RegulonDB RegulonDB 10.8: Gene Form
   

araF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

araG araF ftnB CpxR AraC AraC AraC AraC CRP TSS_2238 TSS_2238 TSS_2237 TSS_2237 ftnBp2 ftnBp2 TSS_2236 TSS_2236 ftnBp ftnBp araFp araFp araFp2 araFp2 araHp7 araHp7

Gene      
Name: araF    Texpresso search in the literature
Synonym(s): ECK1899, EG10057, b1901
Genome position(nucleotides): 1985139 <-- 1986128 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.82
External database links:  
ASAP:
 ABE-0006330
CGSC:
 1023
ECHOBASE:
 EB0055
OU-MICROARRAY:
 b1901
PortEco:
 araF
STRING:
 511145.b1901
COLOMBOS: araF


Product      
Name: arabinose ABC transporter periplasmic binding protein
Synonym(s): AraF
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 35.541
Isoelectric point: 6.547
Motif(s):
 
Type Positions Sequence
277 -> 277 P
24 -> 329 ENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPMDTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQGFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKFTEVTDVVLITRDNFKEELEKKGLGGK
194 -> 194 Q
1 -> 23 MHKFTKALAAIGLAAVMSQSAMA
281 -> 281 V

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.1 - carbon compounds
  4 - transport --> 4.3 - Primary Active Transporters --> 4.3.A - Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters --> 4.3.A.1 - The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases --> 4.3.A.1.p - ABC superfamily, periplasmic binding component
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0030246 - carbohydrate binding
GO:0015407 - ATPase-coupled monosaccharide transmembrane transporter activity
GO:0048029 - monosaccharide binding
biological_process GO:0008643 - carbohydrate transport
GO:0042882 - L-arabinose transmembrane transport
Note(s): Note(s): ...[more].
Reference(s): [1] Clark AF., et al., 1981
External database links:  
ECOCYC:
 ARAF-MONOMER
ECOLIWIKI:
 b1901
INTERPRO:
 IPR001761
INTERPRO:
 IPR028082
INTERPRO:
 IPR026266
MODBASE:
 P02924
PDB:
 2WRZ
PDB:
 5ABP
PDB:
 6ABP
PDB:
 8ABP
PDB:
 9ABP
PDB:
 1BAP
PDB:
 1APB
PDB:
 1ABF
PDB:
 1ABE
PDB:
 7ABP
PFAM:
 PF00532
PRIDE:
 P02924
PRODB:
 PRO_000022119
REFSEQ:
 NP_416414
SMR:
 P02924
UNIPROT:
 P02924


Operon      
Name: araFGH         
Operon arrangement:
Transcription unit        Promoter
araFGH
araFGH


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, AraC


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 araHp7 1983560 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter TSS_2236 1986797 forward nd [RS-EPT-CBR] [3]
  promoter TSS_2237 1986863 forward nd [RS-EPT-CBR] [3]
  promoter TSS_2238 1987007 forward nd [RS-EPT-CBR] [3]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] Clark AF., Hogg RW., 1981, High-affinity arabinose transport mutants of Escherichia coli: isolation and gene location., J Bacteriol 147(3):920-4

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [3] 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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