L-arabinose degradation I

MetaCyc:ARABCAT-PWY

L-arabinose degradation I isomerizes beta-L-arabinopyranose to L-ribulose, phosphorylates L-ribulose with ATP to form L-ribulose 5-phosphate, and epimerizes that phosphoketose to D-xylulose 5-phosphate for entry into pentose phosphate metabolism.

Pathway type

carbohydrate degradation

Organism scope

Escherichia coli NCBITaxon:562

Read the source YAML

Pathway network

20 nodes · 23 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Reaction / activity
Chemical / cofactor
Protein / complex
Other participant
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

Show at full size (scroll to explore)

Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Escherichia coli `NCBITaxon:562`	taxon
L-arabinose isomerase `EC:5.3.1.4`	molecular activity
ribulokinase `EC:2.7.1.16`	molecular activity
L-ribulose-5-phosphate 4-epimerase `EC:5.1.3.4`	molecular activity
beta-L-arabinopyranose `CHEBI:40886`	small molecule
L-ribulose `CHEBI:16880`	small molecule
ATP `CHEBI:30616`	small molecule
L-ribulose 5-phosphate `CHEBI:58226`	small molecule
ADP `CHEBI:456216`	small molecule
H(+) `CHEBI:15378`	small molecule
D-xylulose 5-phosphate `CHEBI:57737`	small molecule
L-arabinose isomerase `UniProtKB:P08202`	protein
manganese(2+) `CHEBI:29035`	cofactor
L-ribulose-5-phosphate 4-epimerase AraD `UniProtKB:P08203`	protein
zinc(2+) `CHEBI:29105`	cofactor
Ribulokinase `UniProtKB:P08204`	protein
L-ribulose-5-phosphate 4-epimerase SgbE `UniProtKB:P37680`	protein
L-ribulose-5-phosphate 4-epimerase UlaF `UniProtKB:P39306`	protein
ribulokinase reaction `RHEA:22073`	reaction	left to right
L-arabinose isomerase reaction `RHEA:14822`	reaction	left to right
L-ribulose-5-phosphate 4-epimerase reaction `RHEA:22369`	reaction	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
L-ribulose `CHEBI:16880`	consumes	ribulokinase reaction `RHEA:22073`	RHEA:22073 Source assertion: Rhea lists CHEBI:16880 on the substrates side of RHEA:22073 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22073']/rh:substrates; rh:contains/rh:compound/rh:accession`
ATP `CHEBI:30616`	consumes	ribulokinase reaction `RHEA:22073`	RHEA:22073 Source assertion: Rhea lists CHEBI:30616 on the substrates side of RHEA:22073 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22073']/rh:substrates; rh:contains/rh:compound/rh:accession`
ribulokinase reaction `RHEA:22073`	produces	H(+) `CHEBI:15378`	RHEA:22073 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:22073 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22073']/rh:products; rh:contains/rh:compound/rh:accession`
ribulokinase reaction `RHEA:22073`	produces	ADP `CHEBI:456216`	RHEA:22073 Source assertion: Rhea lists CHEBI:456216 on the products side of RHEA:22073 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22073']/rh:products; rh:contains/rh:compound/rh:accession`
ribulokinase reaction `RHEA:22073`	produces	L-ribulose 5-phosphate `CHEBI:58226`	RHEA:22073 Source assertion: Rhea lists CHEBI:58226 on the products side of RHEA:22073 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22073']/rh:products; rh:contains/rh:compound/rh:accession`
beta-L-arabinopyranose `CHEBI:40886`	consumes	L-arabinose isomerase reaction `RHEA:14822`	RHEA:14822 Source assertion: Rhea lists CHEBI:40886 on the substrates side of RHEA:14822 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/14822']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-arabinose isomerase reaction `RHEA:14822`	produces	L-ribulose `CHEBI:16880`	RHEA:14822 Source assertion: Rhea lists CHEBI:16880 on the products side of RHEA:14822 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/14822']/rh:products; rh:contains/rh:compound/rh:accession`
L-ribulose 5-phosphate `CHEBI:58226`	consumes	L-ribulose-5-phosphate 4-epimerase reaction `RHEA:22369`	RHEA:22369 Source assertion: Rhea lists CHEBI:58226 on the substrates side of RHEA:22369 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22369']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-ribulose-5-phosphate 4-epimerase reaction `RHEA:22369`	produces	D-xylulose 5-phosphate `CHEBI:57737`	RHEA:22369 Source assertion: Rhea lists CHEBI:57737 on the products side of RHEA:22369 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22369']/rh:products; rh:contains/rh:compound/rh:accession`
L-arabinose isomerase `EC:5.3.1.4`	catalyzes	L-arabinose isomerase reaction `RHEA:14822`	RHEA:14821 Source assertion: Rhea associates EC:5.3.1.4 with the reaction family containing RHEA:14822. Source location `rh:ec`
ribulokinase `EC:2.7.1.16`	catalyzes	ribulokinase reaction `RHEA:22073`	RHEA:22072 Source assertion: Rhea associates EC:2.7.1.16 with the reaction family containing RHEA:22073. Source location `rh:ec`
L-ribulose-5-phosphate 4-epimerase `EC:5.1.3.4`	catalyzes	L-ribulose-5-phosphate 4-epimerase reaction `RHEA:22369`	RHEA:22368 Source assertion: Rhea associates EC:5.1.3.4 with the reaction family containing RHEA:22369. Source location `rh:ec`
L-arabinose isomerase reaction `RHEA:14822`	precedes	ribulokinase reaction `RHEA:22073`	MetaCyc:ARABCAT-PWY Source assertion: MetaCyc pathway ordering places RHEA:14822 before RHEA:22073 in this pathway. Shared intermediate: CHEBI:16880. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
ribulokinase reaction `RHEA:22073`	precedes	L-ribulose-5-phosphate 4-epimerase reaction `RHEA:22369`	MetaCyc:ARABCAT-PWY Source assertion: MetaCyc pathway ordering places RHEA:22073 before RHEA:22369 in this pathway. Shared intermediate: CHEBI:58226. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
L-arabinose isomerase `UniProtKB:P08202`	enables	L-arabinose isomerase reaction `RHEA:14822`	UniProtKB:P08202 Source assertion: UniProt annotates UniProtKB:P08202 with catalytic activity for the reaction family of RHEA:14822. Annotation evidence: curated source annotation; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
L-arabinose isomerase `UniProtKB:P08202`	has_cofactor	manganese(2+) `CHEBI:29035`	UniProtKB:P08202 Source assertion: UniProt lists CHEBI:29035 as a cofactor of UniProtKB:P08202 (evidence: curated annotation). Binds 1 Mn(2+) ion per subunit. Source location `comments[commentType='COFACTOR'].cofactors and note`
L-ribulose-5-phosphate 4-epimerase AraD `UniProtKB:P08203`	enables	L-ribulose-5-phosphate 4-epimerase reaction `RHEA:22369`	UniProtKB:P08203 Source assertion: UniProt annotates UniProtKB:P08203 with catalytic activity for the reaction family of RHEA:22369. Annotation evidence: ECO:0000255, ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
L-ribulose-5-phosphate 4-epimerase AraD `UniProtKB:P08203`	has_cofactor	zinc(2+) `CHEBI:29105`	UniProtKB:P08203 Source assertion: UniProt lists CHEBI:29105 as a cofactor of UniProtKB:P08203 (evidence: ECO:0000255, ECO:0000269). Binds 1 zinc ion per subunit (PubMed:10769139, PubMed:11732895, PubMed:11732896, PubMed:9548961). Also able to use cobalt and manganese ions, but less efficiently (PubMed:10769139). Source location `comments[commentType='COFACTOR'].cofactors and note`
Ribulokinase `UniProtKB:P08204`	enables	ribulokinase reaction `RHEA:22073`	UniProtKB:P08204 Source assertion: UniProt annotates UniProtKB:P08204 with catalytic activity for the reaction family of RHEA:22073. Annotation evidence: curated source annotation; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
L-ribulose-5-phosphate 4-epimerase SgbE `UniProtKB:P37680`	enables	L-ribulose-5-phosphate 4-epimerase reaction `RHEA:22369`	UniProtKB:P37680 Source assertion: UniProt annotates UniProtKB:P37680 with catalytic activity for the reaction family of RHEA:22369. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
L-ribulose-5-phosphate 4-epimerase SgbE `UniProtKB:P37680`	has_cofactor	zinc(2+) `CHEBI:29105`	UniProtKB:P37680 Source assertion: UniProt lists CHEBI:29105 as a cofactor of UniProtKB:P37680 (evidence: ECO:0000250). Binds 1 zinc ion per subunit. Source location `comments[commentType='COFACTOR'].cofactors and note`
L-ribulose-5-phosphate 4-epimerase UlaF `UniProtKB:P39306`	enables	L-ribulose-5-phosphate 4-epimerase reaction `RHEA:22369`	UniProtKB:P39306 Source assertion: UniProt annotates UniProtKB:P39306 with catalytic activity for the reaction family of RHEA:22369. Annotation evidence: ECO:0000255, ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
L-ribulose-5-phosphate 4-epimerase UlaF `UniProtKB:P39306`	has_cofactor	zinc(2+) `CHEBI:29105`	UniProtKB:P39306 Source assertion: UniProt lists CHEBI:29105 as a cofactor of UniProtKB:P39306 (evidence: ECO:0000250, ECO:0000255). Binds 1 zinc ion per subunit. Source location `comments[commentType='COFACTOR'].cofactors and note`

References

MetaCyc:ARABCAT-PWY MetaCyc L-arabinose degradation I (source version: 22.5)
RHEA:14821 Rhea L-arabinose isomerase reaction (source version: 139)
RHEA:14824 Rhea bidirectional L-arabinose isomerase reaction (source version: 139)
RHEA:22072 Rhea ribulokinase reaction (source version: 139)
RHEA:22073 Rhea L-ribulose-5-phosphate-forming direction (source version: 139)
RHEA:22368 Rhea L-ribulose-5-phosphate 4-epimerase reaction (source version: 139)
RHEA:22371 Rhea bidirectional L-ribulose-5-phosphate 4-epimerase reaction (source version: 139)
RHEA:14822 RHEA:14822 authority record (source version: 139)
RHEA:22369 RHEA:22369 authority record (source version: 139)
UniProtKB:P08202 UniProtKB:P08202 authority record (source version: 2026_03)
UniProtKB:P08203 UniProtKB:P08203 authority record (source version: 2026_03)
UniProtKB:P08204 UniProtKB:P08204 authority record (source version: 2026_03)
UniProtKB:P37680 UniProtKB:P37680 authority record (source version: 2026_03)
UniProtKB:P39306 UniProtKB:P39306 authority record (source version: 2026_03)

Curation history

2026-10-05T06:25:52Z codex
- EDIT — Review causal chemistry and add sourced molecular context
  Reviewed the entire record against MetaCyc 22.5 native pathway XML (including nested pathways), Rhea 139 explicit sides and directions, ENZYME 02-Sep-2026, PubMed records, and reviewed UniProt 2026_03 annotations within the record's taxon scope. Replaced generated structured-source quotations with source_assertion and source_locator. Typed molecular activities and participants. Reaction count 3 to 3; 2 directed-ID corrections; 5 protein annotations, 4 cofactor annotations and 0 sourced locations. All Rhea reaction substrate/product sets checked against independent Rhea authority; native pathway leaf coverage and source exceptions recorded in reports/causal_graph_review/metacyc-review.json. Full source URLs, versions and byte hashes are in metacyc-sources.json. All 50 MetaCyc records passed native schema validation; six targeted chemistry/evidence regression tests passed. Missing protein or cofactor annotations are not treated as biological absence; qualifications and exclusions are preserved in the ledger.
Read this curation session