RegulonDB RegulonDB 10.7: Gene Form
   

caiF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

carB caiE caiF CRP FNR caiFp caiFp TSS_79 TSS_79 TSS_78 TSS_78 TSS_77 TSS_77

Gene      
Name: caiF    Texpresso search in the literature
Synonym(s): ECK0035, G6088, b0034
Genome position(nucleotides): 34300 --> 34695 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
45.96
Reference(s): [1] Eichler K., et al., 1996
External database links:  
ASAP:
ABE-0000125
ECHOBASE:
EB3224
OU-MICROARRAY:
b0034
PORTECO:
caiF
REGULONDB:
b0034
STRING:
511145.b0034
M3D: caiF
COLOMBOS: caiF
PortEco: b0034


Product      
Name: DNA-binding transcriptional activator CaiF
Synonym(s): CaiF
Sequence: Get amino acid sequence Fasta Format
Regulator Family: CaiF
Cellular location: cytosol
Molecular weight: 15.436
Isoelectric point: 8.946
Motif(s):
 
Type Positions Sequence
5 -> 61 YVEKPLYLLIAEWMMAENRWVIAREISIHFDIEHSKAVNTLTYILSEVTEISCEVKM

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.4 - amines
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.1 - unassigned reversible reactions
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0009437 - carnitine metabolic process
Reference(s): [2] Buchet A., et al., 1998
[3] Buchet A., et al., 1999
[1] Eichler K., et al., 1996
External database links:  
ECOCYC:
G6088-MONOMER
ECOLIWIKI:
b0034
INTERPRO:
IPR020357
INTERPRO:
IPR036388
PFAM:
PF07180
PRIDE:
P0AE58
PRODB:
PRO_000022245
PRODOM:
PD081346
PROTEINMODELPORTAL:
P0AE58
REFSEQ:
NP_414576
SMR:
P0AE58
UNIPROT:
P0AE58


Operon      
Name: caiF         
Operon arrangement:
Transcription unit        Promoter
caiF


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, FNR
Repressed by: H-NS, NarL


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_77 31596 forward nd [RS-EPT-CBR] [4]
  promoter TSS_78 31603 forward nd [RS-EPT-CBR] [4]
  promoter TSS_79 34216 forward nd [RS-EPT-CBR] [4]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Eichler K., Buchet A., Lemke R., Kleber HP., Mandrand-Berthelot MA., 1996, Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli., J Bacteriol 178(5):1248-57

 [2] Buchet A., Eichler K., Mandrand-Berthelot MA., 1998, Regulation of the carnitine pathway in Escherichia coli: investigation of the cai-fix divergent promoter region., J Bacteriol 180(10):2599-608

 [3] Buchet A., Nasser W., Eichler K., Mandrand-Berthelot MA., 1999, Positive co-regulation of the Escherichia coli carnitine pathway cai and fix operons by CRP and the CaiF activator., Mol Microbiol 34(3):562-75

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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