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CaiF Genetic Sensory Response Unit in Escherichia coli K-12 genome


Gensor Unit Map          
gamma-butyrobetaine gamma-butyrobetaine_Ext gamma-butyrobetainyl-CoA CaiA CaiB CaiC CaiD CaiE CaiF CaiT FixA FixB FixC FixX vitamin Bt vitamin Bt_Ext L-carnityl-CoA a reduced electron acceptor an oxidized electron acceptor caiTABCDE caiTABCDE_mRNA CoA crotonobetainyl-CoA PP fixABCX fixABCX_mRNA CaiF vitamin Bt


Gensor Unit       
Name: CaiF
Description: Molecular biology level
Detailed: In the presence of L-carnitine and under anaerobic conditions, CaiF positively regulates the expression of genes required for carnitine transport and catabolic process. Under this condition, CaiF is modified to CaiF-L-carnitine, binds its targets sites enabling the expression of its regulated genes.
Less detailed: In the presence of L-carnitine (under anaerobic conditions), CaiF positively regulates the expression of genes needed for carnitine transport and catabolic process

Physiology level
Detailed: L-carnitine cannot be utilized as carbon or nitrogen source, however under anaerobic conditions, the presence of this compound induces the expression of genes involved with L-carnitine catabolic process. Under this condition, genes the genes necessary for transport and conversion of L-carnitine to γ-butyrobetaine and its efflux, are expressed.
Less detailed: The presence of L-carnitine induces the expression of genes needful for the metabolism of carnitine to γ-butyrobetaine and its efflux.
Classification:
Groups: Unclassified Gensor Units
Gene Ontology Terms (GO): biological_process GO:1902270 - (R)-carnitine transmembrane transport
GO:1900751 - 4-(trimethylammonio)butanoate transport
GO:0042413 - carnitine catabolic process
GO:0009437 - carnitine metabolic process
GO:1902603 - carnitine transmembrane transport
GO:0015879 - carnitine transport
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cellular_component GO:0005829 - cytosol
GO:0016021 - integral component of membrane
GO:0016020 - membrane
GO:0005886 - plasma membrane
molecular_function GO:0044667 - (R)-carnitine:4-(trimethylammonio)butanoate antiporter activity
GO:0015297 - antiporter activity
GO:0008735 - carnitine dehydratase activity
GO:0008809 - carnitine racemase activity
GO:0015226 - carnitine transmembrane transporter activity
GO:0051108 - carnitine-CoA ligase activity
GO:0051109 - crotonobetaine-CoA ligase activity
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Components: Show/Hide Components Table (26 more...)
Function Name Type
simple_molecule γ-butyrobetaine simple_molecule
simple_molecule γ-butyrobetaine-CoA simple_molecule
simple_molecule γ-butyrobetaine_Ext simple_molecule
simple_molecule A(H2) simple_molecule
protein CaiA protein
protein CaiB protein
protein CaiC protein
protein CaiD protein
protein CaiE protein
protein CaiF protein
protein CaiT protein
protein FixA protein
protein FixB protein
protein FixC protein
protein FixX protein
simple_molecule acceptors simple_molecule
gene caiTABCDE gene
RNA caiTABCDE_mRNA RNA
simple_molecule carnityl-CoA simple_molecule
simple_molecule coenzyme A simple_molecule
simple_molecule crotonobetainyl-CoA simple_molecule
simple_molecule diphosphate simple_molecule
gene fixABCX gene
RNA fixABCX_mRNA RNA
simple_molecule vitamin Bt simple_molecule
simple_molecule vitamin Bt_Ext simple_molecule


Reactions       
Showing 17 reactions
CaiF caiTABCDE caiTABCDE_mRNA
Name: caiTABCDE -> caiTABCDE_mRNA
Description: Transcription of transcription unit caiTABCDE. Reaction activation by CaiF.
Type: transcription
Pathway Components: caiTABCDE - CaiF -> caiTABCDE_mRNA
Components:
Function Name Type Evidence Reference(s)
activator CaiF protein nd nd
reactant caiTABCDE gene nd nd
product caiTABCDE_mRNA RNA nd nd
CaiF fixABCX fixABCX_mRNA
Name: fixABCX -> fixABCX_mRNA
Description: Transcription of transcription unit fixABCX. Reaction activation by CaiF.
Type: transcription
Pathway Components: fixABCX - CaiF -> fixABCX_mRNA
Components:
Function Name Type Evidence Reference(s)
activator CaiF protein nd nd
reactant fixABCX gene nd nd
product fixABCX_mRNA RNA nd nd
fixABCX_mRNA FixA
Name: fixABCX_mRNA -> FixA
Description: Translation of FixA
Type: translation
Pathway Components: fixABCX_mRNA -> FixA
Components:
Function Name Type Evidence Reference(s)
product FixA protein nd nd
reactant fixABCX_mRNA RNA nd nd
fixABCX_mRNA FixB
Name: fixABCX_mRNA -> FixB
Description: Translation of FixB
Type: translation
Pathway Components: fixABCX_mRNA -> FixB
Components:
Function Name Type Evidence Reference(s)
product FixB protein nd nd
reactant fixABCX_mRNA RNA nd nd
fixABCX_mRNA FixC
Name: fixABCX_mRNA -> FixC
Description: Translation of FixC
Type: translation
Pathway Components: fixABCX_mRNA -> FixC
Components:
Function Name Type Evidence Reference(s)
product FixC protein nd nd
reactant fixABCX_mRNA RNA nd nd
fixABCX_mRNA FixX
Name: fixABCX_mRNA -> FixX
Description: Translation of FixX
Type: translation
Pathway Components: fixABCX_mRNA -> FixX
Components:
Function Name Type Evidence Reference(s)
product FixX protein nd nd
reactant fixABCX_mRNA RNA nd nd
caiTABCDE_mRNA CaiT
Name: caiTABCDE_mRNA -> CaiT
Description: Translation of CaiT
Type: translation
Pathway Components: caiTABCDE_mRNA -> CaiT
Components:
Function Name Type Evidence Reference(s)
product CaiT protein nd nd
reactant caiTABCDE_mRNA RNA nd nd
CaiT γ-butyrobetaine_Ext + vitamin Bt_Ext γ-butyrobetaine + vitamin Bt
Name: γ-butyrobetaine_Ext + vitamin Bt_Ext -> γ-butyrobetaine + vitamin Bt
Description: Transport of γ-butyrobetaine_Ext, vitamin Bt_Ext through a bacterial membrane, leading to the presence of γ-butyrobetaine, vitamin Bt inside the cell.
Type: transport
Pathway Components: γ-butyrobetaine_Ext + vitamin Bt_Ext - CaiT -> γ-butyrobetaine + vitamin Bt
Components:
Function Name Type Evidence Reference(s)
product γ-butyrobetaine simple_molecule nd nd
reactant γ-butyrobetaine_Ext simple_molecule nd nd
catalyzer CaiT protein nd nd
product vitamin Bt simple_molecule nd nd
reactant vitamin Bt_Ext simple_molecule nd nd
caiTABCDE_mRNA CaiA
Name: caiTABCDE_mRNA -> CaiA
Description: Translation of CaiA
Type: translation
Pathway Components: caiTABCDE_mRNA -> CaiA
Components:
Function Name Type Evidence Reference(s)
product CaiA protein nd nd
reactant caiTABCDE_mRNA RNA nd nd
γ-butyrobetaine CaiA crotonobetainyl-CoA + A(H2) γ-butyrobetaine-CoA + acceptors
Name: crotonobetainyl-CoA + A(H2) -> γ-butyrobetaine-CoA + acceptors
Description: Reaction transforming crotonobetainyl-CoA, A(H2) into γ-butyrobetaine-CoA, acceptors
Type: state transition
Pathway Components: crotonobetainyl-CoA + A(H2) - CaiA - γ-butyrobetaine -> γ-butyrobetaine-CoA + acceptors
Components:
Function Name Type Evidence Reference(s)
inhibitor γ-butyrobetaine simple_molecule nd nd
product γ-butyrobetaine-CoA simple_molecule nd nd
reactant A(H2) simple_molecule nd nd
catalyzer CaiA protein nd nd
product acceptors simple_molecule nd nd
reactant crotonobetainyl-CoA simple_molecule nd nd
caiTABCDE_mRNA CaiB
Name: caiTABCDE_mRNA -> CaiB
Description: Translation of CaiB
Type: translation
Pathway Components: caiTABCDE_mRNA -> CaiB
Components:
Function Name Type Evidence Reference(s)
product CaiB protein nd nd
reactant caiTABCDE_mRNA RNA nd nd
CaiB γ-butyrobetaine-CoA + vitamin Bt γ-butyrobetaine + carnityl-CoA
Name: γ-butyrobetaine-CoA + vitamin Bt -> γ-butyrobetaine + carnityl-CoA
Description: Reaction transforming γ-butyrobetaine-CoA, vitamin Bt into γ-butyrobetaine, carnityl-CoA
Type: state transition
Pathway Components: γ-butyrobetaine-CoA + vitamin Bt - CaiB -> γ-butyrobetaine + carnityl-CoA
Components:
Function Name Type Evidence Reference(s)
product γ-butyrobetaine simple_molecule nd nd
reactant γ-butyrobetaine-CoA simple_molecule nd nd
catalyzer CaiB protein nd nd
product carnityl-CoA simple_molecule nd nd
reactant vitamin Bt simple_molecule nd nd
caiTABCDE_mRNA CaiC
Name: caiTABCDE_mRNA -> CaiC
Description: Translation of CaiC
Type: translation
Pathway Components: caiTABCDE_mRNA -> CaiC
Components:
Function Name Type Evidence Reference(s)
product CaiC protein nd nd
reactant caiTABCDE_mRNA RNA nd nd
CaiC vitamin Bt + coenzyme A carnityl-CoA + diphosphate
Name: vitamin Bt + coenzyme A -> carnityl-CoA + diphosphate
Description: Reaction transforming vitamin Bt, coenzyme A into carnityl-CoA, diphosphate
Type: state transition
Pathway Components: vitamin Bt + coenzyme A - CaiC -> carnityl-CoA + diphosphate
Components:
Function Name Type Evidence Reference(s)
catalyzer CaiC protein nd nd
product carnityl-CoA simple_molecule nd nd
reactant coenzyme A simple_molecule nd nd
product diphosphate simple_molecule nd nd
reactant vitamin Bt simple_molecule nd nd
caiTABCDE_mRNA CaiD
Name: caiTABCDE_mRNA -> CaiD
Description: Translation of CaiD
Type: translation
Pathway Components: caiTABCDE_mRNA -> CaiD
Components:
Function Name Type Evidence Reference(s)
product CaiD protein nd nd
reactant caiTABCDE_mRNA RNA nd nd
CaiD carnityl-CoA crotonobetainyl-CoA
Name: carnityl-CoA -> crotonobetainyl-CoA
Description: Reaction transforming carnityl-CoA into crotonobetainyl-CoA
Type: state transition
Pathway Components: carnityl-CoA - CaiD -> crotonobetainyl-CoA
Components:
Function Name Type Evidence Reference(s)
catalyzer CaiD protein nd nd
reactant carnityl-CoA simple_molecule nd nd
product crotonobetainyl-CoA simple_molecule nd nd
caiTABCDE_mRNA CaiE
Name: caiTABCDE_mRNA -> CaiE
Description: Translation of CaiE
Type: translation
Pathway Components: caiTABCDE_mRNA -> CaiE
Components:
Function Name Type Evidence Reference(s)
product CaiE protein nd nd
reactant caiTABCDE_mRNA RNA nd nd



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