PlantSME Plant secondary metabolism enzyme database
Flavonoid portable pathway

Flavonoid portable pathway

Category：Flavonoid 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
01
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.
02
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.
03
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.
04
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.
05
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.
06
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.
07
Substrate
Flavanones/dihydroflavonols
C15H12O5-6
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
C15H12O6-7
3'/3'5'-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
08
Substrate
Flavanones/dihydroflavonols
C15 flavonoids
C6-C3-C6 oxygen heterocycle
Flavone, isoflavonoid, and flavonol branches
FNS359 IFS541 IFR11814 FLS124
Product
Flavones/isoflavones/flavonols
C15H10O5-7
oxidized C6-C3-C6 flavonoids
Branch enzymes route shared intermediates into distinct flavonoid subclasses.
09
Substrate
Dihydroflavonols
C15H12O6-7
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)
Algae
Hits327
Bryophytes
Hits11036
Lycophytes/Ferns
Hits622
Gymnosperms
Hits2088
Basal angiosperms
Hits2815
Monocots
Hits36340
Eudicots
Hits124277
Species Distribution
Triticum turgidum
Triticum aestivum
Hordeum vulgare
Aegilops tauschii
Rhynchospora pubera
Avena sativa
Fragaria ananassa
Eragrostis nindensis
Pinus taeda
Diospyros kaki
Lineage Summary
Algae
327
Bryophytes
11036
Lycophytes/Ferns
622
Gymnosperms
2088
Basal angiosperms
2815
Monocots
36340
Eudicots
124277
Module Gene List
GeneSpeciesProtein ID
acer_truncatum_Atru.chr12.583 acer_truncatum acer_truncatum_Atru.chr12.583
acer_truncatum_Atru.chr12.698 acer_truncatum acer_truncatum_Atru.chr12.698
acer_truncatum_Atru.chr12.710 acer_truncatum acer_truncatum_Atru.chr12.710
acer_truncatum_Atru.chr12.896 acer_truncatum acer_truncatum_Atru.chr12.896
acer_truncatum_Atru.chr12.897 acer_truncatum acer_truncatum_Atru.chr12.897
acer_truncatum_Atru.chr13.1147 acer_truncatum acer_truncatum_Atru.chr13.1147
acer_truncatum_Atru.chr13.1152 acer_truncatum acer_truncatum_Atru.chr13.1152
acer_truncatum_Atru.chr13.1157_Atru.chr13.1155 acer_truncatum acer_truncatum_Atru.chr13.1157_Atru.chr13.1155
acer_truncatum_Atru.chr13.1160 acer_truncatum acer_truncatum_Atru.chr13.1160
acer_truncatum_Atru.chr13.1163 acer_truncatum acer_truncatum_Atru.chr13.1163
acer_truncatum_Atru.chr13.136 acer_truncatum acer_truncatum_Atru.chr13.136
acer_truncatum_Atru.chr13.1409 acer_truncatum acer_truncatum_Atru.chr13.1409
acer_truncatum_Atru.chr13.1449 acer_truncatum acer_truncatum_Atru.chr13.1449
acer_truncatum_Atru.chr13.1473 acer_truncatum acer_truncatum_Atru.chr13.1473
acer_truncatum_Atru.chr13.1597 acer_truncatum acer_truncatum_Atru.chr13.1597
acer_truncatum_Atru.chr13.1598 acer_truncatum acer_truncatum_Atru.chr13.1598
acer_truncatum_Atru.chr13.163 acer_truncatum acer_truncatum_Atru.chr13.163
acer_truncatum_Atru.chr13.164 acer_truncatum acer_truncatum_Atru.chr13.164
acer_truncatum_Atru.chr13.1708 acer_truncatum acer_truncatum_Atru.chr13.1708
acer_truncatum_Atru.chr13.1755 acer_truncatum acer_truncatum_Atru.chr13.1755
acer_truncatum_Atru.chr13.1756 acer_truncatum acer_truncatum_Atru.chr13.1756
acer_truncatum_Atru.chr13.2194 acer_truncatum acer_truncatum_Atru.chr13.2194
acer_truncatum_Atru.chr13.455 acer_truncatum acer_truncatum_Atru.chr13.455
acer_truncatum_Atru.chr13.46 acer_truncatum acer_truncatum_Atru.chr13.46
acer_truncatum_Atru.chr13.49 acer_truncatum acer_truncatum_Atru.chr13.49
acer_truncatum_Atru.chr13.50 acer_truncatum acer_truncatum_Atru.chr13.50
acer_truncatum_Atru.chr13.53 acer_truncatum acer_truncatum_Atru.chr13.53
acer_truncatum_Atru.chr13.533 acer_truncatum acer_truncatum_Atru.chr13.533
acer_truncatum_Atru.chr13.57 acer_truncatum acer_truncatum_Atru.chr13.57
acer_truncatum_Atru.chr13.598 acer_truncatum acer_truncatum_Atru.chr13.598