RegulonDB RegulonDB 10.8: Gene Form
   

rclR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rclA rclR ykgE anti-anti-terminator anti-terminator terminator ykgEp10 ykgEp10 ykgEp7 ykgEp7 ykgEp8 ykgEp8 ykgEp9 ykgEp9 ykgCp1 ykgCp1 ykgDp2 ykgDp2 ykgCp4 ykgCp4 ykgDp3 ykgDp3 ykgCp8 ykgCp8 TSS_478 TSS_478

Gene      
Name: rclR    Texpresso search in the literature
Synonym(s): ECK0304, G6175, b0305, ykgD
Genome position(nucleotides): 320227 --> 321081 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.23
External database links:  
ASAP:
ABE-0001054
ECHOBASE:
EB3351
OU-MICROARRAY:
b0305
PortEco:
ykgD
STRING:
511145.b0305
COLOMBOS: rclR


Product      
Name: DNA-binding transcriptional activator RclR
Synonym(s): RclR, YkgD
Sequence: Get amino acid sequence Fasta Format
Regulator Family: AraC/XylS
Cellular location: cytosol
Molecular weight: 31.474
Isoelectric point: 7.293
Motif(s):
 
Type Positions Sequence
197 -> 218 ESLASIAHMSRASFAQLFRDVS
245 -> 268 VVVIAESVGYASESSFHKAFVREF
42 -> 42 H
199 -> 278 LASIAHMSRASFAQLFRDVSGTTPLAVLTKLRLQIAAQMFSRETLPVVVIAESVGYASESSFHKAFVREFGCTPGEYRER
89 -> 89 C

 

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
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
GO:0001216 - DNA-binding transcription activator activity
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0090347 - regulation of cellular organohalogen metabolic process
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
Reference(s): [1] Perez-Rueda E., et al., 2000
[2] Perez-Rueda E., et al., 2004
External database links:  
ECOCYC:
G6175-MONOMER
ECOLIWIKI:
b0305
INTERPRO:
IPR018060
INTERPRO:
IPR032783
INTERPRO:
IPR020449
INTERPRO:
IPR011051
INTERPRO:
IPR009057
MODBASE:
P77379
PFAM:
PF12852
PFAM:
PF12833
PRIDE:
P77379
PRINTS:
PR00032
PROSITE:
PS01124
REFSEQ:
NP_414839
SMART:
SM00342
SMR:
P77379
UNIPROT:
P77379


Operon      
Name: rclR         
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 TSS_478 320033 reverse nd [RS-EPT-CBR] [3]
  promoter ykgCp8 320088 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ykgDp3 320116 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ykgCp4 320170 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ykgDp2 320193 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ykgEp9 321481 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ykgEp8 321484 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ykgEp7 321511 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ykgEp10 321537 forward Similarity to the consensus
Read more >
[ICWHO] [4]


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] 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

 [2] 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

 [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.

 [4] 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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