RegulonDB RegulonDB 10.8: Gene Form
   

ycfJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ndh comR ycfJ terminator TSS_1442 TSS_1442 ycfJp3 ycfJp3

Gene      
Name: ycfJ    Texpresso search in the literature
Synonym(s): ECK1096, EG12444, b1110
Genome position(nucleotides): 1167599 --> 1168138 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.7
External database links:  
ASAP:
 ABE-0003752
ECHOBASE:
 EB2338
OU-MICROARRAY:
 b1110
PortEco:
 ycfJ
STRING:
 511145.b1110
COLOMBOS: ycfJ


Product      
Name: PF05433 family protein YcfJ
Synonym(s): YcfJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 18.92
Isoelectric point: 9.648
Motif(s):
 
Type Positions Sequence
5 -> 25 MLAGIGIGVAAALGVAAVASL
73 -> 113 GSVLGAVAGGVIGHQFGGGRGKDVATVVGALGGGYAGNQIQ

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0019867 - outer membrane
GO:0016020 - membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
biological_process GO:1900190 - regulation of single-species biofilm formation
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Beloin C., et al., 2004
External database links:  
ECOCYC:
 EG12444-MONOMER
ECOLIWIKI:
 b1110
INTERPRO:
 IPR008816
PFAM:
 PF05433
PRIDE:
 P0AB35
REFSEQ:
 NP_415628
UNIPROT:
 P0AB35


Operon      
Name: ycfJ         
Operon arrangement:
Transcription unit        Promoter
 


RNA cis-regulatory element    
Attenuation: Translational


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 ycfJp3 1167407 forward Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter TSS_1442 1168035 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] Beloin C., Valle J., Latour-Lambert P., Faure P., Kzreminski M., Balestrino D., Haagensen JA., Molin S., Prensier G., Arbeille B., Ghigo JM., 2004, Global impact of mature biofilm lifestyle on Escherichia coli K-12 gene expression., Mol Microbiol 51(3):659-74

 [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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