RegulonDB RegulonDB 10.9: Gene Form
   

ybfA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rhsC unknown ybfA kdpF KdpE terminator anti-terminator anti-anti-terminator anti-anti-terminator anti-terminator terminator terminator terminator rhsCp3 rhsCp3 TSS_830 TSS_830 ybfAp8 ybfAp8 TSS_828 (cluster) TSS_828 (cluster) ybfAp7 ybfAp7 kdpFp kdpFp

Gene      
Name: ybfA    Texpresso search in the literature
Synonym(s): ECK0688, EG11521, b0699
Genome position(nucleotides): 729134 --> 729340 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.24
External database links:  
ASAP:
ABE-0002386
ECHOBASE:
EB1483
ECOLIHUB:
ybfA
OU-MICROARRAY:
b0699
STRING:
511145.b0699
COLOMBOS: ybfA


Product      
Name: DUF2517 domain-containing protein YbfA
Synonym(s): YbfA
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,cytosol
Molecular weight: 8.275
Isoelectric point: 9.721
Motif(s):
 
Type Positions Sequence
13 -> 34 FLRRTYAVAAGVLALPFMLFWK
22 -> 68 AGVLALPFMLFWKDRARFYSYLHRVWSKTSDKPVWMDQAEKATGDFY
1 -> 21 MELYREYPAWLIFLRRTYAVA
4 -> 63 YREYPAWLIFLRRTYAVAAGVLALPFMLFWKDRARFYSYLHRVWSKTSDKPVWMDQAEKA

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0005887 - integral component of plasma membrane
biological_process GO:0009314 - response to radiation
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
EG11521-MONOMER
ECOLIWIKI:
b0699
INTERPRO:
IPR019663
PFAM:
PF10725
PRIDE:
P0AAU2
REFSEQ:
NP_415228
UNIPROT:
P0AAU2


Operon      
Name: ybfA         
Operon arrangement:
Transcription unit        Promoter
ybfA


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 ybfAp7 729037 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter TSS_828 (cluster) 729071 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter ybfAp8 729082 forward Similarity to the consensus
Read more >
[ICWHO], [RS-EPT-CBR] [1], [2]
  promoter TSS_830 729088 forward nd [RS-EPT-CBR] [2]
  promoter rhsCp3 729379 forward Similarity to the consensus
Read more >
[ICWHO] [1]


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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