RegulonDB RegulonDB 10.9: Gene Form
   

ydbJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydbK ldhA hslJ ydbJ CysB SoxS SoxS anti-anti-terminator anti-terminator terminator hslJp hslJp ydbJp ydbJp TSS_1788 (cluster) TSS_1788 (cluster) ydbJp1 ydbJp1 ydbKp4 ydbKp4 TSS_1787 TSS_1787 ydbKp ydbKp TSS_1786 TSS_1786 TSS_1785 TSS_1785 TSS_1784 TSS_1784

Gene      
Name: ydbJ    Texpresso search in the literature
Synonym(s): ECK1375, G0-10450, b4529
Genome position(nucleotides): 1441058 --> 1441324 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.68
External database links:  
ASAP:
ABE-0285050
ECHOBASE:
EB2974
ECOLIHUB:
ydbJ
STRING:
511145.b4529
COLOMBOS: ydbJ


Product      
Name: DUF333 domain-containing protein YdbJ
Synonym(s): YdbJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 8.696
Isoelectric point: 7.761
Motif(s):
 
Type Positions Sequence
26 -> 88 TAAHVAPGLKASMSSSGEANCAMIGGSLSVARQLDGTAIGMCALPNGKRCSEQSLAAGSCGSY
1 -> 25 MRAAFWVGCAALLLSACSSEPVQQA
38 -> 83 MSSSGEANCAMIGGSLSVARQLDGTAIGMCALPNGKRCSEQSLAAG

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
MONOMER0-2672
ECOLIWIKI:
b4529
INTERPRO:
IPR005590
PFAM:
PF03891
PRIDE:
P0ACW2
REFSEQ:
YP_588453
UNIPROT:
P0ACW2


Operon      
Name: ydbJ         
Operon arrangement:
Transcription unit        Promoter
ydbJ


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_1784 1438596 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1785 1438744 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1786 1438759 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1787 1440845 reverse nd [RS-EPT-CBR] [1]
  promoter ydbJp1 1440856 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1788 (cluster) 1441022 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]


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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