RegulonDB RegulonDB 10.8: Gene Form
   

yobB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

exoX yobB holE ptrB TSS_2187 (cluster) TSS_2187 (cluster) TSS_2186 TSS_2186 yobBp5 yobBp5 TSS_2185 TSS_2185 yobBp8 yobBp8

Gene      
Name: yobB    Texpresso search in the literature
Synonym(s): ECK1844, G7015, b1843
Genome position(nucleotides): 1925440 --> 1926096 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.05
External database links:  
ASAP:
 ABE-0006129
ECHOBASE:
 EB3784
OU-MICROARRAY:
 b1843
PortEco:
 yobB
STRING:
 511145.b1843
COLOMBOS: yobB


Product      
Name: putative carbon-nitrogen hydrolase family protein YobB
Synonym(s): YobB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 24.395
Isoelectric point: 8.814
Motif(s):
 
Type Positions Sequence
4 -> 207 WKVAAAQYEPRKTSLTEQVAHHLEFVRAAARQQCQLLVFPSLSLLGCDYSRRALPAPPDLSLLDPLCYAATTWRMTIIAGLPVEYNDRFIRGIAVFAPWRKTPGIYHQSHGACLGRRSRTITVVDEQPQGMDMDPTCSLFTTGQCLGEPDLLASARRLQFFSHQYSIAVLMANARGNSALWDEYGRLIVRADRGSLLLVGQRSS
5 -> 113 KVAAAQYEPRKTSLTEQVAHHLEFVRAAARQQCQLLVFPSLSLLGCDYSRRALPAPPDLSLLDPLCYAATTWRMTIIAGLPVEYNDRFIRGIAVFAPWRKTPGIYHQSH

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
biological_process GO:0006807 - nitrogen compound metabolic process
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
External database links:  
ECOCYC:
 G7015-MONOMER
ECOLIWIKI:
 b1843
INTERPRO:
 IPR003010
INTERPRO:
 IPR036526
MODBASE:
 P76280
PFAM:
 PF00795
PRIDE:
 P76280
PROSITE:
 PS50263
REFSEQ:
 NP_416357
UNIPROT:
 P76280


Operon      
Name: yobB-exoX         
Operon arrangement:
Transcription unit        Promoter
 


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 yobBp8 1925209 forward Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter TSS_2185 1925307 reverse nd [RS-EPT-CBR] [3]
  promoter yobBp5 1925364 forward Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter TSS_2186 1925389 forward nd [RS-EPT-CBR] [3]
  promoter TSS_2187 (cluster) 1926096 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [3]


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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [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

 [3] 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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