RegulonDB RegulonDB 11.1: Gene Form
   

yfiR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dgcN yfiR yfiB yfiL YjjQ TSS_2946 TSS_2946 TSS_2945 TSS_2945 yfiRp yfiRp yfiRp3 yfiRp3 yfiRp5 yfiRp5 yfiRp6 yfiRp6 yfiRp8 yfiRp8 yfiRp7 yfiRp7

Gene      
Name: yfiR    Texpresso search in the literature
Synonym(s): ECK2600, G7354, b2603
Genome position(nucleotides): 2741875 --> 2742393
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 45.66
External database links:  
ASAP:
 ABE-0008568
ECHOBASE:
 EB3977
ECOLIHUB:
 yfiR
OU-MICROARRAY:
 b2603
STRING:
 511145.b2603
COLOMBOS: yfiR


Product      
Name: DUF4154 domain-containing protein YfiR
Synonym(s): YfiR, putative periplasmic protein involved in swarming motility
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space,cytosol
Molecular weight: 18.978
Isoelectric point: 7.951
Motif(s):
 
Type Positions Sequence Comment
1 -> 22 MRFSHRLFLLLILLLTGAPILA
23 -> 172 QEPSDVAKNVRMMVSGIVSYTRWPALSGPPKLCIFSSSRFSTALQENAATSLPYLPVIIHTQQEAMISGCNGFYFGNESPTFQMELTEQYPSKALLLIAEQNTECIIGSAFCLIIHNNDVRFAVNLDALSRSGVKVNPDVLMLARKKNDG UniProt: Protein YfiR.
34 -> 167 MMVSGIVSYTRWPALSGPPKLCIFSSSRFSTALQENAATSLPYLPVIIHTQQEAMISGCNGFYFGNESPTFQMELTEQYPSKALLLIAEQNTECIIGSAFCLIIHNNDVRFAVNLDALSRSGVKVNPDVLMLAR

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.3 - motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0042597 - periplasmic space
biological_process GO:0071978 - bacterial-type flagellum-dependent swarming motility
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Girgis HS., et al., 2007
External database links:  
ALPHAFOLD:
 P64548
ECOCYC:
 G7354-MONOMER
ECOLIWIKI:
 b2603
INTERPRO:
 IPR025293
PFAM:
 PF13689
PRIDE:
 P64548
REFSEQ:
 NP_417094
SMR:
 P64548
UNIPROT:
 P64548


Operon      
Name: yfiR-dgcN-yfiB         
Operon arrangement:
Transcription unit        Promoter
yfiR-dgcN-yfiB
yfiRN


Transcriptional Regulation      
Display Regulation             
Repressed by: YjjQ


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 yfiRp7 2741677 forward nd [COMP-AINF] [2]
  promoter yfiRp8 2741702 forward nd [COMP-AINF] [2]
  promoter yfiRp6 2741751 forward nd [COMP-AINF] [2]
  promoter yfiRp5 2741762 forward nd [COMP-AINF] [2]
  promoter yfiRp3 2741822 forward nd [COMP-AINF] [2]
  promoter TSS_2945 2743141 forward nd [RS-EPT-CBR] [3]
  promoter TSS_2946 2743327 forward nd [RS-EPT-CBR] [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Girgis HS., Liu Y., Ryu WS., Tavazoie S., 2007, A comprehensive genetic characterization of bacterial motility., PLoS Genet 3(9):1644-60

 [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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