RegulonDB RegulonDB 10.6.3: 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 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.17
External database links:  
ASAP:
ABE-0002711
ECHOBASE:
EB2306
ECOCYC:
EG12406
ECOLIHUB:
ybiH
OU-MICROARRAY:
b0796
REGULONDB:
b0796
STRING:
511145.b0796
M3D: cecR
COLOMBOS: cecR
PortEco: b0796


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
17 -> 62 LIAAALAQFGEYGMNATTREIAAQAGQNIAAITYYFGSKEDLYLAC
11 -> 70 EQAKKQLIAAALAQFGEYGMNATTREIAAQAGQNIAAITYYFGSKEDLYLACAQWIADFI
33 -> 52 TTREIAAQAGQNIAAITYYF
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:0042802 - identical protein binding
biological_process GO:0006351 - 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: [AUPEINH] Assay of unpurified protein expressed in its native host
[HIFS] Human inference of function from sequence
[IEP] Inferred from expression pattern
Reference(s): [1] Griffith JM., et al., 2018
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
[4] Yamanaka Y., et al., 2016
External database links:  
ECOCYC:
EG12406-MONOMER
ECOLIWIKI:
b0796
INTERPRO:
IPR039419
INTERPRO:
IPR036271
INTERPRO:
IPR023772
INTERPRO:
IPR015292
INTERPRO:
IPR009057
INTERPRO:
IPR001647
MODBASE:
P0ACU0
PANTHER:
PTHR30328
PFAM:
PF09209
PFAM:
PF00440
PRIDE:
P0ACU0
PRINTS:
PR00455
PROSITE:
PS01081
PROSITE:
PS50977
PROTEINMODELPORTAL:
P0ACU0
REFSEQ:
NP_415317
SMR:
P0ACU0
SWISSMODEL:
P0ACU0
UNIPROT:
P0ACU0


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


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] [5]
  promoter TSS_954 829469 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_955 829473 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_956 830082 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_957 830088 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_958 830670 reverse nd [RS-EPT-CBR] [5]
  promoter rhlEp5 830783 forward Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter TSS_959 830785 forward nd [RS-EPT-CBR] [5]


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] Griffith JM., Basting PJ., Bischof KM., Wrona EP., Kunka KS., Tancredi AC., Moore JP., Hyman MRL., Slonczewski JL., 2018, Experimental evolution of Escherichia coli K-12 in the presence of PMF uncoupler CCCP selects for mutations affecting PMF-driven drug efflux pumps., Appl Environ Microbiol

 [2] 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

 [3] 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

 [4] 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

 [5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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.

 [6] 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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