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\|1129\|g6677.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|1129\|g6677.t1
jgi\|Chlsc1\|13657\|g1689.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|13657\|g1689.t1
jgi\|Chlsc1\|13854\|g14821.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|13854\|g14821.t1
jgi\|Chlsc1\|14418\|g17239.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|14418\|g17239.t1
jgi\|Chlsc1\|14432\|g17253.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|14432\|g17253.t1
jgi\|Chlsc1\|14624\|g1125.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|14624\|g1125.t1
jgi\|Chlsc1\|2318\|g7719.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|2318\|g7719.t1
jgi\|Chlsc1\|2590\|g14472.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|2590\|g14472.t1
jgi\|Chlsc1\|2591\|g14472.t2	chlamydomonas_schloesseri	jgi\|Chlsc1\|2591\|g14472.t2
jgi\|Chlsc1\|2673\|g14555.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|2673\|g14555.t1
jgi\|Chlsc1\|2858\|g16890.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|2858\|g16890.t1
jgi\|Chlsc1\|4192\|g2903.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|4192\|g2903.t1
jgi\|Chlsc1\|6026\|g10063.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|6026\|g10063.t1
jgi\|Chlsc1\|6413\|g5683.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|6413\|g5683.t1
jgi\|Chlsc1\|6775\|g15178.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|6775\|g15178.t1
jgi\|Chlsc1\|726\|g7929.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|726\|g7929.t1
jgi\|Chlsc1\|7507\|g11074.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|7507\|g11074.t1
jgi\|Chlsc1\|7733\|g11299.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|7733\|g11299.t1
jgi\|Chlsc1\|9555\|g3358.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|9555\|g3358.t1
jgi\|Chlsc1\|9695\|g3495.t1	chlamydomonas_schloesseri	jgi\|Chlsc1\|9695\|g3495.t1
Catmscaffold104_pilon0003670	chlorokybus_atmophyticus	Catmscaffold104_pilon0003670
Catmscaffold10_pilon0007190	chlorokybus_atmophyticus	Catmscaffold10_pilon0007190
Catmscaffold110_pilon0007560	chlorokybus_atmophyticus	Catmscaffold110_pilon0007560
Catmscaffold115_pilon0009670	chlorokybus_atmophyticus	Catmscaffold115_pilon0009670
Catmscaffold118_pilon0010450	chlorokybus_atmophyticus	Catmscaffold118_pilon0010450
Catmscaffold17_pilon0023260	chlorokybus_atmophyticus	Catmscaffold17_pilon0023260
Catmscaffold1_pilon0028040	chlorokybus_atmophyticus	Catmscaffold1_pilon0028040
Catmscaffold1_pilon0028780	chlorokybus_atmophyticus	Catmscaffold1_pilon0028780
Catmscaffold22_pilon0030610	chlorokybus_atmophyticus	Catmscaffold22_pilon0030610
Catmscaffold234_pilon0032450	chlorokybus_atmophyticus	Catmscaffold234_pilon0032450