Flavonoid portable pathway

Flavonoid pathway definition imported from the 2026-05-17 portable BLAST/HMM package.

Representative Flavonoid Reaction Route

Phenylpropanoid entry, flavonoid scaffold, and anthocyanin branches. The flavonoid pathway is branched; this view arranges the main scaffold and common branches into a readable representative route without forcing all branches into one linear pathway.

9 curated steps/modules

From Phenylpropanoid Entry To Flavonoid Scaffold

Substrate

L-Phenylalanine

C₉H₁₁NO₂

C₆H₅-CH₂-CH(NH₂)-COOH

Deamination to the cinnamate entry point

PAL104

Product

trans-Cinnamic acid

C₉H₈O₂

C₆H₅-CH=CH-COOH

PAL commits L-phenylalanine to the phenylpropanoid entry route that supplies the flavonoid acyl donor.

Substrate

trans-Cinnamic acid

C₉H₈O₂

C₆H₅-CH=CH-COOH

Para-hydroxylation of cinnamate

C4H2

Product

p-Coumaric acid

C₉H₈O₃

4-HO-C₆H₄-CH=CH-COOH

C4H/CYP73A hydroxylates cinnamate to p-coumarate, a required phenylpropanoid step toward the flavonoid donor.

Substrate

p-Coumaric acid

C₉H₈O₃

4-HO-C₆H₄-CH=CH-COOH

Substrate

CoA

C₂₁H₃₆N₇O₁₆P₃S

CoA-SH

CoA ligation to form the flavonoid acyl donor

4CL308

Product

p-Coumaroyl-CoA

C₃₀H₃₈N₇O₁₈P₃S

4-HO-C₆H₄-CH=CH-C(=O)-SCoA

4CL activates p-coumarate to p-coumaroyl-CoA for CHS-mediated flavonoid scaffold formation.

Substrate

p-Coumaroyl-CoA

C₃₀H₃₈N₇O₁₈P₃S

4-HO-C₆H₄-CH=CH-C(=O)-SCoA

Substrate

Malonyl-CoA

C₂₄H₃₈N₇O₁₉P₃S

HOOC-CH₂-C(=O)-SCoA

Condensation of the C6-C3-C6 scaffold

CHS55

Product

Naringenin chalcone

C₁₅H₁₂O₅

HO-Ar-CO-CH=CH-Ar-(OH)₂

CHS condenses one p-coumaroyl-CoA with three malonyl-CoA units to form a chalcone scaffold.

Substrate

Naringenin chalcone

C₁₅H₁₂O₅

HO-Ar-CO-CH=CH-Ar-(OH)₂

Chalcone cyclization

CHI56

Product

Naringenin

C₁₅H₁₂O₅

flavanone C₆-C₃-C₆ ring

CHI converts the open-chain chalcone into the flavanone core.

Substrate

Naringenin

C₁₅H₁₂O₅

flavanone C₆-C₃-C₆ ring

C-ring 3-hydroxylation to dihydroflavonols

F3H111

Product

Dihydrokaempferol

C₁₅H₁₂O₆

dihydroflavonol C-ring

F3H is a 2-oxoglutarate-dependent dioxygenase that converts flavanones into the dihydroflavonol pool.

Substrate

Flavanones/dihydroflavonols

C₁₅H₁₂O_5-6

C₆-C₃-C₆ oxygen heterocycle

B-ring hydroxylation shapes flavonoid hydroxylation patterns

F3'H/CYP75B169 F3'5'H/CYP75A11

Product

B-ring hydroxylated flavonoid intermediates

C₁₅H₁₂O_6-7

3&#x₂₇;/3&#x₂₇;5&#x₂₇;-hydroxylated flavonoids

CYP75B/F3'H and CYP75A/F3'5'H alter B-ring hydroxylation and generate precursors for quercetin- and myricetin-type branches.

Flavone, Anthocyanin, And Proanthocyanidin Branches

Substrate

Flavanones/dihydroflavonols

C₁₅ flavonoids

C₆-C₃-C₆ oxygen heterocycle

Flavone, isoflavonoid, and flavonol branches

FNS1 IFS IFR50 FLS

Product

Flavones/isoflavones/flavonols

C₁₅H₁₀O_5-7

oxidized C₆-C₃-C₆ flavonoids

Branch enzymes route shared intermediates into distinct flavonoid subclasses.

Substrate

Dihydroflavonols

C₁₅H₁₂O_6-7

dihydroflavonol C-ring

Anthocyanin and proanthocyanidin direction

DFR47 ANS/LDOX8 UFGT73 ANR4

Product

Anthocyanin glycosides/proanthocyanidins

C₁₅ glycosides/polymers

flavylium-glycoside / flavan-3-ol polymer

DFR/ANS/UFGT/ANR route the dihydroflavonol pool toward pigments and condensed tannins.

Lineage Distribution

Assignments under this module are distributed across the following plant lineages.

All Lineages Algae (999)

Current lineage filter: Algae. All species, family, module, and gene statistics below have been narrowed to this lineage.

Species Distribution

Takakia lepidozioides

Botryococcus braunii

Ptychomnion cygnisetum

Chromochloris zofingiensis

Chlamydomonas reinhardtii

Dunaliella salina

Cyanophora paradoxa

Chlamydomonas schloesseri

Chlorokybus atmophyticus

Lineage Summary

Algae

999

Module Gene List

Gene	Species	Protein ID
jgi\|Chlsc1\|3235\|g6141.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|3235\|g6141.t1
jgi\|Chlsc1\|3771\|g623.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|3771\|g623.t1
jgi\|Chlsc1\|3911\|g4002.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|3911\|g4002.t1
jgi\|Chlsc1\|4337\|g3049.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|4337\|g3049.t1
jgi\|Chlsc1\|7705\|g11269.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|7705\|g11269.t1
jgi\|Chlsc1\|8001\|g11567.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|8001\|g11567.t1
jgi\|Chlsc1\|8121\|g13045.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|8121\|g13045.t1
jgi\|Chlsc1\|8928\|g6623.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|8928\|g6623.t1
jgi\|Chlsc1\|8990\|g2447.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|8990\|g2447.t1
jgi\|Chlsc1\|9467\|g10527.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|9467\|g10527.t1
Catmscaffold104_pilon0003300	chlorokybus_atmophyticus	Catmscaffold104_pilon0003300
Catmscaffold108_pilon0006360	chlorokybus_atmophyticus	Catmscaffold108_pilon0006360
Catmscaffold110_pilon0008150	chlorokybus_atmophyticus	Catmscaffold110_pilon0008150
Catmscaffold127_pilon0012540	chlorokybus_atmophyticus	Catmscaffold127_pilon0012540
Catmscaffold127_pilon0012600	chlorokybus_atmophyticus	Catmscaffold127_pilon0012600
Catmscaffold12_pilon0014090	chlorokybus_atmophyticus	Catmscaffold12_pilon0014090
Catmscaffold175_pilon0018920	chlorokybus_atmophyticus	Catmscaffold175_pilon0018920
Catmscaffold17_pilon0020600	chlorokybus_atmophyticus	Catmscaffold17_pilon0020600
Catmscaffold180_pilon0023990	chlorokybus_atmophyticus	Catmscaffold180_pilon0023990
Catmscaffold195_pilon0025880	chlorokybus_atmophyticus	Catmscaffold195_pilon0025880
Catmscaffold23_pilon0034110	chlorokybus_atmophyticus	Catmscaffold23_pilon0034110
Catmscaffold26_pilon0039440	chlorokybus_atmophyticus	Catmscaffold26_pilon0039440
Catmscaffold32_pilon0049520	chlorokybus_atmophyticus	Catmscaffold32_pilon0049520
Catmscaffold61_pilon0074070	chlorokybus_atmophyticus	Catmscaffold61_pilon0074070
Catmscaffold71_pilon0079810	chlorokybus_atmophyticus	Catmscaffold71_pilon0079810
Catmscaffold73_pilon0079900	chlorokybus_atmophyticus	Catmscaffold73_pilon0079900
Catmscaffold75_pilon0080350	chlorokybus_atmophyticus	Catmscaffold75_pilon0080350
Catmscaffold87_pilon0086200	chlorokybus_atmophyticus	Catmscaffold87_pilon0086200
Catmscaffold88_pilon0086560	chlorokybus_atmophyticus	Catmscaffold88_pilon0086560
Catmscaffold9_pilon0092740	chlorokybus_atmophyticus	Catmscaffold9_pilon0092740