RegulonDB RegulonDB 10.7: Gene Form
   

decR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

mdlA cof decR mdlB SoxS MarA terminator anti-terminator anti-anti-terminator TSS_608 TSS_608 decRp decRp

Gene      
Name: decR    Texpresso search in the literature
Synonym(s): ECK0441, G6247, b0447, cyuR, ybaO
Genome position(nucleotides): 468383 --> 468841 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.85
External database links:  
ASAP:
ABE-0001553
ECHOBASE:
EB3009
OU-MICROARRAY:
b0447
PORTECO:
ybaO
REGULONDB:
b0447
STRING:
511145.b0447
M3D: decR
COLOMBOS: decR
PortEco: b0447


Product      
Name: DNA-binding transcriptional activator DecR
Synonym(s): CyuR, DecR, YbaO
Sequence: Get amino acid sequence Fasta Format
Regulator Family: AsnC
Cellular location: cytosol
Molecular weight: 17.437
Isoelectric point: 5.792
Motif(s):
 
Type Positions Sequence
68 -> 142 VLIKTQHHSSEWYCRFVTVVTEMPEVLGFWRMAGEYDYLMRVQVADMKRYDEFYKRLVNSVPGLSDVTSSFAMEQ
2 -> 63 LDKIDRKLLALLQQDCTLSLQALAEAVNLTTTPCWKRLKRLEDDGILIGKVALLDPEKIGLG
21 -> 40 LQALAEAVNLTTTPCWKRLK

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0043565 - sequence-specific DNA binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:2000144 - positive regulation of DNA-templated transcription, initiation
GO:0009093 - cysteine catabolic process
Note(s): Note(s): ...[more].
Evidence: [APPINH] Assay of protein partially-purified from its native host
[HIFS] Human inference of function from sequence
[IEP] Inferred from expression pattern
[IPI] Inferred from physical interaction
Reference(s): [1] Bennik MH., et al., 2000
[2] Gao Y., et al., 2018
[3] Perez-Rueda E., et al., 2000
[4] Perez-Rueda E., et al., 2004
[5] Shimada T., et al., 2016
External database links:  
DIP:
DIP-11303N
ECOCYC:
G6247-MONOMER
ECOLIWIKI:
b0447
INTERPRO:
IPR019885
INTERPRO:
IPR019887
INTERPRO:
IPR019888
INTERPRO:
IPR036388
INTERPRO:
IPR036390
INTERPRO:
IPR011008
INTERPRO:
IPR000485
INTERPRO:
IPR011991
MODBASE:
P0ACJ5
PFAM:
PF01037
PRIDE:
P0ACJ5
PRINTS:
PR00033
PROSITE:
PS00519
PROSITE:
PS50956
PROTEINMODELPORTAL:
P0ACJ5
REFSEQ:
NP_414981
SMART:
SM00344
SMR:
P0ACJ5
UNIPROT:
P0ACJ5


Operon      
Name: decR         
Operon arrangement:
Transcription unit        Promoter
 


Transcriptional Regulation      
Display Regulation             
Activated by: MarA, SoxS


RNA cis-regulatory element    
Attenuation: Transcriptional


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_608 468357 forward nd [RS-EPT-CBR] [6]


Evidence    

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



Reference(s)    

 [1] Bennik MH., Pomposiello PJ., Thorne DF., Demple B., 2000, Defining a rob regulon in Escherichia coli by using transposon mutagenesis., J Bacteriol 182(13):3794-801

 [2] Gao Y., Yurkovich JT., Seo SW., Kabimoldayev I., Drager A., Chen K., Sastry AV., Fang X., Mih N., Yang L., Eichner J., Cho BK., Kim D., Palsson BO., 2018, Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655., Nucleic Acids Res 46(20):10682-10696

 [3] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [4] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [5] Shimada T., Tanaka K., Ishihama A., 2016, Transcription factor DecR (YbaO) controls detoxification of L-cysteine in Escherichia coli., Microbiology 162(9):1698-1707

 [6] 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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