RegulonDB RegulonDB 10.9: Gene Form
   

ybdF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nfsB ybdF ybdJ SoxS Rob MarA ybdFp5 ybdFp5 TSS_722 TSS_722 nfsBp nfsBp

Gene      
Name: ybdF    Texpresso search in the literature
Synonym(s): ECK0571, G6324, b0579
Genome position(nucleotides): 605518 <-- 605886 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
47.15
External database links:  
ASAP:
ABE-0001986
ECHOBASE:
EB2503
ECOLIHUB:
ybdF
OU-MICROARRAY:
b0579
STRING:
511145.b0579
COLOMBOS: ybdF


Product      
Name: PF04237 family protein YbdF
Synonym(s): YbdF
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 14.05
Isoelectric point: 9.077
Motif(s):
 
Type Positions Sequence
15 -> 106 LELPFVELCWPFGPEFDVFKIGGKIFMLSSELRGVPFINLKSDPQKSLLNQQIYPSIKPGYHMNKKHWISVYPGEEISEALLRDLINDSWNL
93 -> 93 E

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-48140N
ECOCYC:
G6324-MONOMER
ECOLIWIKI:
b0579
INTERPRO:
IPR007351
INTERPRO:
IPR038056
MODBASE:
P0AAT2
PANTHER:
PTHR35145
PFAM:
PF04237
PRIDE:
P0AAT2
REFSEQ:
NP_415111
SMR:
P0AAT2
UNIPROT:
P0AAT2


Operon      
Name: ybdF         
Operon arrangement:
Transcription unit        Promoter
ybdF


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 TSS_722 605482 reverse nd [RS-EPT-CBR] [1]
  promoter ybdFp5 606053 reverse Similarity to the consensus
Read more >
[ICWHO] [2]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] 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.

 [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


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