L-Carnitine Degradation I

PathBank:SMP0002051

The four-reaction PathBank route represents anaerobic L-carnitine reduction to gamma-butyrobetaine through CoA thioesters, using characterized Escherichia coli K-12 Cai proteins. CaiC supplies the initial carnitinyl-CoA pool; CaiD dehydrates it, CaiA reduces crotonobetainyl-CoA, and the CaiB homodimer transfers CoA to another carnitine molecule, releasing gamma-butyrobetaine and regenerating carnitinyl-CoA. Thus ATP-dependent initiation is distinct from the recycling loop. Rhea charge forms and both generic electron-transfer flavoprotein redox states are retained; the exact physiological donor complex is unresolved. FAD bound to CaiA is a separate cofactor. Selected catabolic directions do not imply irreversibility of CaiD or CaiB. This enzyme mechanism does not establish growth or expression in every K-12 strain, and is distinct from aerobic carnitine assimilation. The older native map defines the route boundary; its erroneous or underspecified chemical xrefs are not adopted as exact identities.

Pathway type
anaerobic carnitine catabolism
Organism scope

Read the source YAML

Pathway network

24 nodes · 32 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.

Pathway network: L-Carnitine Degradation I 24 nodes · 32 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. CHEBI:16347 — consumes → RHEA:28515; Evidence: RHEA:28515consumes CHEBI:30616 — consumes → RHEA:28515; Evidence: RHEA:28515consumes CHEBI:57287 — consumes → RHEA:28515; Evidence: RHEA:28515consumes RHEA:28515 — produces → CHEBI:60932; Evidence: RHEA:28515produces RHEA:28515 — produces → CHEBI:456215; Evidence: RHEA:28515produces RHEA:28515 — produces → CHEBI:33019; Evidence: RHEA:28515produces CHEBI:60932 — consumes → RHEA:28339; Evidence: RHEA:28339consumes RHEA:28339 — produces → CHEBI:60933; Evidence: RHEA:28339produces RHEA:28339 — produces → CHEBI:15377; Evidence: RHEA:28339produces CHEBI:60933 — consumes → RHEA:51586; Evidence: RHEA:51586consumes RHEA-COMP:10686 — consumes → RHEA:51586; This is a whole generic electron-transfer flavoprotein redox state, not free FAD/FADH2 and not an identified FixA/FixB complex. Coefficient 1 belongs to the Rhea reference equation.; Evidence: RHEA:51586, UniProtKB:P60584consumes RHEA:51586 — produces → CHEBI:61513; Evidence: RHEA:51586produces RHEA:51586 — produces → RHEA-COMP:10685; This is a whole generic electron-transfer flavoprotein redox state, not free FAD/FADH2 and not an identified FixA/FixB complex. Coefficient 1 belongs to the Rhea reference equation.; Evidence: RHEA:51586, UniProtKB:P60584produces RHEA:51586 — produces → CHEBI:15378; Evidence: RHEA:51586produces CHEBI:61513 — consumes → RHEA:28419; Evidence: RHEA:28419consumes CHEBI:16347 — consumes → RHEA:28419; Evidence: RHEA:28419consumes RHEA:28419 — produces → CHEBI:60932; Evidence: RHEA:28419produces RHEA:28419 — produces → CHEBI:16244; Evidence: RHEA:28419produces UniProtKB:P31552 — catalyzes → RHEA:28515; CaiC primes the CoA-linked cycle; this ATP-dependent step does not imply one ATP hydrolyzed per subsequent carnitine reduction. Its other betaine substrates lie outside this native four-reaction route.; Evidence: UniProtKB:P31552, RHEA:28515, PMID:18266698catalyzes UniProtKB:P31551 — catalyzes → RHEA:28339; The protein accession denotes CaiD enzyme identity; UniProt describes a homotrimer. The catabolic dehydration direction is selected from a reversible hydration/dehydration reaction, not a free-carnitine dehydratase reaction.; Evidence: UniProtKB:P31551, RHEA:28339, PMID:11551212catalyzes UniProtKB:P60584 — catalyzes → RHEA:51586; The protein accession denotes CaiA enzyme identity; UniProt describes a homotetramer. The selected right-to-left direction of Rhea 51584 reduces crotonobetainyl-CoA. Genetic requirement for fixA/fixB does not identify a directly measured physiological carrier complex or its electron-transfer stoichiometry.; Evidence: UniProtKB:P60584, RHEA:51586, PMID:12081978catalyzes PathBank:SMP0002051/ProteinComplex/4010 — catalyzes → RHEA:28419; The native CaiB homodimer transfers CoA from gamma-butyrobetainyl-CoA to fresh carnitine. The selected direction releases gamma-butyrobetaine and regenerates carnitinyl-CoA; the characterized CoA transfer is reversible.; Evidence: UniProtKB:P31572, RHEA:28419, PathBank:SMP0002051catalyzes PathBank:SMP0002051/ProteinComplex/4010 — has_part → UniProtKB:P31572; Two copies of CaiB form the source-defined homodimer; the graph represents membership once and preserves the copy number here and in the evidence.; Evidence: PathBank:SMP0002051, UniProtKB:P31572, PMID:15518548has part UniProtKB:P60584 — has_cofactor → CHEBI:57692; This is FAD bound to CaiA, separate from the flavin reactive part of the generic electron-transfer flavoprotein in the Rhea redox reaction. The ChEBI charge form follows the curated cofactor cross-reference.; Evidence: UniProtKB:P60584, PMID:10209289has cofactor RHEA:28515 — part_of → PathBank:SMP0002051; Manual source correspondence based on the native catalyst and biochemical transformation, not a native Rhea cross-reference or exactMatch. Current Rhea chemistry supplies explicit charge/stereo forms and corrects the older map's chemical-identity defects.; Evidence: PathBank:SMP0002051, UniProtKB:P31552part of RHEA:28339 — part_of → PathBank:SMP0002051; Manual source correspondence based on the native catalyst and biochemical transformation, not a native Rhea cross-reference or exactMatch. Current Rhea chemistry supplies explicit charge/stereo forms and corrects the older map's chemical-identity defects.; Evidence: PathBank:SMP0002051, UniProtKB:P31551part of RHEA:51586 — part_of → PathBank:SMP0002051; Manual source correspondence based on the native catalyst and biochemical transformation, not a native Rhea cross-reference or exactMatch. Current Rhea chemistry supplies explicit charge/stereo forms and corrects the older map's chemical-identity defects.; Evidence: PathBank:SMP0002051, UniProtKB:P60584part of RHEA:28419 — part_of → PathBank:SMP0002051; Manual source correspondence based on the native catalyst and biochemical transformation, not a native Rhea cross-reference or exactMatch. Current Rhea chemistry supplies explicit charge/stereo forms and corrects the older map's chemical-identity defects.; Evidence: PathBank:SMP0002051, UniProtKB:P31572part of RHEA:28515 — provides_input_for → RHEA:28339; CaiC supplies the initial carnitinyl-CoA pool for CaiD; the subsequent CaiB loop recycles that pool.; Evidence: RHEA:28515, RHEA:28339provides input for RHEA:28339 — provides_input_for → RHEA:51586; The product CHEBI:60933 is the next selected reaction substrate.; Evidence: RHEA:28339, RHEA:51586provides input for RHEA:51586 — provides_input_for → RHEA:28419; The product CHEBI:61513 is the next selected reaction substrate.; Evidence: RHEA:51586, RHEA:28419provides input for RHEA:28419 — provides_input_for → RHEA:28339; CaiB regenerates carnitinyl-CoA for another cycle; this material-flow loop does not assert a temporal order from the native pathwayOrder array.; Evidence: RHEA:28419, RHEA:28339provides input for (R)-carnitine; CHEBI:16347; Declared type: small_molecule small molecule (R)-carnitine ATP(4-); CHEBI:30616; Declared type: small_molecule small molecule ATP(4-) coenzyme A(4-); CHEBI:57287; Declared type: small_molecule small molecule coenzyme A(4-) (R)-carnitinyl-CoA(3-); CHEBI:60932; Declared type: small_molecule small molecule (R)-carnitinyl-CoA(3-) adenosine 5'-monophosphate(2-); CHEBI:456215; Declared type: small_molecule small molecule adenosine 5'-monophosphate(2-) diphosphate(3-); CHEBI:33019; Declared type: small_molecule small molecule diphosphate(3-) (E)-4-(trimethylammonio)but-2-enoyl-CoA(3-); CHEBI:60933; Declared type: small_molecule small molecule (E)-4-(trimethylammonio)but- 2-enoyl-CoA(3-) water; CHEBI:15377; Declared type: small_molecule small molecule water gamma-butyrobetainyl-CoA(3-); CHEBI:61513; Declared type: small_molecule small molecule gamma-butyrobetainyl-CoA(3-) hydron; CHEBI:15378; Declared type: small_molecule small molecule hydron 4-(trimethylammonio)butanoate; CHEBI:16244; Declared type: small_molecule small molecule 4- (trimethylammonio)butanoate FAD(3-); CHEBI:57692; Declared type: cofactor cofactor FAD(3-) oxidized [electron-transfer flavoprotein]; RHEA-COMP:10685; Declared type: protein protein oxidized [electron-transfer flavoprotein] reduced [electron-transfer flavoprotein]; RHEA-COMP:10686; Declared type: protein protein reduced [electron-transfer flavoprotein] Crotonobetaine/carnitine--CoA ligase; UniProtKB:P31552; Declared type: protein protein Crotonobetaine/carnitine-- CoA ligase Carnitinyl-CoA dehydratase; UniProtKB:P31551; Declared type: protein protein Carnitinyl-CoA dehydratase Crotonobetainyl-CoA reductase; UniProtKB:P60584; Declared type: protein protein Crotonobetainyl-CoA reductase L-carnitine CoA-transferase; UniProtKB:P31572; Declared type: protein protein L-carnitine CoA-transferase γ-butyrobetainyl-CoA:carnitine CoA transferase; PathBank:SMP0002051/ProteinComplex/4010; Declared type: complex complex γ-butyrobetainyl- CoA:carnitine CoA transferase CaiC ATP-dependent initial carnitinyl-CoA formation; RHEA:28515; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity CaiC ATP-dependent initial carnitinyl-CoA formation CaiD carnitinyl-CoA dehydration; RHEA:28339; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity CaiD carnitinyl-CoA dehydration CaiA crotonobetainyl-CoA reduction; RHEA:51586; Declared type: molecular_activity; Source reaction direction: right_to_left molecular activity CaiA crotonobetainyl-CoA reduction CaiB CoA transfer to carnitine and gamma-butyrobetaine release; RHEA:28419; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity CaiB CoA transfer to carnitine and gamma- butyrobetaine release L-Carnitine Degradation I; PathBank:SMP0002051; Declared type: pathway pathway L-Carnitine Degradation I

Components and activities

Declared biological components and source reaction directions
NodeKind or roleSource direction
Escherichia coli K-12
NCBITaxon:83333		taxon
(R)-carnitine
CHEBI:16347		small molecule
ATP(4-)
CHEBI:30616		small molecule
coenzyme A(4-)
CHEBI:57287		small molecule
(R)-carnitinyl-CoA(3-)
CHEBI:60932		small molecule
adenosine 5'-monophosphate(2-)
CHEBI:456215		small molecule
diphosphate(3-)
CHEBI:33019		small molecule
(E)-4-(trimethylammonio)but-2-enoyl-CoA(3-)
CHEBI:60933		small molecule
water
CHEBI:15377		small molecule
gamma-butyrobetainyl-CoA(3-)
CHEBI:61513		small molecule
hydron
CHEBI:15378		small molecule
4-(trimethylammonio)butanoate
CHEBI:16244		small molecule
FAD(3-)
CHEBI:57692		cofactor
oxidized [electron-transfer flavoprotein]
RHEA-COMP:10685		protein
reduced [electron-transfer flavoprotein]
RHEA-COMP:10686		protein
Crotonobetaine/carnitine--CoA ligase
UniProtKB:P31552		protein
Carnitinyl-CoA dehydratase
UniProtKB:P31551		protein
Crotonobetainyl-CoA reductase
UniProtKB:P60584		protein
L-carnitine CoA-transferase
UniProtKB:P31572		protein
γ-butyrobetainyl-CoA:carnitine CoA transferase
PathBank:SMP0002051/ProteinComplex/4010		complex
CaiC ATP-dependent initial carnitinyl-CoA formation
RHEA:28515		molecular activityleft to right
CaiD carnitinyl-CoA dehydration
RHEA:28339		molecular activityleft to right
CaiA crotonobetainyl-CoA reduction
RHEA:51586		molecular activityright to left
CaiB CoA transfer to carnitine and gamma-butyrobetaine release
RHEA:28419		molecular activityleft to right

Mechanistic edges

Mechanistic edges and their cited evidence
SubjectPredicate and descriptionObjectEvidence
(R)-carnitine
CHEBI:16347		consumes

CaiC ATP-dependent initial carnitinyl-CoA formation
RHEA:28515
  • RHEA:28515

    Source assertion: Rhea places CHEBI:16347 on the substrates side of directed RHEA:28515, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28515"]/rh:substrates; http://rdf.rhea-db.org/28514_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_28514_compound_4231/rh:compound -> http://rdf.rhea-db.org/Compound_4231/rh:chebi
ATP(4-)
CHEBI:30616		consumes

CaiC ATP-dependent initial carnitinyl-CoA formation
RHEA:28515
  • RHEA:28515

    Source assertion: Rhea places CHEBI:30616 on the substrates side of directed RHEA:28515, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28515"]/rh:substrates; http://rdf.rhea-db.org/28514_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_28514_compound_6372/rh:compound -> http://rdf.rhea-db.org/Compound_6372/rh:chebi
coenzyme A(4-)
CHEBI:57287		consumes

CaiC ATP-dependent initial carnitinyl-CoA formation
RHEA:28515
  • RHEA:28515

    Source assertion: Rhea places CHEBI:57287 on the substrates side of directed RHEA:28515, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28515"]/rh:substrates; http://rdf.rhea-db.org/28514_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_28514_compound_1264/rh:compound -> http://rdf.rhea-db.org/Compound_1264/rh:chebi
CaiC ATP-dependent initial carnitinyl-CoA formation
RHEA:28515		produces

(R)-carnitinyl-CoA(3-)
CHEBI:60932
  • RHEA:28515

    Source assertion: Rhea places CHEBI:60932 on the products side of directed RHEA:28515, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28515"]/rh:products; http://rdf.rhea-db.org/28514_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_28514_compound_6425/rh:compound -> http://rdf.rhea-db.org/Compound_6425/rh:chebi
CaiC ATP-dependent initial carnitinyl-CoA formation
RHEA:28515		produces

adenosine 5'-monophosphate(2-)
CHEBI:456215
  • RHEA:28515

    Source assertion: Rhea places CHEBI:456215 on the products side of directed RHEA:28515, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28515"]/rh:products; http://rdf.rhea-db.org/28514_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_28514_compound_2590/rh:compound -> http://rdf.rhea-db.org/Compound_2590/rh:chebi
CaiC ATP-dependent initial carnitinyl-CoA formation
RHEA:28515		produces

diphosphate(3-)
CHEBI:33019
  • RHEA:28515

    Source assertion: Rhea places CHEBI:33019 on the products side of directed RHEA:28515, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28515"]/rh:products; http://rdf.rhea-db.org/28514_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_28514_compound_2106/rh:compound -> http://rdf.rhea-db.org/Compound_2106/rh:chebi
(R)-carnitinyl-CoA(3-)
CHEBI:60932		consumes

CaiD carnitinyl-CoA dehydration
RHEA:28339
  • RHEA:28339

    Source assertion: Rhea places CHEBI:60932 on the substrates side of directed RHEA:28339, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28339"]/rh:substrates; http://rdf.rhea-db.org/28338_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_28338_compound_6425/rh:compound -> http://rdf.rhea-db.org/Compound_6425/rh:chebi
CaiD carnitinyl-CoA dehydration
RHEA:28339		produces

(E)-4-(trimethylammonio)but-2-enoyl-CoA(3-)
CHEBI:60933
  • RHEA:28339

    Source assertion: Rhea places CHEBI:60933 on the products side of directed RHEA:28339, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28339"]/rh:products; http://rdf.rhea-db.org/28338_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_28338_compound_6426/rh:compound -> http://rdf.rhea-db.org/Compound_6426/rh:chebi
CaiD carnitinyl-CoA dehydration
RHEA:28339		produces

water
CHEBI:15377
  • RHEA:28339

    Source assertion: Rhea places CHEBI:15377 on the products side of directed RHEA:28339, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28339"]/rh:products; http://rdf.rhea-db.org/28338_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_28338_compound_1283/rh:compound -> http://rdf.rhea-db.org/Compound_1283/rh:chebi
(E)-4-(trimethylammonio)but-2-enoyl-CoA(3-)
CHEBI:60933		consumes

CaiA crotonobetainyl-CoA reduction
RHEA:51586
  • RHEA:51586

    Source assertion: Rhea places CHEBI:60933 on the substrates side of directed RHEA:51586, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/51586"]/rh:substrates; http://rdf.rhea-db.org/51584_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_51584_compound_6426/rh:compound -> http://rdf.rhea-db.org/Compound_6426/rh:chebi
reduced [electron-transfer flavoprotein]
RHEA-COMP:10686		consumes

This is a whole generic electron-transfer flavoprotein redox state, not free FAD/FADH2 and not an identified FixA/FixB complex. Coefficient 1 belongs to the Rhea reference equation.

CaiA crotonobetainyl-CoA reduction
RHEA:51586
  • RHEA:51586

    Source assertion: Rhea places RHEA-COMP:10686 on the substrates side of directed RHEA:51586, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/51586"]/rh:substrates; http://rdf.rhea-db.org/51584_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_51584_compound_10686/rh:compound -> http://rdf.rhea-db.org/Compound_10686/rh:id, rh:name, rdfs:subClassOf
  • UniProtKB:P60584

    Source assertion: CaiA catalytic activity cross-references RHEA-COMP:10686 as a Rhea component of the electron-transfer flavoprotein reaction. The function annotation proposes, but does not establish, FixA/FixB as donor.

    Source locationcomments[1].reaction.reactionCrossReferences; comments[0].texts[0] (FUNCTION)
CaiA crotonobetainyl-CoA reduction
RHEA:51586		produces

gamma-butyrobetainyl-CoA(3-)
CHEBI:61513
  • RHEA:51586

    Source assertion: Rhea places CHEBI:61513 on the products side of directed RHEA:51586, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/51586"]/rh:products; http://rdf.rhea-db.org/51584_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_51584_compound_6459/rh:compound -> http://rdf.rhea-db.org/Compound_6459/rh:chebi
CaiA crotonobetainyl-CoA reduction
RHEA:51586		produces

This is a whole generic electron-transfer flavoprotein redox state, not free FAD/FADH2 and not an identified FixA/FixB complex. Coefficient 1 belongs to the Rhea reference equation.

oxidized [electron-transfer flavoprotein]
RHEA-COMP:10685
  • RHEA:51586

    Source assertion: Rhea places RHEA-COMP:10685 on the products side of directed RHEA:51586, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/51586"]/rh:products; http://rdf.rhea-db.org/51584_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_51584_compound_10685/rh:compound -> http://rdf.rhea-db.org/Compound_10685/rh:id, rh:name, rdfs:subClassOf
  • UniProtKB:P60584

    Source assertion: CaiA catalytic activity cross-references RHEA-COMP:10685 as a Rhea component of the electron-transfer flavoprotein reaction. The function annotation proposes, but does not establish, FixA/FixB as donor.

    Source locationcomments[1].reaction.reactionCrossReferences; comments[0].texts[0] (FUNCTION)
CaiA crotonobetainyl-CoA reduction
RHEA:51586		produces

hydron
CHEBI:15378
  • RHEA:51586

    Source assertion: Rhea places CHEBI:15378 on the products side of directed RHEA:51586, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/51586"]/rh:products; http://rdf.rhea-db.org/51584_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_51584_compound_3249/rh:compound -> http://rdf.rhea-db.org/Compound_3249/rh:chebi
gamma-butyrobetainyl-CoA(3-)
CHEBI:61513		consumes

CaiB CoA transfer to carnitine and gamma-butyrobetaine release
RHEA:28419
  • RHEA:28419

    Source assertion: Rhea places CHEBI:61513 on the substrates side of directed RHEA:28419, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28419"]/rh:substrates; http://rdf.rhea-db.org/28418_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_28418_compound_6459/rh:compound -> http://rdf.rhea-db.org/Compound_6459/rh:chebi
(R)-carnitine
CHEBI:16347		consumes

CaiB CoA transfer to carnitine and gamma-butyrobetaine release
RHEA:28419
  • RHEA:28419

    Source assertion: Rhea places CHEBI:16347 on the substrates side of directed RHEA:28419, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28419"]/rh:substrates; http://rdf.rhea-db.org/28418_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_28418_compound_4231/rh:compound -> http://rdf.rhea-db.org/Compound_4231/rh:chebi
CaiB CoA transfer to carnitine and gamma-butyrobetaine release
RHEA:28419		produces

(R)-carnitinyl-CoA(3-)
CHEBI:60932
  • RHEA:28419

    Source assertion: Rhea places CHEBI:60932 on the products side of directed RHEA:28419, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28419"]/rh:products; http://rdf.rhea-db.org/28418_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_28418_compound_6425/rh:compound -> http://rdf.rhea-db.org/Compound_6425/rh:chebi
CaiB CoA transfer to carnitine and gamma-butyrobetaine release
RHEA:28419		produces

4-(trimethylammonio)butanoate
CHEBI:16244
  • RHEA:28419

    Source assertion: Rhea places CHEBI:16244 on the products side of directed RHEA:28419, with coefficient 1.

    Source locationrdf:Description[@rdf:about="http://rdf.rhea-db.org/28419"]/rh:products; http://rdf.rhea-db.org/28418_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_28418_compound_5286/rh:compound -> http://rdf.rhea-db.org/Compound_5286/rh:chebi
Crotonobetaine/carnitine--CoA ligase
UniProtKB:P31552		catalyzes

CaiC primes the CoA-linked cycle; this ATP-dependent step does not imply one ATP hydrolyzed per subsequent carnitine reduction. Its other betaine substrates lie outside this native four-reaction route.

CaiC ATP-dependent initial carnitinyl-CoA formation
RHEA:28515
  • UniProtKB:P31552

    Source assertion: UniProt assigns RHEA:28514 catalytic activity to P31552 with ECO:0000269/PubMed:18266698 and ECO:0000255/HAMAP-Rule:MF_01524; its function supports the selected pathway transformation.

    Source locationcomments[3].reaction.reactionCrossReferences; comments[3].reaction.evidences; comments[0].texts[0]
  • RHEA:28515

    Source assertion: Rhea identifies RHEA:28515 as the left_to_right directed form of RHEA:28514.

    Source locationhttp://rdf.rhea-db.org/28514/rh:directionalReaction; http://rdf.rhea-db.org/28515/rh:substrates, rh:products
  • PMID:18266698
    the main in vivo role of CaiC was found to be the synthesis of betainyl-CoAs
Carnitinyl-CoA dehydratase
UniProtKB:P31551		catalyzes

The protein accession denotes CaiD enzyme identity; UniProt describes a homotrimer. The catabolic dehydration direction is selected from a reversible hydration/dehydration reaction, not a free-carnitine dehydratase reaction.

CaiD carnitinyl-CoA dehydration
RHEA:28339
  • UniProtKB:P31551

    Source assertion: UniProt assigns RHEA:28338 catalytic activity to P31551 with ECO:0000269/PubMed:11551212 and ECO:0000255/HAMAP-Rule:MF_01051; its function supports the selected pathway transformation.

    Source locationcomments[1].reaction.reactionCrossReferences; comments[1].reaction.evidences; comments[0].texts[0]
  • RHEA:28339

    Source assertion: Rhea identifies RHEA:28339 as the left_to_right directed form of RHEA:28338.

    Source locationhttp://rdf.rhea-db.org/28338/rh:directionalReaction; http://rdf.rhea-db.org/28339/rh:substrates, rh:products
  • PMID:11551212
    CaiD was shown to be a crotonobetainyl-CoA hydratase
Crotonobetainyl-CoA reductase
UniProtKB:P60584		catalyzes

The protein accession denotes CaiA enzyme identity; UniProt describes a homotetramer. The selected right-to-left direction of Rhea 51584 reduces crotonobetainyl-CoA. Genetic requirement for fixA/fixB does not identify a directly measured physiological carrier complex or its electron-transfer stoichiometry.

CaiA crotonobetainyl-CoA reduction
RHEA:51586
  • UniProtKB:P60584

    Source assertion: UniProt assigns RHEA:51584 catalytic activity to P60584 with ECO:0000269/PubMed:10978161 and ECO:0000255/HAMAP-Rule:MF_01052; its function supports the selected pathway transformation.

    Source locationcomments[1].reaction.reactionCrossReferences; comments[1].reaction.evidences; comments[0].texts[0]
  • RHEA:51586

    Source assertion: Rhea identifies RHEA:51586 as the right_to_left directed form of RHEA:51584.

    Source locationhttp://rdf.rhea-db.org/51584/rh:directionalReaction; http://rdf.rhea-db.org/51586/rh:substrates, rh:products
  • PMID:12081978

    Source assertion: E. coli fixA and fixB mutants failed to reduce carnitine to gamma-butyrobetaine anaerobically. Electron provision by the neighboring fix operon was proposed, rather than a particular donor-protein reaction being directly established.

    Source locationAbstract, final two sentences; Europe PMC resultList.result[id=12081978].abstractText
γ-butyrobetainyl-CoA:carnitine CoA transferase
PathBank:SMP0002051/ProteinComplex/4010		catalyzes

The native CaiB homodimer transfers CoA from gamma-butyrobetainyl-CoA to fresh carnitine. The selected direction releases gamma-butyrobetaine and regenerates carnitinyl-CoA; the characterized CoA transfer is reversible.

CaiB CoA transfer to carnitine and gamma-butyrobetaine release
RHEA:28419
  • UniProtKB:P31572

    Source assertion: UniProt assigns RHEA:28418 catalytic activity to P31572 with ECO:0000269/PubMed:11551212 and ECO:0000255/HAMAP-Rule:MF_01050; its function supports the selected pathway transformation.

    Source locationcomments[2].reaction.reactionCrossReferences; comments[2].reaction.evidences; comments[0].texts[0]
  • RHEA:28419

    Source assertion: Rhea identifies RHEA:28419 as the left_to_right directed form of RHEA:28418.

    Source locationhttp://rdf.rhea-db.org/28418/rh:directionalReaction; http://rdf.rhea-db.org/28419/rh:substrates, rh:products
  • PathBank:SMP0002051

    Source assertion: Native ReactionCatalysis/5916 connects ProteinComplex/4010 to Reactions/5953; its single protein component is CaiB (UniProt P31572), with stoichiometric coefficient 2.

    Source locationPW002037.owl: ReactionCatalysis/5916/bp:controller, bp:controlled; ProteinComplex/4010/bp:component, bp:componentStoichiometry
γ-butyrobetainyl-CoA:carnitine CoA transferase
PathBank:SMP0002051/ProteinComplex/4010		has_part

Two copies of CaiB form the source-defined homodimer; the graph represents membership once and preserves the copy number here and in the evidence.

L-carnitine CoA-transferase
UniProtKB:P31572
  • PathBank:SMP0002051

    Source assertion: The native complex has component Protein/6507, linked to UniProt P31572, with stoichiometric coefficient 2.

    Source locationPW002037.owl: ProteinComplex/4010/bp:component; Protein/6507/Stoichiometry/2.0/bp:stoichiometricCoefficient; ProteinReference/6507/bp:xref
  • UniProtKB:P31572

    Source assertion: CaiB is a homodimer, supported by ECO:0000269/PubMed:15518548 and ECO:0000255/HAMAP-Rule:MF_01050.

    Source locationcomments[4].texts[0] (SUBUNIT)
  • PMID:15518548
    two monomers are interlaced to form an interlocked dimer
Crotonobetainyl-CoA reductase
UniProtKB:P60584		has_cofactor

This is FAD bound to CaiA, separate from the flavin reactive part of the generic electron-transfer flavoprotein in the Rhea redox reaction. The ChEBI charge form follows the curated cofactor cross-reference.

FAD(3-)
CHEBI:57692
  • UniProtKB:P60584

    Source assertion: CaiA has FAD (CHEBI:57692) as cofactor and binds one FAD per subunit; the annotation cites ECO:0000269/PubMed:10209289 and ECO:0000255/HAMAP-Rule:MF_01052.

    Source locationcomments[2].cofactors[0]; comments[2].note.texts[0]
  • PMID:10209289
    CII contains non-covalently bound FAD in a molar ratio of 1:1.
CaiC ATP-dependent initial carnitinyl-CoA formation
RHEA:28515		part_of

Manual source correspondence based on the native catalyst and biochemical transformation, not a native Rhea cross-reference or exactMatch. Current Rhea chemistry supplies explicit charge/stereo forms and corrects the older map's chemical-identity defects.

PathBank:SMP0002051
  • PathBank:SMP0002051

    Source assertion: PathBank SMP0002051 explicitly includes native Reactions/5950 and its associated catalysis; the controller resolves to P31552.

    Source locationPW002037.owl: Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002051"]/bp:pathwayComponent; ReactionCatalysis/5913/bp:controller, bp:controlled
  • UniProtKB:P31552

    Source assertion: The corresponding enzyme annotation identifies RHEA:28514; this provides the independent reaction-family bridge to RHEA:28515, selected in the native catabolic direction.

    Source locationcomments[3].reaction.reactionCrossReferences; comments[0]
CaiD carnitinyl-CoA dehydration
RHEA:28339		part_of

Manual source correspondence based on the native catalyst and biochemical transformation, not a native Rhea cross-reference or exactMatch. Current Rhea chemistry supplies explicit charge/stereo forms and corrects the older map's chemical-identity defects.

PathBank:SMP0002051
  • PathBank:SMP0002051

    Source assertion: PathBank SMP0002051 explicitly includes native Reactions/5951 and its associated catalysis; the controller resolves to P31551.

    Source locationPW002037.owl: Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002051"]/bp:pathwayComponent; ReactionCatalysis/5914/bp:controller, bp:controlled
  • UniProtKB:P31551

    Source assertion: The corresponding enzyme annotation identifies RHEA:28338; this provides the independent reaction-family bridge to RHEA:28339, selected in the native catabolic direction.

    Source locationcomments[1].reaction.reactionCrossReferences; comments[0]
CaiA crotonobetainyl-CoA reduction
RHEA:51586		part_of

Manual source correspondence based on the native catalyst and biochemical transformation, not a native Rhea cross-reference or exactMatch. Current Rhea chemistry supplies explicit charge/stereo forms and corrects the older map's chemical-identity defects.

PathBank:SMP0002051
  • PathBank:SMP0002051

    Source assertion: PathBank SMP0002051 explicitly includes native Reactions/5952 and its associated catalysis; the controller resolves to P60584.

    Source locationPW002037.owl: Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002051"]/bp:pathwayComponent; ReactionCatalysis/5915/bp:controller, bp:controlled
  • UniProtKB:P60584

    Source assertion: The corresponding enzyme annotation identifies RHEA:51584; this provides the independent reaction-family bridge to RHEA:51586, selected in the native catabolic direction.

    Source locationcomments[1].reaction.reactionCrossReferences; comments[0]
CaiB CoA transfer to carnitine and gamma-butyrobetaine release
RHEA:28419		part_of

Manual source correspondence based on the native catalyst and biochemical transformation, not a native Rhea cross-reference or exactMatch. Current Rhea chemistry supplies explicit charge/stereo forms and corrects the older map's chemical-identity defects.

PathBank:SMP0002051
  • PathBank:SMP0002051

    Source assertion: PathBank SMP0002051 explicitly includes native Reactions/5953 and its associated catalysis; the controller resolves to P31572 through complex ProteinComplex/4010.

    Source locationPW002037.owl: Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002051"]/bp:pathwayComponent; ReactionCatalysis/5916/bp:controller, bp:controlled
  • UniProtKB:P31572

    Source assertion: The corresponding enzyme annotation identifies RHEA:28418; this provides the independent reaction-family bridge to RHEA:28419, selected in the native catabolic direction.

    Source locationcomments[2].reaction.reactionCrossReferences; comments[0]
CaiC ATP-dependent initial carnitinyl-CoA formation
RHEA:28515		provides_input_for

CaiC supplies the initial carnitinyl-CoA pool for CaiD; the subsequent CaiB loop recycles that pool.

CaiD carnitinyl-CoA dehydration
RHEA:28339
  • RHEA:28515

    Source assertion: CHEBI:60932 is a coefficient-1 product of RHEA:28515; this shared chemical provides the material connection between the selected reactions.

    Source locationhttp://rdf.rhea-db.org/28515/rh:products; http://rdf.rhea-db.org/28514_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_28514_compound_6425/rh:compound -> http://rdf.rhea-db.org/Compound_6425/rh:chebi
  • RHEA:28339

    Source assertion: CHEBI:60932 is a coefficient-1 substrate of RHEA:28339; this shared chemical provides the material connection between the selected reactions.

    Source locationhttp://rdf.rhea-db.org/28339/rh:substrates; http://rdf.rhea-db.org/28338_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_28338_compound_6425/rh:compound -> http://rdf.rhea-db.org/Compound_6425/rh:chebi
CaiD carnitinyl-CoA dehydration
RHEA:28339		provides_input_for

The product CHEBI:60933 is the next selected reaction substrate.

CaiA crotonobetainyl-CoA reduction
RHEA:51586
  • RHEA:28339

    Source assertion: CHEBI:60933 is a coefficient-1 product of RHEA:28339; this shared chemical provides the material connection between the selected reactions.

    Source locationhttp://rdf.rhea-db.org/28339/rh:products; http://rdf.rhea-db.org/28338_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_28338_compound_6426/rh:compound -> http://rdf.rhea-db.org/Compound_6426/rh:chebi
  • RHEA:51586

    Source assertion: CHEBI:60933 is a coefficient-1 substrate of RHEA:51586; this shared chemical provides the material connection between the selected reactions.

    Source locationhttp://rdf.rhea-db.org/51586/rh:substrates; http://rdf.rhea-db.org/51584_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_51584_compound_6426/rh:compound -> http://rdf.rhea-db.org/Compound_6426/rh:chebi
CaiA crotonobetainyl-CoA reduction
RHEA:51586		provides_input_for

The product CHEBI:61513 is the next selected reaction substrate.

CaiB CoA transfer to carnitine and gamma-butyrobetaine release
RHEA:28419
  • RHEA:51586

    Source assertion: CHEBI:61513 is a coefficient-1 product of RHEA:51586; this shared chemical provides the material connection between the selected reactions.

    Source locationhttp://rdf.rhea-db.org/51586/rh:products; http://rdf.rhea-db.org/51584_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_51584_compound_6459/rh:compound -> http://rdf.rhea-db.org/Compound_6459/rh:chebi
  • RHEA:28419

    Source assertion: CHEBI:61513 is a coefficient-1 substrate of RHEA:28419; this shared chemical provides the material connection between the selected reactions.

    Source locationhttp://rdf.rhea-db.org/28419/rh:substrates; http://rdf.rhea-db.org/28418_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_28418_compound_6459/rh:compound -> http://rdf.rhea-db.org/Compound_6459/rh:chebi
CaiB CoA transfer to carnitine and gamma-butyrobetaine release
RHEA:28419		provides_input_for

CaiB regenerates carnitinyl-CoA for another cycle; this material-flow loop does not assert a temporal order from the native pathwayOrder array.

CaiD carnitinyl-CoA dehydration
RHEA:28339
  • RHEA:28419

    Source assertion: CHEBI:60932 is a coefficient-1 product of RHEA:28419; this shared chemical provides the material connection between the selected reactions.

    Source locationhttp://rdf.rhea-db.org/28419/rh:products; http://rdf.rhea-db.org/28418_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_28418_compound_6425/rh:compound -> http://rdf.rhea-db.org/Compound_6425/rh:chebi
  • RHEA:28339

    Source assertion: CHEBI:60932 is a coefficient-1 substrate of RHEA:28339; this shared chemical provides the material connection between the selected reactions.

    Source locationhttp://rdf.rhea-db.org/28339/rh:substrates; http://rdf.rhea-db.org/28338_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_28338_compound_6425/rh:compound -> http://rdf.rhea-db.org/Compound_6425/rh:chebi

References

Curation history