Funneling pathway: m-cresol
type: Pathway
id: P00021
name: funnel_m_cresol
funneling branch: gentisate branch
pathway component: 3-methylphenol → 3-hydroxybenzyl alcohol
pathway component: 3-hydroxybenzyl alcohol → 3-hydroxybenzaldehyde
pathway component: 3-hydroxybenzaldehyde → 3-hydroxybenzoic acid
pathway component: 3-hydroxybenzoic acid → gentisate
pathway component: 3-hydroxybenzoic acid → protocatechuic acid
pathway order: BiochemicalPathwayStep
  step conversion: 3-methylphenol → 3-hydroxybenzyl alcohol
  reac id: R00063
  step order: 1
  next step: 3-hydroxybenzyl alcohol → 3-hydroxybenzaldehyde
pathway order: BiochemicalPathwayStep
  step conversion: 3-hydroxybenzyl alcohol → 3-hydroxybenzaldehyde
  reac id: R00064
  step order: 2
  next step: 3-hydroxybenzaldehyde → 3-hydroxybenzoic acid
pathway order: BiochemicalPathwayStep
  step conversion: 3-hydroxybenzaldehyde → 3-hydroxybenzoic acid
  reac id: R00065
  step order: 3
  next step: 3-hydroxybenzoic acid → gentisate
pathway order: BiochemicalPathwayStep
  step conversion: 3-hydroxybenzoic acid → gentisate
  reac id: R00042
  step order: 4a
  next step: 3-hydroxybenzoic acid → protocatechuic acid
pathway order: BiochemicalPathwayStep
  step conversion: 3-hydroxybenzoic acid → protocatechuic acid
  reac id: R00066
  step order: 4b
connections: beta-ketoadipate (all branches)
  type: PathwayConnection
  direction: downstream
  id: P00001
  pathway type: Fission
  connecting substrate id: S00002
connections: protocatechuate 4,5-cleavage
  type: PathwayConnection
  direction: downstream
  id: P00002
  pathway type: Fission
  connecting substrate id: S00002
connections: protocatechuate 2,3-cleavage
  type: PathwayConnection
  direction: downstream
  id: P00012
  pathway type: Fission
  connecting substrate id: S00002
connections: beta-ketoadipate: Protocatechuate branch
  type: PathwayConnection
  direction: downstream
  id: P00004
  pathway type: Fission
  connecting substrate id: S00002
connections: gentisate-cleavage
  type: PathwayConnection
  direction: upstream
  id: P00015
  pathway type: Fission
  connecting substrate id: S00017
created: 2026-02-28T10:42:00.413854+00:00
elignin note: This file is JSON-LD based on BioPAX Level 3 naming conventions. It is NOT a standards-compliant BioPAX OWL/RDF document. eLignin-specific extensions (elignin_id, connections, genes, …) are mapped to the http://www.elignindatabase.com/ontology# namespace. To convert to canonical BioPAX RDF/XML use pybiopax or a compatible RDF serialiser.

3-methylphenol → 3-hydroxybenzyl alcohol
type: BiochemicalReaction
id: R00063
left: 3-methylphenol
right: 3-hydroxybenzyl alcohol

3-hydroxybenzyl alcohol → 3-hydroxybenzaldehyde
type: BiochemicalReaction
id: R00064
left: 3-hydroxybenzyl alcohol
right: 3-hydroxybenzaldehyde

3-hydroxybenzaldehyde → 3-hydroxybenzoic acid
type: BiochemicalReaction
id: R00065
left: 3-hydroxybenzaldehyde
right: 3-hydroxybenzoic acid

3-hydroxybenzoic acid
type: SmallMolecule
id: S00023
chemical formula: C7H6O3
molecular weight: 138.12
xref: UnificationXref
  db: PubChem Compound
  id: 7420
xref: UnificationXref
  db: ChEBI
  id: 30764
xref: UnificationXref
  db: KEGG Compound
  id: C00587
xref: UnificationXref
  db: CAS
  id: 99-06-9
xref: UnificationXref
  db: PubChem Compound
  id: 7420
xref: UnificationXref
  db: ChEBI
  id: 30764
xref: UnificationXref
  db: KEGG Compound
  id: C00587
xref: UnificationXref
  db: CAS
  id: 99-06-9
xref: UnificationXref
  db: PubChem Compound
  id: 7420
xref: UnificationXref
  db: ChEBI
  id: 30764
xref: UnificationXref
  db: KEGG Compound
  id: C00587
xref: UnificationXref
  db: CAS
  id: 99-06-9

3-hydroxybenzoic acid → gentisate
type: BiochemicalReaction
id: R00042
left: 3-hydroxybenzoic acid
right: gentisate
catalysis: Catalysis
  controller: 3-hydroxybenzoate 6-hydroxylase
  controlled: 3-hydroxybenzoic acid → gentisate

gentisate
type: SmallMolecule
id: S00017
chemical formula: C7H6O4
molecular weight: 154.12
xref: UnificationXref
  db: PubChem Compound
  id: 3469
xref: UnificationXref
  db: ChEBI
  id: 17189
xref: UnificationXref
  db: KEGG Compound
  id: C00628
xref: UnificationXref
  db: CAS
  id: 490-79-9

3-hydroxybenzoate 6-hydroxylase
type: Protein
id: E00033
EC number: 1.14.13.24

3-hydroxybenzoic acid → protocatechuic acid
type: BiochemicalReaction
id: R00066
left: 3-hydroxybenzoic acid
right: protocatechuic acid

protocatechuic acid
type: SmallMolecule
id: S00002
chemical formula: C7H6O4
molecular weight: 153.11
xref: UnificationXref
  db: PubChem Compound
  id: 72
xref: UnificationXref
  db: ChEBI
  id: 36062
xref: UnificationXref
  db: KEGG Compound
  id: C00230
xref: UnificationXref
  db: CAS
  id: 99-50-3