC8113886 Figure 1 legend`
Probable malonic semialdehyde reductase RutE `UniProtKB:P75894`	has_cofactor Predicted FMN requirement retained with its original evidence tier.	FMN(3-) `CHEBI:58210`	UniProtKB:P75894 Source assertion: RutE FMN cofactor annotation has ECO:0000305 curator inference, not a direct cofactor-binding assay. Source location `/comments/2/cofactors/0`
FMN + NADH + 2 H(+) => FMNH2 + NAD(+) `RHEA:21622`	part_of Modern biochemical reconstruction of the same uracil-to-3-hydroxypropionate boundary; native22.5 peracid and RutC/RutD assignments are superseded, not asserted equivalent elementary reactions.	`MetaCyc:PWY0-1471`	PMID:28661684 Source assertion: Figure 1 identifies RutF as the flavin reductase that supplies the reduced cofactor for the first RutA step. Source location `PMC6040642 Figure 1 legend` RHEA:21622 Source assertion: Rhea master 21620 explicitly links directed member 21622; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/21620 rh:directionalReaction http://rdf.rhea-db.org/21622; http://rdf.rhea-db.org/21622 rh:substrates; rh:products; rh:equation`
uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	part_of Modern biochemical reconstruction of the same uracil-to-3-hydroxypropionate boundary; native22.5 peracid and RutC/RutD assignments are superseded, not asserted equivalent elementary reactions.	`MetaCyc:PWY0-1471`	PMID:33839153 Source assertion: The revised Rut model covers ureidoacrylate formation, RutB cleavage, 3-aminoacrylate deamination, carbamate decay and terminal malonate-semialdehyde reduction. Source location `PMC8113886 Figure 1 and legend; Introduction; Results` RHEA:31588 Source assertion: Rhea master 31587 explicitly links directed member 31588; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/31587 rh:directionalReaction http://rdf.rhea-db.org/31588; http://rdf.rhea-db.org/31588 rh:substrates; rh:products; rh:equation`
(Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) `RHEA:31604`	part_of Modern biochemical reconstruction of the same uracil-to-3-hydroxypropionate boundary; native22.5 peracid and RutC/RutD assignments are superseded, not asserted equivalent elementary reactions.	`MetaCyc:PWY0-1471`	PMID:33839153 Source assertion: The revised Rut model covers ureidoacrylate formation, RutB cleavage, 3-aminoacrylate deamination, carbamate decay and terminal malonate-semialdehyde reduction. Source location `PMC8113886 Figure 1 and legend; Introduction; Results` RHEA:31604 Source assertion: Rhea master 31603 explicitly links directed member 31604; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/31603 rh:directionalReaction http://rdf.rhea-db.org/31604; http://rdf.rhea-db.org/31604 rh:substrates; rh:products; rh:equation`
carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	part_of Modern biochemical reconstruction of the same uracil-to-3-hydroxypropionate boundary; native22.5 peracid and RutC/RutD assignments are superseded, not asserted equivalent elementary reactions.	`MetaCyc:PWY0-1471`	PMID:33839153 Source assertion: The revised Rut model covers ureidoacrylate formation, RutB cleavage, 3-aminoacrylate deamination, carbamate decay and terminal malonate-semialdehyde reduction. Source location `PMC8113886 Figure 1 and legend; Introduction; Results` RHEA:15650 Source assertion: Rhea master 15649 explicitly links directed member 15650; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/15649 rh:directionalReaction http://rdf.rhea-db.org/15650; http://rdf.rhea-db.org/15650 rh:substrates; rh:products; rh:equation`
(Z)-3-aminoacrylate + H2O + H(+) => 3-oxopropanoate + NH4(+) `RHEA:34948`	part_of Modern biochemical reconstruction of the same uracil-to-3-hydroxypropionate boundary; native22.5 peracid and RutC/RutD assignments are superseded, not asserted equivalent elementary reactions.	`MetaCyc:PWY0-1471`	PMID:33839153 Source assertion: The revised Rut model covers ureidoacrylate formation, RutB cleavage, 3-aminoacrylate deamination, carbamate decay and terminal malonate-semialdehyde reduction. Source location `PMC8113886 Figure 1 and legend; Introduction; Results` RHEA:34948 Source assertion: Rhea master 34947 explicitly links directed member 34948; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/34947 rh:directionalReaction http://rdf.rhea-db.org/34948; http://rdf.rhea-db.org/34948 rh:substrates; rh:products; rh:equation`
3-oxopropanoate + NADPH + H(+) => 3-hydroxypropanoate + NADP(+) `RHEA:26440`	part_of Modern biochemical reconstruction of the same uracil-to-3-hydroxypropionate boundary; native22.5 peracid and RutC/RutD assignments are superseded, not asserted equivalent elementary reactions.	`MetaCyc:PWY0-1471`	PMID:33839153 Source assertion: The revised Rut model covers ureidoacrylate formation, RutB cleavage, 3-aminoacrylate deamination, carbamate decay and terminal malonate-semialdehyde reduction. Source location `PMC8113886 Figure 1 and legend; Introduction; Results` RHEA:26440 Source assertion: Rhea master 26438 explicitly links directed member 26440; its substrates and products define the selected pathway orientation. Source location `http://rdf.rhea-db.org/26438 rh:directionalReaction http://rdf.rhea-db.org/26440; http://rdf.rhea-db.org/26440 rh:substrates; rh:products; rh:equation`
FMN + NADH + 2 H(+) => FMNH2 + NAD(+) `RHEA:21622`	provides_input_for Dependency inferred from the inspected pathway and matching current Rhea chemical identities; no physical enzyme channeling is asserted.	uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	PMID:33839153 Source assertion: The revised pathway diagram places FMN-dependent uracil opening before RutB cleavage, branches carbamate decay from aminoacrylate deamination, and ends with semialdehyde reduction. Source location `PMC8113886 Figure 1 and legend` RHEA:21622 Source assertion: The selected upstream reaction produces CHEBI:57618. Source location `http://rdf.rhea-db.org/21622 rh:products; corresponding rh:contains/rh:compound/rh:chebi` RHEA:31588 Source assertion: The selected downstream reaction consumes the same CHEBI:57618. Source location `http://rdf.rhea-db.org/31588 rh:substrates; corresponding rh:contains/rh:compound/rh:chebi`
uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	provides_input_for Dependency inferred from the inspected pathway and matching current Rhea chemical identities; no physical enzyme channeling is asserted.	FMN + NADH + 2 H(+) => FMNH2 + NAD(+) `RHEA:21622`	PMID:33839153 Source assertion: The revised pathway diagram places FMN-dependent uracil opening before RutB cleavage, branches carbamate decay from aminoacrylate deamination, and ends with semialdehyde reduction. Source location `PMC8113886 Figure 1 and legend` RHEA:31588 Source assertion: The selected upstream reaction produces CHEBI:58210. Source location `http://rdf.rhea-db.org/31588 rh:products; corresponding rh:contains/rh:compound/rh:chebi` RHEA:21622 Source assertion: The selected downstream reaction consumes the same CHEBI:58210. Source location `http://rdf.rhea-db.org/21622 rh:substrates; corresponding rh:contains/rh:compound/rh:chebi`
uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) `RHEA:31588`	provides_input_for Dependency inferred from the inspected pathway and matching current Rhea chemical identities; no physical enzyme channeling is asserted.	(Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) `RHEA:31604`	PMID:33839153 Source assertion: The revised pathway diagram places FMN-dependent uracil opening before RutB cleavage, branches carbamate decay from aminoacrylate deamination, and ends with semialdehyde reduction. Source location `PMC8113886 Figure 1 and legend` RHEA:31588 Source assertion: The selected upstream reaction produces CHEBI:59891. Source location `http://rdf.rhea-db.org/31588 rh:products; corresponding rh:contains/rh:compound/rh:chebi` RHEA:31604 Source assertion: The selected downstream reaction consumes the same CHEBI:59891. Source location `http://rdf.rhea-db.org/31604 rh:substrates; corresponding rh:contains/rh:compound/rh:chebi`
(Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) `RHEA:31604`	provides_input_for Dependency inferred from the inspected pathway and matching current Rhea chemical identities; no physical enzyme channeling is asserted.	carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	PMID:33839153 Source assertion: The revised pathway diagram places FMN-dependent uracil opening before RutB cleavage, branches carbamate decay from aminoacrylate deamination, and ends with semialdehyde reduction. Source location `PMC8113886 Figure 1 and legend` RHEA:31604 Source assertion: The selected upstream reaction produces CHEBI:13941. Source location `http://rdf.rhea-db.org/31604 rh:products; corresponding rh:contains/rh:compound/rh:chebi` RHEA:15650 Source assertion: The selected downstream reaction consumes the same CHEBI:13941. Source location `http://rdf.rhea-db.org/15650 rh:substrates; corresponding rh:contains/rh:compound/rh:chebi`
(Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) `RHEA:31604`	provides_input_for Dependency inferred from the inspected pathway and matching current Rhea chemical identities; no physical enzyme channeling is asserted.	(Z)-3-aminoacrylate + H2O + H(+) => 3-oxopropanoate + NH4(+) `RHEA:34948`	PMID:33839153 Source assertion: The revised pathway diagram places FMN-dependent uracil opening before RutB cleavage, branches carbamate decay from aminoacrylate deamination, and ends with semialdehyde reduction. Source location `PMC8113886 Figure 1 and legend` RHEA:31604 Source assertion: The selected upstream reaction produces CHEBI:59894. Source location `http://rdf.rhea-db.org/31604 rh:products; corresponding rh:contains/rh:compound/rh:chebi` RHEA:34948 Source assertion: The selected downstream reaction consumes the same CHEBI:59894. Source location `http://rdf.rhea-db.org/34948 rh:substrates; corresponding rh:contains/rh:compound/rh:chebi`
(Z)-3-aminoacrylate + H2O + H(+) => 3-oxopropanoate + NH4(+) `RHEA:34948`	provides_input_for Dependency inferred from the inspected pathway and matching current Rhea chemical identities; no physical enzyme channeling is asserted.	3-oxopropanoate + NADPH + H(+) => 3-hydroxypropanoate + NADP(+) `RHEA:26440`	PMID:33839153 Source assertion: The revised pathway diagram places FMN-dependent uracil opening before RutB cleavage, branches carbamate decay from aminoacrylate deamination, and ends with semialdehyde reduction. Source location `PMC8113886 Figure 1 and legend` RHEA:34948 Source assertion: The selected upstream reaction produces CHEBI:33190. Source location `http://rdf.rhea-db.org/34948 rh:products; corresponding rh:contains/rh:compound/rh:chebi` RHEA:26440 Source assertion: The selected downstream reaction consumes the same CHEBI:33190. Source location `http://rdf.rhea-db.org/26440 rh:substrates; corresponding rh:contains/rh:compound/rh:chebi`

References

MetaCyc:PWY0-1471 uracil degradation III (source version: MetaCyc 22.5; original native XML retrieved 2026-10-11)
MetaCyc:CPLX0-1962 3-hydroxy acid dehydrogenase (source version: MetaCyc 22.5; original native XML retrieved 2026-10-11)
MetaCyc:EG12345-MONOMER YdfG native subunit identity (source version: MetaCyc 22.5; original native XML retrieved 2026-10-11)
MetaCyc:RXN0-5222 spontaneous carbamate decomposition (source version: MetaCyc 22.5; original native XML retrieved 2026-10-11)
MetaCyc:RXN-8974 3-hydroxypropionate:NADP+ oxidoreductase (source version: MetaCyc 22.5; original native XML retrieved 2026-10-11)
UniProtKB:P75893 FMN reductase (NADH) RutF (source version: Reviewed entry version 152, sequence version 3; retrieved 2026-10-11)
UniProtKB:P75898 Pyrimidine monooxygenase RutA (source version: Reviewed entry version 160, sequence version 3; retrieved 2026-10-11)
UniProtKB:P75897 Ureidoacrylate amidohydrolase RutB (source version: Reviewed entry version 153, sequence version 2; retrieved 2026-10-11)
UniProtKB:P0AFQ5 3-aminoacrylate deaminase RutC (source version: Reviewed entry version 120, sequence version 1; retrieved 2026-10-11)
UniProtKB:P39831 NADP-dependent 3-hydroxy acid dehydrogenase YdfG (source version: Reviewed entry version 171, sequence version 2; retrieved 2026-10-11)
UniProtKB:P75894 Probable malonic semialdehyde reductase RutE (source version: Reviewed entry version 150, sequence version 1; retrieved 2026-10-11)
PMID:20369853 Catalysis of a flavoenzyme-mediated amide hydrolysis (source version: Complete primary article HTML retrieved 2026-10-11)
PMID:20400551 The Rut Pathway for Pyrimidine Degradation: Novel Chemistry and Toxicity Problems (source version: Complete primary article HTML retrieved 2026-10-11)
PMID:28661684 RutA-Catalyzed Oxidative Cleavage of the Uracil Amide Involves Formation of a Flavin-N5-oxide (source version: Complete primary article HTML retrieved 2026-10-11)
PMID:33839153 The Rid family member RutC of Escherichia coli is a 3-aminoacrylate deaminase (source version: Complete primary article XML retrieved 2026-10-11)
PMID:23143235 Structure of Escherichia coli RutC, a member of the YjgF family and putative aminoacrylate peracid reductase of the rut operon (source version: Complete primary article HTML retrieved 2026-10-11)
RHEA:21622 FMN + NADH + 2 H(+) => FMNH2 + NAD(+) (source version: Rhea release 142; digest covers original complete RDF gzip)
RHEA:31588 uracil + FMNH2 + NADH + O2 => (Z)-3-ureidoacrylate + FMN + NAD(+) + H2O + H(+) (source version: Rhea release 142; digest covers original complete RDF gzip)
RHEA:31604 (Z)-3-ureidoacrylate + H2O => (Z)-3-aminoacrylate + carbamate + H(+) (source version: Rhea release 142; digest covers original complete RDF gzip)
RHEA:15650 carbamate + 2 H(+) => NH4(+) + CO2 (source version: Rhea release 142; digest covers original complete RDF gzip)
RHEA:34948 (Z)-3-aminoacrylate + H2O + H(+) => 3-oxopropanoate + NH4(+) (source version: Rhea release 142; digest covers original complete RDF gzip)
RHEA:26440 3-oxopropanoate + NADPH + H(+) => 3-hydroxypropanoate + NADP(+) (source version: Rhea release 142; digest covers original complete RDF gzip)

Curation history

2026-10-11T03:11:19Z Codex
- CREATE — Add the complete corrected uracil degradation III pathway.
  Retained six chemical reactions including FMN recycling and spontaneous carbamate decay. Used modern RutC deaminase experiments and YdfG terminal reduction, qualified RutE predictions, rejected unmeasured RutD catalysis and preserved temperature/strain/polarity limits. Source dossiers and verification receipts are in research/pathway_additions/2026-10-11-next-184; independent scientific assessments are saved separately.
Read this curation session