RegulonDB RegulonDB 10.9: Gene Form
   

ybaB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dnaX htpG recR ybaB AscG Cis-reg; frameshift_element anti-terminator anti-anti-terminator TSS_640 TSS_640 htpGp2 htpGp2 TSS_639 TSS_639 TSS_638 TSS_638 htpGp1 htpGp1 htpGp3 htpGp3 TSS_637 (cluster) TSS_637 (cluster) TSS_636 TSS_636 TSS_635 (cluster) TSS_635 (cluster) ybaBp ybaBp TSS_634 TSS_634 TSS_633 TSS_633

Gene      
Name: ybaB    Texpresso search in the literature
Synonym(s): ECK0465, EG11100, b0471
Genome position(nucleotides): 494076 --> 494405 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.73
External database links:  
ASAP:
ABE-0001636
ECHOBASE:
EB1092
ECOLIHUB:
ybaB
OU-MICROARRAY:
b0471
STRING:
511145.b0471
COLOMBOS: ybaB


Product      
Name: putative nucleoid-associated protein YbaB
Synonym(s): YbaB, conserved DNA-binding protein YbaB
Sequence: Get amino acid sequence Fasta Format
Cellular location: bacterial nucleoid,cytosol
Molecular weight: 12.015
Isoelectric point: 4.724
Motif(s):
 
Type Positions Sequence
11 -> 99 MKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLEDDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGM

 

Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.5 - adaptations
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0009295 - nucleoid
GO:0043590 - bacterial nucleoid
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
biological_process GO:0006950 - response to stress
GO:0009314 - response to radiation
External database links:  
DIP:
DIP-48059N
ECOCYC:
EG11100-MONOMER
ECOLIWIKI:
b0471
INTERPRO:
IPR036894
INTERPRO:
IPR004401
MODBASE:
P0A8B5
PANTHER:
PTHR33449
PDB:
1PUG
PFAM:
PF02575
PRIDE:
P0A8B5
REFSEQ:
NP_415004
SMR:
P0A8B5
UNIPROT:
P0A8B5


Operon      
Name: ybaB-recR         
Operon arrangement:
Transcription unit        Promoter
ybaB-recR


RNA cis-regulatory element    
   
Cis-reg; frameshift_element DnaX ribosomal frameshifting element
   
   


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_633 493064 forward nd [RS-EPT-CBR] [1]
  promoter TSS_634 493071 forward nd [RS-EPT-CBR] [1]
  promoter TSS_635 (cluster) 493804 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_636 494018 forward nd [RS-EPT-CBR] [1]
  promoter TSS_637 (cluster) 494051 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_638 495076 forward nd [RS-EPT-CBR] [1]
  promoter TSS_639 495082 forward nd [RS-EPT-CBR] [1]
  promoter TSS_640 495090 forward nd [RS-EPT-CBR] [1]


Evidence    

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



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.


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