L-arginine degradation V (arginine deiminase pathway)

MetaCyc:ARGDEGRAD-PWY

L-arginine degradation through the arginine deiminase pathway converts L-arginine to L-citrulline, L-ornithine, ammonium, hydrogencarbonate, and ATP through arginine deiminase, catabolic ornithine carbamoyltransferase, and carbamate kinase.

Pathway type

amino acid degradation

Organism scope

Halobacterium salinarum NCBITaxon:2242

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Pathway network

23 nodes · 28 asserted directed edges

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Chemical / cofactor
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Cell / process context
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Dashed arrow: membership, location or cofactor relation

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Halobacterium salinarum `NCBITaxon:2242`	taxon
arginine deiminase `EC:3.5.3.6`	molecular activity
ornithine carbamoyltransferase `EC:2.1.3.3`	molecular activity
carbamate kinase `EC:2.7.2.2`	molecular activity
L-arginine `CHEBI:32682`	small molecule
H2O `CHEBI:15377`	small molecule
L-citrulline `CHEBI:57743`	small molecule
ammonium `CHEBI:28938`	small molecule
phosphate `CHEBI:43474`	small molecule
H+ `CHEBI:15378`	small molecule
carbamoyl phosphate `CHEBI:58228`	small molecule
L-ornithine `CHEBI:46911`	small molecule
ADP `CHEBI:456216`	small molecule
ATP `CHEBI:30616`	small molecule
hydrogencarbonate `CHEBI:17544`	small molecule
carbamate `CHEBI:13941`	small molecule
carbon dioxide `CHEBI:16526`	small molecule
Carbamate kinase `UniProtKB:Q48295`	protein
cytoplasm `GO:0005737`	cellular component
Ornithine carbamoyltransferase, catabolic `UniProtKB:Q48296`	protein
L-arginine deiminase reaction `RHEA:19598`	reaction	left to right
catabolic ornithine carbamoyltransferase reaction `RHEA:19515`	reaction	right to left
carbamoyl phosphate + ADP => carbamate + ATP `RHEA:30757`	reaction	right to left
carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	reaction	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
H2O `CHEBI:15377`	consumes	L-arginine deiminase reaction `RHEA:19598`	RHEA:19598 Source assertion: Rhea lists CHEBI:15377 on the substrates side of RHEA:19598 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19598']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-arginine `CHEBI:32682`	consumes	L-arginine deiminase reaction `RHEA:19598`	RHEA:19598 Source assertion: Rhea lists CHEBI:32682 on the substrates side of RHEA:19598 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19598']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-arginine deiminase reaction `RHEA:19598`	produces	ammonium `CHEBI:28938`	RHEA:19598 Source assertion: Rhea lists CHEBI:28938 on the products side of RHEA:19598 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19598']/rh:products; rh:contains/rh:compound/rh:accession`
L-arginine deiminase reaction `RHEA:19598`	produces	L-citrulline `CHEBI:57743`	RHEA:19598 Source assertion: Rhea lists CHEBI:57743 on the products side of RHEA:19598 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19598']/rh:products; rh:contains/rh:compound/rh:accession`
H+ `CHEBI:15378`	consumes	catabolic ornithine carbamoyltransferase reaction `RHEA:19515`	RHEA:19515 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:19515 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19515']/rh:substrates; rh:contains/rh:compound/rh:accession`
phosphate `CHEBI:43474`	consumes	catabolic ornithine carbamoyltransferase reaction `RHEA:19515`	RHEA:19515 Source assertion: Rhea lists CHEBI:43474 on the substrates side of RHEA:19515 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19515']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-citrulline `CHEBI:57743`	consumes	catabolic ornithine carbamoyltransferase reaction `RHEA:19515`	RHEA:19515 Source assertion: Rhea lists CHEBI:57743 on the substrates side of RHEA:19515 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19515']/rh:substrates; rh:contains/rh:compound/rh:accession`
catabolic ornithine carbamoyltransferase reaction `RHEA:19515`	produces	L-ornithine `CHEBI:46911`	RHEA:19515 Source assertion: Rhea lists CHEBI:46911 on the products side of RHEA:19515 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19515']/rh:products; rh:contains/rh:compound/rh:accession`
catabolic ornithine carbamoyltransferase reaction `RHEA:19515`	produces	carbamoyl phosphate `CHEBI:58228`	RHEA:19515 Source assertion: Rhea lists CHEBI:58228 on the products side of RHEA:19515 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19515']/rh:products; rh:contains/rh:compound/rh:accession`
ADP `CHEBI:456216`	consumes	carbamoyl phosphate + ADP => carbamate + ATP `RHEA:30757`	RHEA:30757 Source assertion: Rhea lists CHEBI:456216 on the substrates side of RHEA:30757 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/30757']/rh:substrates; rh:contains/rh:compound/rh:accession`
carbamoyl phosphate `CHEBI:58228`	consumes	carbamoyl phosphate + ADP => carbamate + ATP `RHEA:30757`	RHEA:30757 Source assertion: Rhea lists CHEBI:58228 on the substrates side of RHEA:30757 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/30757']/rh:substrates; rh:contains/rh:compound/rh:accession`
carbamoyl phosphate + ADP => carbamate + ATP `RHEA:30757`	produces	carbamate `CHEBI:13941`	RHEA:30757 Source assertion: Rhea lists CHEBI:13941 on the products side of RHEA:30757 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/30757']/rh:products; rh:contains/rh:compound/rh:accession`
carbamoyl phosphate + ADP => carbamate + ATP `RHEA:30757`	produces	ATP `CHEBI:30616`	RHEA:30757 Source assertion: Rhea lists CHEBI:30616 on the products side of RHEA:30757 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/30757']/rh:products; rh:contains/rh:compound/rh:accession`
carbamate `CHEBI:13941`	consumes	carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	RHEA:15650 Source assertion: Rhea lists CHEBI:13941 on the substrates side of RHEA:15650 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/15650']/rh:substrates; rh:contains/rh:compound/rh:accession`
H+ `CHEBI:15378`	consumes	carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	RHEA:15650 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:15650 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/15650']/rh:substrates; rh:contains/rh:compound/rh:accession`
carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	produces	carbon dioxide `CHEBI:16526`	RHEA:15650 Source assertion: Rhea lists CHEBI:16526 on the products side of RHEA:15650 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/15650']/rh:products; rh:contains/rh:compound/rh:accession`
carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	produces	ammonium `CHEBI:28938`	RHEA:15650 Source assertion: Rhea lists CHEBI:28938 on the products side of RHEA:15650 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/15650']/rh:products; rh:contains/rh:compound/rh:accession`
arginine deiminase `EC:3.5.3.6`	catalyzes	L-arginine deiminase reaction `RHEA:19598`	RHEA:19597 Source assertion: Rhea associates EC:3.5.3.6 with the reaction family containing RHEA:19598. Source location `rh:ec` PMID:8759859 arcA gene coding for arginine deiminase Source location `PubMed Abstract`
ornithine carbamoyltransferase `EC:2.1.3.3`	catalyzes	catabolic ornithine carbamoyltransferase reaction `RHEA:19515`	RHEA:19513 Source assertion: Rhea associates EC:2.1.3.3 with the reaction family containing RHEA:19515. Source location `rh:ec` PMID:8759859 catabolic ornithine transcarbamylase and the corresponding gene, arcB Source location `PubMed Abstract`
carbamate kinase `EC:2.7.2.2`	catalyzes	carbamoyl phosphate + ADP => carbamate + ATP `RHEA:30757`	MetaCyc:ARGDEGRAD-PWY Source assertion: The native pathway assigns EC:2.7.2.2 activity to the enzymatic step represented by RHEA:30757; this is a component step when the EC definition is an overall reaction. Source location `Pathway/reaction-layout; Reaction/enzymatic-reaction and component-reaction relationships` PMID:8759859 arcC gene coding for carbamate kinase Source location `PubMed Abstract`
catabolic ornithine carbamoyltransferase reaction `RHEA:19515`	precedes	carbamoyl phosphate + ADP => carbamate + ATP `RHEA:30757`	MetaCyc:ARGDEGRAD-PWY Source assertion: MetaCyc pathway ordering places RHEA:19515 before RHEA:30757 in this pathway. Shared intermediate: CHEBI:58228. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
L-arginine deiminase reaction `RHEA:19598`	precedes	catabolic ornithine carbamoyltransferase reaction `RHEA:19515`	MetaCyc:ARGDEGRAD-PWY Source assertion: MetaCyc pathway ordering places RHEA:19598 before RHEA:19515 in this pathway. Shared intermediate: CHEBI:57743. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
carbamoyl phosphate + ADP => carbamate + ATP `RHEA:30757`	precedes	carbamate + 2 H(+) => NH4(+) + CO2 `RHEA:15650`	MetaCyc:ARGDEGRAD-PWY Source assertion: MetaCyc pathway ordering places RHEA:30757 before RHEA:15650 in this pathway. Shared intermediate: CHEBI:13941. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
Carbamate kinase `UniProtKB:Q48295`	enables	carbamoyl phosphate + ADP => carbamate + ATP `RHEA:30757`	UniProtKB:Q48295 Source assertion: UniProt annotates UniProtKB:Q48295 with catalytic activity for the overall reaction containing the native MetaCyc enzymatic component RHEA:30757. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:64091. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Carbamate kinase `UniProtKB:Q48295`	located_in	cytoplasm `GO:0005737`	UniProtKB:Q48295 Source assertion: UniProt locates UniProtKB:Q48295 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: ECO:0000305. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
Ornithine carbamoyltransferase, catabolic `UniProtKB:Q48296`	enables	catabolic ornithine carbamoyltransferase reaction `RHEA:19515`	UniProtKB:Q48296 Source assertion: UniProt annotates UniProtKB:Q48296 with catalytic activity for the reaction family of RHEA:19515. Annotation evidence: curated source annotation; organism taxon: NCBITaxon:64091. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
L-arginine `CHEBI:32682`	activates	Ornithine carbamoyltransferase, catabolic `UniProtKB:Q48296`	UniProtKB:Q48296 Source assertion: UniProt activity-regulation annotation: Arginine lead to a slight activation. Inhibited by all nucleotide phosphates Source location `comments[commentType='ACTIVITY REGULATION'].texts`
Ornithine carbamoyltransferase, catabolic `UniProtKB:Q48296`	located_in	cytoplasm `GO:0005737`	UniProtKB:Q48296 Source assertion: UniProt locates UniProtKB:Q48296 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: ECO:0000305. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`

References

MetaCyc:ARGDEGRAD-PWY MetaCyc L-arginine degradation V pathway (source version: 22.5)
RHEA:19598 Rhea L-arginine deiminase direction (source version: 139)
RHEA:19515 Rhea catabolic ornithine carbamoyltransferase direction (source version: 139)
RHEA:10154 Rhea ATP-forming carbamate kinase direction (source version: 139)
PMID:8759859 Ruepp and Soppa, Journal of Bacteriology, 1996
RHEA:30757 RHEA:30757 authority record (source version: 139)
RHEA:15650 RHEA:15650 authority record (source version: 139)
RHEA:19597 RHEA:19597 authority record (source version: 139)
RHEA:19513 RHEA:19513 authority record (source version: 139)
UniProtKB:Q48295 UniProtKB:Q48295 authority record (source version: 2026_03)
UniProtKB:Q48296 UniProtKB:Q48296 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 4; 0 directed-ID corrections; 2 protein annotations, 0 cofactor annotations and 2 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. Expanded combined reaction steps: RHEA:10154.
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