RegulonDB RegulonDB 11.1: Gene Form
   

perR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

insI1 perR ykfA anti-anti-terminator anti-terminator terminator anti-anti-terminator anti-terminator terminator TSS_465 TSS_465 insN-1p insN-1p

Gene      
Name: perR    Texpresso search in the literature
Synonym(s): ECK0256, G6129, b0254
Genome position(nucleotides): 269289 <-- 270182
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 47.99
External database links:  
ASAP:
 ABE-0000862
ECHOBASE:
 EB3124
ECOLIHUB:
 perR
ECOO157CYC:
 Z0885
ECOO157CYC:
 Z0346
OU-MICROARRAY:
 b0254
STRING:
 511145.b0254
COLOMBOS: perR


Product      
Name: CP4-6 prophage; putative transcriptional regulator PerR
Synonym(s): PerR
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 33.639
Isoelectric point: 6.605
Motif(s):
 
Type Positions Sequence Comment
7 -> 64 APLNLLRAFEAAGRTGAFALAASELELSPSAISHAIRKLENLLDVRLFQRSTREITLT UniProt: HTH lysR-type.
9 -> 68 LNLLRAFEAAGRTGAFALAASELELSPSAISHAIRKLENLLDVRLFQRSTREITLTKEGE
24 -> 44 FALAASELELSPSAISHAIRK UniProt: H-T-H motif.
91 -> 291 DESRPLRLHTAPSFAHQWLLPRLGKFIRENPSIDLRLSASTEYARFEQDDFDLDIVYGEPRPSPYEKIPLAVEELTPLCSPQLAERLKKPEDLYALTLIQCDVQLYQWKGWFEANKMTPPNNYGLRFDRSFMAIAAAVDGLGVVLESKLLAEREIASGKLVCPLVNSTSEIHYIGHYLVFPQHQHMHSALDVFKTWLLNEL

 
Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
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:0042802 - identical protein binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [COMP-AINF-FN-FROM-SEQ] Automated inference of function from sequence
Reference(s): [1] Perez-Rueda E., et al., 2004
External database links:  
ALPHAFOLD:
 Q57083
DIP:
 DIP-10463N
ECOCYC:
 G6129-MONOMER
ECOLIWIKI:
 b0254
ECOO157CYC:
 Z0885-MONOMER
ECOO157CYC:
 Z0346-MONOMER
INTERPRO:
 IPR036388
INTERPRO:
 IPR036390
INTERPRO:
 IPR005119
INTERPRO:
 IPR000847
MODBASE:
 Q57083
PFAM:
 PF03466
PFAM:
 PF00126
PRIDE:
 Q57083
PRINTS:
 PR00039
PRODB:
 PRO_000023513
PROSITE:
 PS50931
REFSEQ:
 NP_414788
SMR:
 Q57083
UNIPROT:
 Q57083


Operon      
Name: perR         
Operon arrangement:
Transcription unit        Promoter
perR


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 insN-1p 270226 forward nd [COMP-HINF], [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP], [EXP-IEP] [2]
  promoter TSS_465 270588 forward nd [RS-EPT-CBR] [3]


Evidence    

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [EXP-IEP] Inferred from expression pattern

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


Reference(s)    

 [1] 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

 [2] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [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.

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