RegulonDB RegulonDB 11.1: Gene Form
   

cecR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybhF rhlE ybhG cecR ybhS CecR TSS_959 TSS_959 rhlEp5 rhlEp5 TSS_958 TSS_958 cecRp cecRp TSS_957 TSS_957 TSS_956 TSS_956 TSS_955 TSS_955 TSS_954 TSS_954 TSS_953 TSS_953

Gene      
Name: cecR    Texpresso search in the literature
Synonym(s): ECK0785, EG12406, b0796, ybiH
Genome position(nucleotides): 829972 <-- 830643
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.17
External database links:  
ASAP:
 ABE-0002711
ECHOBASE:
 EB2306
ECOLIHUB:
 ybiH
OU-MICROARRAY:
 b0796
STRING:
 511145.b0796
COLOMBOS: cecR


Product      
Name: DNA-binding transcriptional dual regulator CecR
Synonym(s): CecR, YbiH
Sequence: Get amino acid sequence Fasta Format
Regulator Family: TetR/AcrR
Cellular location: cytosol
Molecular weight: 25.017
Isoelectric point: 6.504
Motif(s):
 
Type Positions Sequence Comment
11 -> 70 EQAKKQLIAAALAQFGEYGMNATTREIAAQAGQNIAAITYYFGSKEDLYLACAQWIADFI UniProt: HTH tetR-type.
17 -> 62 LIAAALAQFGEYGMNATTREIAAQAGQNIAAITYYFGSKEDLYLAC
33 -> 52 TTREIAAQAGQNIAAITYYF UniProt: H-T-H motif.
96 -> 218 RELILRACRNMIKLLTQDDTVNLSKFISREQLSPTAAYHLVHEQVISPLHSHLTRLIAAWTGCDANDTRMILHTHALIGEILAFRLGKETILLRTGWTAFDEEKTELINQTVTCHIDLILQGL

 
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
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0042802 - identical protein binding
GO:0000976 - transcription cis-regulatory region binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:2000143 - negative regulation of DNA-templated transcription, initiation
GO:2000144 - positive regulation of DNA-templated transcription, initiation
Note(s): Note(s): ...[more].
Evidence: [COMP-HINF-FN-FROM-SEQ] Human inference of function from sequence
[EXP-IDA-UNPURIFIED-PROTEIN-NH] Assay of unpurified protein expressed in its native host
[EXP-IEP] Inferred from expression pattern
[EXP-IPI] Inferred from physical interaction
Reference(s): [1] Gao Y., et al., 2018
[2] Griffith JM., et al., 2019
[3] Perez-Rueda E., et al., 2000
[4] Perez-Rueda E., et al., 2004
[5] Yamanaka Y., et al., 2016
External database links:  
ALPHAFOLD:
 P0ACU0
ECOCYC:
 EG12406-MONOMER
ECOLIWIKI:
 b0796
INTERPRO:
 IPR023772
INTERPRO:
 IPR036271
INTERPRO:
 IPR015292
INTERPRO:
 IPR009057
INTERPRO:
 IPR001647
MODBASE:
 P0ACU0
PFAM:
 PF09209
PFAM:
 PF00440
PRIDE:
 P0ACU0
PRINTS:
 PR00455
PROSITE:
 PS50977
PROSITE:
 PS01081
REFSEQ:
 NP_415317
SMR:
 P0ACU0
SWISSMODEL:
 P0ACU0
UNIPROT:
 P0ACU0


Operon      
Name: cecR-ybhGFSR         
Operon arrangement:
Transcription unit        Promoter
cecR-ybhGFSR


Transcriptional Regulation      
Display Regulation             
Repressed by: CecR


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_953 829107 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_954 829469 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_955 829473 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_956 830082 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_957 830088 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_958 830670 reverse nd [RS-EPT-CBR] [6]
  promoter rhlEp5 830783 forward nd [COMP-AINF] [7]
  promoter TSS_959 830785 forward nd [RS-EPT-CBR] [6]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] 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

 [2] Griffith JM., Basting PJ., Bischof KM., Wrona EP., Kunka KS., Tancredi AC., Moore JP., Hyman MRL., Slonczewski JL., 2019, Experimental Evolution of Escherichia coli K-12 in the Presence of Proton Motive Force (PMF) Uncoupler Carbonyl Cyanide m -Chlorophenylhydrazone Selects for Mutations Affecting PMF-Driven Drug Efflux Pumps., Appl Environ Microbiol 85(5)

 [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] Yamanaka Y., Shimada T., Yamamoto K., Ishihama A., 2016, Transcription factor CecR (YbiH) regulates a set of genes affecting the sensitivity of Escherichia coli against cefoperazone and chloramphenicol., Microbiology 162(7):1253-64

 [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.

 [7] 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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