RegulonDB RegulonDB 10.7: Gene Form
   

ydfH gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydfG ydfH ydfZ PhoB terminator TSS_1851 TSS_1851 ydfHp ydfHp

Gene      
Name: ydfH    Texpresso search in the literature
Synonym(s): ECK1533, G6814, b1540
Genome position(nucleotides): 1628352 --> 1629038 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.07
External database links:  
ASAP:
ABE-0005144
ECHOBASE:
EB3581
OU-MICROARRAY:
b1540
PORTECO:
ydfH
REGULONDB:
b1540
STRING:
511145.b1540
M3D: ydfH
COLOMBOS: ydfH
PortEco: b1540


Product      
Name: DNA-binding transcriptional repressor YdfH
Synonym(s): YdfH
Sequence: Get amino acid sequence Fasta Format
Regulator Family: GntR
Cellular location: cytosol
Molecular weight: 26.565
Isoelectric point: 6.249
Motif(s):
 
Type Positions Sequence
38 -> 57 EKEVSVRFNVSRQPVREAFI
11 -> 78 QPVNQQIYRILRRDIVHCLIAPGTPLSEKEVSVRFNVSRQPVREAFIKLAENGLIQIRPQRGSYVNKI
15 -> 75 QQIYRILRRDIVHCLIAPGTPLSEKEVSVRFNVSRQPVREAFIKLAENGLIQIRPQRGSYV
89 -> 208 IRQAIECAVARRAASMITESQCYQLEQNLHQQRIAIERKQLDDFFELDDNFHQLLTQIADCQLAWDTIENLKATVDRVRYMSFDHVSPPEMLLRQHLDIFSALQKRDGDAVERAMTQHLQ

 

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
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [APPHINH] Assay of protein purified to homogeneity from its native host
[HIFS] Human inference of function from sequence
[IEP] Inferred from expression pattern
Reference(s): [1] Perez-Rueda E., et al., 2000
[2] Perez-Rueda E., et al., 2004
[3] Sakihama Y., et al., 2012
External database links:  
ECOCYC:
G6814-MONOMER
ECOLIWIKI:
b1540
INTERPRO:
IPR011711
INTERPRO:
IPR036390
INTERPRO:
IPR036388
INTERPRO:
IPR008920
INTERPRO:
IPR000524
MODBASE:
P0ACM2
PFAM:
PF00392
PFAM:
PF07729
PRIDE:
P0ACM2
PRINTS:
PR00035
PROSITE:
PS50949
PROTEINMODELPORTAL:
P0ACM2
REFSEQ:
NP_416058
SMART:
SM00895
SMART:
SM00345
SMR:
P0ACM2
UNIPROT:
P0ACM2


Operon      
Name: ydfH         
Operon arrangement:
Transcription unit        Promoter
 


Transcriptional Regulation      
Display Regulation             
Activated by: PhoB


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_1851 1629168 forward nd [RS-EPT-CBR] [4]


Evidence    

 [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] Sakihama Y., Mizoguchi H., Oshima T., Ogasawara N., 2012, YdfH identified as a repressor of rspA by the use of reduced genome Escherichia coli MGF-01., Biosci Biotechnol Biochem 76(9):1688-93

 [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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