Phenylpropanoid portable pathway

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

Representative Phenylpropanoid Reaction Route

Entry backbone to monolignol/lignin branches. Substrates, products, and condensed structural formulae show representative conversions; resolved reactions are shown as single enzymes, whereas multi-enzyme branches are shown as curated modules. Member counts come from public annotations.

6 curated steps/modules

Entry Backbone And Lignin Direction

Substrate

L-Phenylalanine

C₉H₁₁NO₂

C₆H₅-CH₂-CH(NH₂)-COOH

Deamination to form the phenylpropene acid scaffold

PAL105

Product

trans-Cinnamic acid

C₉H₈O₂

C₆H₅-CH=CH-COOH

PAL commits the amino-acid substrate to phenylpropanoid metabolism.

Substrate

trans-Cinnamic acid

C₉H₈O₂

C₆H₅-CH=CH-COOH

Para-hydroxylation of the aromatic ring

C4H12

Product

p-Coumaric acid

C₉H₈O₃

4-HO-C₆H₄-CH=CH-COOH

C4H/CYP73A introduces the 4-hydroxyl group for downstream CoA activation.

Substrate

p-Coumaric acid

C₉H₈O₃

4-HO-C₆H₄-CH=CH-COOH

Substrate

CoA

C₂₁H₃₆N₇O₁₆P₃S

CoA-SH

CoA ligation and activation

4CL309

Product

p-Coumaroyl-CoA

C₃₀H₃₈N₇O₁₈P₃S

4-HO-C₆H₄-CH=CH-C(=O)-SCoA

4CL converts the free acid into a thioester used by condensation, acyltransfer, and reduction reactions.

Substrate

p-Coumaroyl-CoA

C₃₀H₃₈N₇O₁₈P₃S

4-HO-C₆H₄-CH=CH-C(=O)-SCoA

Hydroxylation, acyl transfer, and methylation

HCT41 C3'H/CYP98A671 CSE272 CCoAOMT44

Product

Feruloyl-CoA-type intermediates

C₃₁H₄₀N₇O₁₉P₃S

3-MeO-4-HO-C₆H₃-CH=CH-C(=O)-SCoA

This segment remodels the p-coumaroyl scaffold into caffeoyl/feruloyl-type intermediates.

Substrate

Hydroxycinnamoyl-CoA

C_30-31 CoA thioesters

Ar-CH=CH-C(=O)-SCoA

Reduction and S/G monolignol formation

CCR262 CAD165 F5H/CYP84A13 COMT64

Product

Coniferyl/sinapyl alcohol

C₁₀H₁₂O₃ / C₁₁H₁₄O₄

Ar-CH=CH-CH₂OH

CCR/CAD and related steps route CoA thioesters toward monolignol monomers.

Substrate

Monolignols

C₉-C₁₁ phenylpropanoids

Ar-CH=CH-CH₂OH

Oxidative coupling and polymerization

LAC195 POD3241

Product

Lignin polymer

(C₉ unit)n

[Ar-C₃]n ether/C-C polymer

LAC/POD oxidatively couple monolignols into lignin polymers.

Lineage Distribution

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

All Lineages Algae (5394)

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

Species Distribution

Chromochloris zofingiensis

Botryococcus braunii

Penium margaritaceum

Takakia lepidozioides

Chlamydomonas reinhardtii

Chlamydomonas schloesseri

Ptychomnion cygnisetum

Dunaliella salina

Caulerpa lentillifera

Lineage Summary

Algae

5394

Module Gene List

Gene	Species	Protein ID
Bbrascaffold_1330024210.1	botryococcus_braunii	Bbrascaffold_1330024210.1
Bbrascaffold_1350025530.1	botryococcus_braunii	Bbrascaffold_1350025530.1
Bbrascaffold_1380027340.1	botryococcus_braunii	Bbrascaffold_1380027340.1
Bbrascaffold_1420030930.1	botryococcus_braunii	Bbrascaffold_1420030930.1
Bbrascaffold_1420031020.1	botryococcus_braunii	Bbrascaffold_1420031020.1
Bbrascaffold_1480036710.1	botryococcus_braunii	Bbrascaffold_1480036710.1
Bbrascaffold_1480036710.3	botryococcus_braunii	Bbrascaffold_1480036710.3
Bbrascaffold_150038940.1	botryococcus_braunii	Bbrascaffold_150038940.1
Bbrascaffold_152_20041350.1	botryococcus_braunii	Bbrascaffold_152_20041350.1
Bbrascaffold_152_30041840.1	botryococcus_braunii	Bbrascaffold_152_30041840.1
Bbrascaffold_1590045680.1	botryococcus_braunii	Bbrascaffold_1590045680.1
Bbrascaffold_1590045850.1	botryococcus_braunii	Bbrascaffold_1590045850.1
Bbrascaffold_1590046040.1	botryococcus_braunii	Bbrascaffold_1590046040.1
Bbrascaffold_160_30049020.1	botryococcus_braunii	Bbrascaffold_160_30049020.1
Bbrascaffold_1620050270.1	botryococcus_braunii	Bbrascaffold_1620050270.1
Bbrascaffold_1690057350.1	botryococcus_braunii	Bbrascaffold_1690057350.1
Bbrascaffold_1730059920.1	botryococcus_braunii	Bbrascaffold_1730059920.1
Bbrascaffold_1790065160.2	botryococcus_braunii	Bbrascaffold_1790065160.2
Bbrascaffold_1790065920.1	botryococcus_braunii	Bbrascaffold_1790065920.1
Bbrascaffold_1790065930.1	botryococcus_braunii	Bbrascaffold_1790065930.1
Bbrascaffold_180066730.1	botryococcus_braunii	Bbrascaffold_180066730.1
Bbrascaffold_180_10067190.1	botryococcus_braunii	Bbrascaffold_180_10067190.1
Bbrascaffold_182_20068850.1	botryococcus_braunii	Bbrascaffold_182_20068850.1
Bbrascaffold_182_30069430.1	botryococcus_braunii	Bbrascaffold_182_30069430.1
Bbrascaffold_1840071880.2	botryococcus_braunii	Bbrascaffold_1840071880.2
Bbrascaffold_1870075300.1	botryococcus_braunii	Bbrascaffold_1870075300.1
Bbrascaffold_1900076760.1	botryococcus_braunii	Bbrascaffold_1900076760.1
Bbrascaffold_2050083640.1	botryococcus_braunii	Bbrascaffold_2050083640.1
Bbrascaffold_2150086990.1	botryococcus_braunii	Bbrascaffold_2150086990.1
Bbrascaffold_2170088250.1	botryococcus_braunii	Bbrascaffold_2170088250.1