RegulonDB RegulonDB 10.8: Gene Form
   

yfeR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yfeH yfeR yfeN ypeB yfeRp1 yfeRp1 yfeHp3 yfeHp3 TSS_2688 TSS_2688 yfeHp5 yfeHp5

Gene      
Name: yfeR    Texpresso search in the literature
Synonym(s): ECK2403, G7257, b2409
Genome position(nucleotides): 2525930 <-- 2526856 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.94
External database links:  
ASAP:
ABE-0007932
ECHOBASE:
EB3911
OU-MICROARRAY:
b2409
PortEco:
yfeR
STRING:
511145.b2409
COLOMBOS: yfeR


Product      
Name: putative LysR-type DNA-binding transcriptional regulator YfeR
Synonym(s): YfeR
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 33.903
Isoelectric point: 6.883
Motif(s):
 
Type Positions Sequence
89 -> 292 QQLSGKVRVAASQTISAHLIPQCIAESHRRYPDIQFVLHDRPQQWVMESIRQGDVDFGIVIDPGPVGDLQCEAILSEPFFLLCHRDSALAVEDYVPWQALQGAKLVLQDYASGSRPLIDAALARNGIQANIVQEIGHPATLFPMVAAGIGISILPALALPLPEGSPLVVKRITPVVERQLMLVRRKNRSLSTAAEALWDVVRDQ
1 -> 60 MNYSLKQLKVFVTVAQEKSFSRAGERIGLSQSAVSHSVKELENHTGVRLLDRTTREVVLT
5 -> 64 LKQLKVFVTVAQEKSFSRAGERIGLSQSAVSHSVKELENHTGVRLLDRTTREVVLTDAGQ
20 -> 39 FSRAGERIGLSQSAVSHSVK

 

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:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0043565 - sequence-specific DNA binding
GO:0000986 - bacterial-type cis-regulatory region sequence-specific DNA binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
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:  
DIP:
DIP-12017N
ECOCYC:
G7257-MONOMER
ECOLIWIKI:
b2409
INTERPRO:
IPR036388
INTERPRO:
IPR036390
INTERPRO:
IPR005119
INTERPRO:
IPR000847
MODBASE:
P0ACR7
PFAM:
PF03466
PFAM:
PF00126
PRIDE:
P0ACR7
PRINTS:
PR00039
PROSITE:
PS50931
REFSEQ:
NP_416904
SMR:
P0ACR7
UNIPROT:
P0ACR7


Operon      
Name: yfeR         
Operon arrangement:
Transcription unit        Promoter
yfeR


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 yfeHp5 2526909 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter TSS_2688 2526926 forward nd [RS-EPT-CBR] [4]
  promoter yfeHp3 2526933 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yfeRp1 2527039 reverse Similarity to the consensus
Read more >
[ICWHO] [3]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [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., 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] 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

 [4] 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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