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

PAL7015

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

C4H464

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

4CL25907

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

CHS11738

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

CHI3089

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

F3H4697

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/CYP75B1332 F3'5'H/CYP75A247

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

FNS359 IFS541 IFR11814 FLS124

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

DFR1310 ANS/LDOX1019 UFGT106747 ANR1183

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 (327) Bryophytes (11036) Lycophytes/Ferns (622) Gymnosperms (2088) Basal angiosperms (2815) Monocots (36340) Eudicots (124277)

Species Distribution

Lineage Summary

Module Gene List

Gene	Species	Protein ID
Aalbaalba5_s000502220251220.1	abies_alba	Aalbaalba5_s000502220251220.1
Aalbaalba5_s000502220251230.1	abies_alba	Aalbaalba5_s000502220251230.1
Aalbaalba5_s000502330251330.1	abies_alba	Aalbaalba5_s000502330251330.1
Aalbaalba5_s000534210263000.1	abies_alba	Aalbaalba5_s000534210263000.1
Aalbaalba5_s000542850266080.1	abies_alba	Aalbaalba5_s000542850266080.1
Aalbaalba5_s000581520279800.1	abies_alba	Aalbaalba5_s000581520279800.1
Aalbaalba5_s000595840284700.1	abies_alba	Aalbaalba5_s000595840284700.1
Aalbaalba5_s000607030288480.1	abies_alba	Aalbaalba5_s000607030288480.1
Aalbaalba5_s000627940295520.1	abies_alba	Aalbaalba5_s000627940295520.1
Aalbaalba5_s000639990299800.1	abies_alba	Aalbaalba5_s000639990299800.1
Aalbaalba5_s000653920304100.1	abies_alba	Aalbaalba5_s000653920304100.1
Aalbaalba5_s000746960332610.1	abies_alba	Aalbaalba5_s000746960332610.1
Aalbaalba5_s000761700337350.1	abies_alba	Aalbaalba5_s000761700337350.1
Aalbaalba5_s000761700337350.2	abies_alba	Aalbaalba5_s000761700337350.2
Aalbaalba5_s000769960339720.1	abies_alba	Aalbaalba5_s000769960339720.1
Aalbaalba5_s000804120350090.1	abies_alba	Aalbaalba5_s000804120350090.1
Aalbaalba5_s000808710351420.1	abies_alba	Aalbaalba5_s000808710351420.1
Aalbaalba5_s000820390354860.1	abies_alba	Aalbaalba5_s000820390354860.1
Aalbaalba5_s000820390354860.2	abies_alba	Aalbaalba5_s000820390354860.2
Aalbaalba5_s000835000358860.1	abies_alba	Aalbaalba5_s000835000358860.1
Aalbaalba5_s000850340362960.1	abies_alba	Aalbaalba5_s000850340362960.1
Aalbaalba5_s000859330365380.1	abies_alba	Aalbaalba5_s000859330365380.1
Aalbaalba5_s000923510383240.1	abies_alba	Aalbaalba5_s000923510383240.1
Aalbaalba5_s000927180384110.1	abies_alba	Aalbaalba5_s000927180384110.1
Aalbaalba5_s000940340387870.1	abies_alba	Aalbaalba5_s000940340387870.1
Aalbaalba5_s000961560393280.1	abies_alba	Aalbaalba5_s000961560393280.1
Aalbaalba5_s000969580395560.1	abies_alba	Aalbaalba5_s000969580395560.1
Aalbaalba5_s000974060396750.1	abies_alba	Aalbaalba5_s000974060396750.1
Aalbaalba5_s001027790410630.1	abies_alba	Aalbaalba5_s001027790410630.1
Aalbaalba5_s001027790410630.2	abies_alba	Aalbaalba5_s001027790410630.2