RegulonDB RegulonDB 11.1: Gene Form
   

ybbJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

qmcA fetA ybbJ cueR fetB fetAp fetAp ybbLp6 ybbLp6 TSS_659 (cluster) TSS_659 (cluster) qmcAp qmcAp ybbJp1 ybbJp1

Gene      
Name: ybbJ    Texpresso search in the literature
Synonym(s): ECK0482, G6264, b0488
Genome position(nucleotides): 514401 <-- 514859
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 57.3
External database links:  
ASAP:
 ABE-0001695
ECHOBASE:
 EB3045
ECOLIHUB:
 ybbJ
OU-MICROARRAY:
 b0488
STRING:
 511145.b0488
COLOMBOS: ybbJ


Product      
Name: NfeD-like family protein YbbJ
Synonym(s): YbbJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 16.939
Isoelectric point: 8.009
Motif(s):
 
Type Positions Sequence Comment
1 -> 21 MMELMVVHPHIFWLSLGGLLL UniProt: Helical.
32 -> 52 LLWSGVAAVITGLVVWLVPLG UniProt: Helical.
55 -> 75 WQGVMFAILTLLAAWLWWKWL UniProt: Helical.
60 -> 148 FAILTLLAAWLWWKWLSRRVREQKHSDSHLNQRGQQLIGRRFVLESPLVNGRGHMRVGDSSWPVSASEDLGAGTHVEVIAIEGITLHIR

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P0AAS3
ECOCYC:
 G6264-MONOMER
ECOLIWIKI:
 b0488
INTERPRO:
 IPR002810
PFAM:
 PF01957
PRIDE:
 P0AAS3
REFSEQ:
 NP_415021
UNIPROT:
 P0AAS3


Operon      
Name: qmcA-ybbJ         
Operon arrangement:
Transcription unit        Promoter
qmcA-ybbJ


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 ybbJp1 515077 reverse nd [COMP-AINF] [1]
  promoter TSS_659 (cluster) 515825 reverse nd [RS-EPT-CBR] [2]
  promoter ybbLp6 515892 forward nd [COMP-AINF], [RS-EPT-CBR] [1], [2]


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] 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

 [2] 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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