RegulonDB RegulonDB 10.8: Gene Form
   

hdfR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hdfR maoP trpT hdfRp6 hdfRp6 TSS_4371 TSS_4371 TSS_4370 TSS_4370 hdfRp hdfRp

Gene      
Name: hdfR    Texpresso search in the literature
Synonym(s): ECK3756, EG11449, b3762, b3763, b4480, yifA, yifD
Genome position(nucleotides): 3947128 <-- 3947967 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.45
External database links:  
ASAP:
ABE-0174109
ECHOBASE:
EB1418
OU-MICROARRAY:
b3763
PortEco:
hdfR
STRING:
511145.b4480
COLOMBOS: hdfR


Product      
Name: DNA-binding transcriptional dual regulator HdfR
Synonym(s): HdfR, YifA, YifD
Sequence: Get amino acid sequence Fasta Format
Regulator Family: LysR
Cellular location: cytosol
Molecular weight: 31.746
Isoelectric point: 7.732
Motif(s):
 
Type Positions Sequence
1 -> 58 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLT
4 -> 62 ELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGE
87 -> 270 RHNEFSIGASASLWECMLNQWLGRLYQNQDAHTGLQFEARIAQRQSLVKQLHERQLDLLITTEAPKMDEFSSQLLGYFTLALYTSAPSKLKGDLNYLRLEWGPDFQQHEAGLIGADEVPILTTSSAELAQQQIAMLNGCTWLPVSWARKKGGLHTVVDSTTLSRPLYAIWLQNSDKNALIRDLL
18 -> 37 FGRAAESLYLTQSAVSFRIR

 

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 --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
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
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[APPINH] Assay of protein partially-purified from its native host
[GEA] Gene expression analysis
Reference(s): [1] Bartoli J., et al., 2017
[2] Ko M., et al., 2000
[3] Krin E., et al., 2010
External database links:  
DIP:
DIP-48185N
ECOCYC:
EG11449-MONOMER
ECOLIWIKI:
b4480
INTERPRO:
IPR036388
INTERPRO:
IPR036390
INTERPRO:
IPR020890
INTERPRO:
IPR005119
INTERPRO:
IPR000847
MODBASE:
P0A8R9
PFAM:
PF03466
PFAM:
PF00126
PRIDE:
P0A8R9
PRINTS:
PR00039
PRODB:
PRO_000022871
PROSITE:
PS50931
REFSEQ:
YP_026246
SMR:
P0A8R9
UNIPROT:
P0A8R9


Operon      
Name: hdfR         
Operon arrangement:
Transcription unit        Promoter
hdfR


Transcriptional Regulation      
Display Regulation             
Repressed by: H-NS


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_4370 3948050 forward nd [RS-EPT-CBR] [4]
  promoter TSS_4371 3948058 forward nd [RS-EPT-CBR] [4]
  promoter hdfRp6 3948160 reverse Similarity to the consensus
Read more >
[ICWHO] [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] Bartoli J., My L., Belmudes L., Coute Y., Viala JP., Bouveret E., 2017, The Long Hunt for pssR -Looking for a Phospholipid Synthesis Transcriptional Regulator, Finding the Ribosome., J Bacteriol 199(14)

 [2] Ko M., Park C., 2000, H-NS-Dependent regulation of flagellar synthesis is mediated by a LysR family protein., J Bacteriol 182(16):4670-2

 [3] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273

 [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.

 [5] 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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