RegulonDB RegulonDB 10.9: Gene Form
   

ybeD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dacA lipB ybeD terminator ybeDp ybeDp TSS_754 (cluster) TSS_754 (cluster) lipBp2 lipBp2 lipBp3 lipBp3

Gene      
Name: ybeD    Texpresso search in the literature
Synonym(s): ECK0624, EG11592, b0631
Genome position(nucleotides): 662379 <-- 662642 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
46.21
External database links:  
ASAP:
ABE-0002162
ECHOBASE:
EB1550
ECOLIHUB:
ybeD
OU-MICROARRAY:
b0631
STRING:
511145.b0631
COLOMBOS: ybeD


Product      
Name: DUF493 domain-containing protein YbeD
Synonym(s): YbeD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 9.827
Isoelectric point: 5.588
Motif(s):
 
Type Positions Sequence
7 -> 87 ELLEFPTPFTYKVMGQALPELVDQVVEVVQRHAPGDYTPTVKPSSKGNYHSVSITINATHIEQVETLYEELGKIDIVRMVL

 

Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
biological_process GO:0034605 - cellular response to heat
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-31839N
ECOCYC:
EG11592-MONOMER
ECOLIWIKI:
b0631
INTERPRO:
IPR027471
INTERPRO:
IPR007454
PANTHER:
PTHR38036
PDB:
1RWU
PFAM:
PF04359
PRIDE:
P0A8J4
REFSEQ:
NP_415164
SMR:
P0A8J4
UNIPROT:
P0A8J4


Operon      
Name: ybeD-lipB         
Operon arrangement:
Transcription unit        Promoter
ybeD-lipB
ybeD-lipB
lipB
ybeD


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 lipBp3 662399 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter lipBp2 662401 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter TSS_754 (cluster) 662704 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [2]


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] 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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