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
PAL34
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
C4H12
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
4CL122
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
CHS67
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
CHI36
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
F3H46
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/CYP75B6 F3'5'H/CYP75A3
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
FNS1 IFS2 IFR23 FLS
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
DFR7 ANS/LDOX16 UFGT359 ANR1
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 Lycophytes/Ferns (735)
Current lineage filter: Lycophytes/Ferns. All species, family, module, and gene statistics below have been narrowed to this lineage.
Algae
Hits0
Bryophytes
Hits0
Lycophytes/Ferns
Hits735
Gymnosperms
Hits0
Basal angiosperms
Hits0
Monocots
Hits0
Eudicots
Hits0
Species Distribution
Isoetes taiwanensis
Selaginella moellendorffii
Azolla filiculoides
Salvinia cucullata
Lineage Summary
Lycophytes/Ferns
735
Module Gene List
Reset
GeneSpeciesProtein ID
ItaiItaiw_v1_contig_5400032970.1 isoetes_taiwanensis ItaiItaiw_v1_contig_5400032970.1
ItaiItaiw_v1_contig_6080035490.1 isoetes_taiwanensis ItaiItaiw_v1_contig_6080035490.1
ItaiItaiw_v1_contig_610035550.1 isoetes_taiwanensis ItaiItaiw_v1_contig_610035550.1
ItaiItaiw_v1_contig_730039660.1 isoetes_taiwanensis ItaiItaiw_v1_contig_730039660.1
ItaiItaiw_v1_contig_730039680.1 isoetes_taiwanensis ItaiItaiw_v1_contig_730039680.1
ItaiItaiw_v1_contig_730039700.1 isoetes_taiwanensis ItaiItaiw_v1_contig_730039700.1
ItaiItaiw_v1_contig_730039720.1 isoetes_taiwanensis ItaiItaiw_v1_contig_730039720.1
ItaiItaiw_v1_contig_730039730.1 isoetes_taiwanensis ItaiItaiw_v1_contig_730039730.1
ItaiItaiw_v1_contig_8170042170.1 isoetes_taiwanensis ItaiItaiw_v1_contig_8170042170.1
ItaiItaiw_v1_contig_880043570.1 isoetes_taiwanensis ItaiItaiw_v1_contig_880043570.1
ItaiItaiw_v1_scaffold_100059440.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_100059440.1
ItaiItaiw_v1_scaffold_100062920.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_100062920.1
ItaiItaiw_v1_scaffold_10047330.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_10047330.1
ItaiItaiw_v1_scaffold_10048300.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_10048300.1
ItaiItaiw_v1_scaffold_10048320.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_10048320.1
ItaiItaiw_v1_scaffold_10048550.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_10048550.1
ItaiItaiw_v1_scaffold_10053090.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_10053090.1
ItaiItaiw_v1_scaffold_10056270.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_10056270.1
ItaiItaiw_v1_scaffold_10056280.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_10056280.1
ItaiItaiw_v1_scaffold_1010066570.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_1010066570.1
ItaiItaiw_v1_scaffold_1010066590.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_1010066590.1
ItaiItaiw_v1_scaffold_1020067360.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_1020067360.1
ItaiItaiw_v1_scaffold_1040070330.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_1040070330.1
ItaiItaiw_v1_scaffold_1070072260.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_1070072260.1
ItaiItaiw_v1_scaffold_1080072870.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_1080072870.1
ItaiItaiw_v1_scaffold_1080072900.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_1080072900.1
ItaiItaiw_v1_scaffold_1080072910.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_1080072910.1
ItaiItaiw_v1_scaffold_1080072920.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_1080072920.1
ItaiItaiw_v1_scaffold_1080072930.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_1080072930.1
ItaiItaiw_v1_scaffold_110076430.1 isoetes_taiwanensis ItaiItaiw_v1_scaffold_110076430.1