RegulonDB RegulonDB 10.8: Gene Form
   

ydeI gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dgcZ ydeJ ydeI FNR CysB CpxR PhoP ydeJp ydeJp ydeIp5 ydeIp5 ydeIp6 ydeIp6 ydeIp1 ydeIp1 dgcZp dgcZp TSS_1844 TSS_1844

Gene      
Name: ydeI    Texpresso search in the literature
Synonym(s): ECK1529, EG11644, b1536
Genome position(nucleotides): 1624105 <-- 1624497 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 47.58
External database links:  
ASAP:
 ABE-0005127
ECHOBASE:
 EB1597
OU-MICROARRAY:
 b1536
PortEco:
 ydeI
STRING:
 511145.b1536
COLOMBOS: ydeI


Product      
Name: BOF family protein YdeI
Synonym(s): YdeI, stress response protein
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 14.121
Isoelectric point: 6.971
Motif(s):
 
Type Positions Sequence
30 -> 130 APPPPHAIEDGYRGTDDAKKMTVDFAKTMHDGASVSLRGNLISHKGEDRYVFRDKSGEINVVIPAAVFDGREVQPDQMINISGSLDKKSAPAVVRVTHLQK
1 -> 19 MKFQAIVLASFLVMPYALA
20 -> 130 DDQGGLKQDAAPPPPHAIEDGYRGTDDAKKMTVDFAKTMHDGASVSLRGNLISHKGEDRYVFRDKSGEINVVIPAAVFDGREVQPDQMINISGSLDKKSAPAVVRVTHLQK

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
biological_process GO:0070301 - cellular response to hydrogen peroxide
GO:0044011 - single-species biofilm formation on inanimate substrate
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Lee J., et al., 2010
External database links:  
DIP:
 DIP-11678N
ECOCYC:
 EG11644-MONOMER
ECOLIWIKI:
 b1536
INTERPRO:
 IPR016052
INTERPRO:
 IPR005220
INTERPRO:
 IPR036700
MINT:
 MINT-1260141
MODBASE:
 P31130
PFAM:
 PF04076
PRIDE:
 P31130
REFSEQ:
 NP_416054
SMR:
 P31130
UNIPROT:
 P31130


Operon      
Name: ydeI         
Operon arrangement:
Transcription unit        Promoter
ydeI
 


Transcriptional Regulation      
Display Regulation             
Activated by: RcdA


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_1844 1623877 reverse nd [RS-EPT-CBR] [2]
  promoter ydeIp1 1624516 reverse Similarity to the consensus
Read more > 		[ICWHO] [3]
  promoter ydeIp6 1624543 reverse Similarity to the consensus
Read more > 		[ICWHO] [3]


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] Lee J., Hiibel SR., Reardon KF., Wood TK., 2010, Identification of stress-related proteins in Escherichia coli using the pollutant cis-dichloroethylene., J Appl Microbiol 108(6):2088-102

 [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.

 [3] 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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