RegulonDB RegulonDB 11.1: Gene Form
   

ynbE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydbH ldhA ydbL ynbE TSS_1789 TSS_1789 ldhAp ldhAp ydbHp9 ydbHp9

Gene      
Name: ynbE    Texpresso search in the literature
Synonym(s): ECK1379, G6704, b1382
Genome position(nucleotides): 1445687 --> 1445872
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
43.01
External database links:  
ASAP:
ABE-0004625
ECHOBASE:
EB4045
ECOLIHUB:
ynbE
OU-MICROARRAY:
b1382
STRING:
511145.b1382
COLOMBOS: ynbE


Product      
Name: lipoprotein YnbE
Synonym(s): YnbE
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 6.84
Isoelectric point: 4.66
Motif(s):
 
Type Positions Sequence Comment
26 -> 59 PKEPITINMNVKIEHEIIIKADKDVEELLETRSD

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
Note(s): Note(s): ...[more].
Reference(s): [1] Murata M., et al., 2011
[2] Rao S., et al., 2020
External database links:  
ALPHAFOLD:
P64448
ECOCYC:
G6704-MONOMER
ECOLIWIKI:
b1382
INTERPRO:
IPR025985
PFAM:
PF13617
PRIDE:
P64448
REFSEQ:
NP_415900
UNIPROT:
P64448


Operon      
Name: ydbH-ynbE-ydbL         
Operon arrangement:
Transcription unit        Promoter
ydbH-ynbE-ydbL


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 ydbHp9 1442900 forward nd [COMP-AINF] [3]
  promoter TSS_1789 1445572 forward nd [RS-EPT-CBR] [4]


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] Murata M., Fujimoto H., Nishimura K., Charoensuk K., Nagamitsu H., Raina S., Kosaka T., Oshima T., Ogasawara N., Yamada M., 2011, Molecular strategy for survival at a critical high temperature in Eschierichia coli., PLoS One 6(6):e20063

 [2] Rao S., Bates GT., Matthews CR., Newport TD., Vickery ON., Stansfeld PJ., 2020, Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations., Structure 28(4):475-487.e3

 [3] 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

 [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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