D-arabinose degradation I

MetaCyc:DARABCAT-PWY

D-arabinose degradation I isomerizes D-arabinose to D-ribulose, then phosphorylates D-ribulose with ATP to form D-ribulose 5-phosphate for entry into pentose phosphate metabolism.

Pathway type

carbohydrate degradation

Organism scope

Escherichia coli B NCBITaxon:37762

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Escherichia coli B `NCBITaxon:37762`	taxon
D-arabinose isomerase `EC:5.3.1.3`	molecular activity
D-ribulokinase `EC:2.7.1.47`	molecular activity
D-arabinose `CHEBI:46994`	small molecule
D-ribulose `CHEBI:17173`	small molecule
ATP `CHEBI:30616`	small molecule
D-ribulose 5-phosphate `CHEBI:58121`	small molecule
ADP `CHEBI:456216`	small molecule
H(+) `CHEBI:15378`	small molecule
D-ribulokinase reaction `RHEA:17602`	reaction	left to right
D-arabinose isomerase reaction `RHEA:13850`	reaction	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
D-ribulose `CHEBI:17173`	consumes	D-ribulokinase reaction `RHEA:17602`	RHEA:17602 Source assertion: Rhea lists CHEBI:17173 on the substrates side of RHEA:17602 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17602']/rh:substrates; rh:contains/rh:compound/rh:accession`
ATP `CHEBI:30616`	consumes	D-ribulokinase reaction `RHEA:17602`	RHEA:17602 Source assertion: Rhea lists CHEBI:30616 on the substrates side of RHEA:17602 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17602']/rh:substrates; rh:contains/rh:compound/rh:accession`
D-ribulokinase reaction `RHEA:17602`	produces	H(+) `CHEBI:15378`	RHEA:17602 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:17602 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17602']/rh:products; rh:contains/rh:compound/rh:accession`
D-ribulokinase reaction `RHEA:17602`	produces	ADP `CHEBI:456216`	RHEA:17602 Source assertion: Rhea lists CHEBI:456216 on the products side of RHEA:17602 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17602']/rh:products; rh:contains/rh:compound/rh:accession`
D-ribulokinase reaction `RHEA:17602`	produces	D-ribulose 5-phosphate `CHEBI:58121`	RHEA:17602 Source assertion: Rhea lists CHEBI:58121 on the products side of RHEA:17602 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/17602']/rh:products; rh:contains/rh:compound/rh:accession`
D-arabinose `CHEBI:46994`	consumes	D-arabinose isomerase reaction `RHEA:13850`	RHEA:13850 Source assertion: Rhea lists CHEBI:46994 on the substrates side of RHEA:13850 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13850']/rh:substrates; rh:contains/rh:compound/rh:accession`
D-arabinose isomerase reaction `RHEA:13850`	produces	D-ribulose `CHEBI:17173`	RHEA:13850 Source assertion: Rhea lists CHEBI:17173 on the products side of RHEA:13850 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13850']/rh:products; rh:contains/rh:compound/rh:accession`
D-arabinose isomerase `EC:5.3.1.3`	catalyzes	D-arabinose isomerase reaction `RHEA:13850`	RHEA:13849 Source assertion: Rhea associates EC:5.3.1.3 with the reaction family containing RHEA:13850. Source location `rh:ec`
D-ribulokinase `EC:2.7.1.47`	catalyzes	D-ribulokinase reaction `RHEA:17602`	RHEA:17601 Source assertion: Rhea associates EC:2.7.1.47 with the reaction family containing RHEA:17602. Source location `rh:ec`
D-arabinose isomerase reaction `RHEA:13850`	precedes	D-ribulokinase reaction `RHEA:17602`	MetaCyc:DARABCAT-PWY Source assertion: MetaCyc pathway ordering places RHEA:13850 before RHEA:17602 in this pathway. Shared intermediate: CHEBI:17173. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`

References

MetaCyc:DARABCAT-PWY MetaCyc D-arabinose degradation I (source version: 22.5)
RHEA:13849 Rhea D-arabinose isomerase reaction (source version: 139)
RHEA:13852 Rhea bidirectional D-arabinose isomerase reaction (source version: 139)
RHEA:17601 Rhea D-ribulokinase reaction (source version: 139)
RHEA:17602 Rhea D-ribulose-5-phosphate-forming direction (source version: 139)
RHEA:13850 RHEA:13850 authority record (source version: 139)

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 2 to 2; 1 directed-ID corrections; 0 protein annotations, 0 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.
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D-arabinose degradation I

Pathway network

Components and activities

Mechanistic edges

References

Curation history