RegulonDB RegulonDB 10.8: Gene Form
   

ydeO gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydeN ydeO safA GadX NagC GadX NagC ydeNp3 ydeNp3 ydeNp ydeNp

Gene      
Name: ydeO    Texpresso search in the literature
Synonym(s): ECK1493, G6789, b1499
Genome position(nucleotides): 1582926 <-- 1583687 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
39.5
External database links:  
ASAP:
ABE-0004992
ECHOBASE:
EB3558
OU-MICROARRAY:
b1499
PortEco:
ydeO
STRING:
511145.b1499
COLOMBOS: ydeO


Product      
Name: DNA-binding transcriptional dual regulator YdeO
Synonym(s): YdeO
Sequence: Get amino acid sequence Fasta Format
Regulator Family: AraC/XylS
Cellular location: cytosol
Molecular weight: 28.725
Isoelectric point: 9.048
Motif(s):
 
Type Positions Sequence
137 -> 233 GKVRNIVNMKPAHPWKLKDICDCLYISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKE
157 -> 230 CDCLYISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRV
200 -> 223 VNKIAEQCGYASTSYFIYAFRKHF
154 -> 175 KDICDCLYISESLLKKKLKQEQ

 

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
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[APPHINH] Assay of protein purified to homogeneity from its native host
[GEA] Gene expression analysis
[HIFS] Human inference of function from sequence
[IEP] Inferred from expression pattern
[IMP] Inferred from mutant phenotype
Reference(s): [1] Burton NA., et al., 2010
[2] Gallegos MT., et al., 1997
[3] Ma Z., et al., 2004
[4] Masuda N., et al., 2002
[5] Masuda N., et al., 2003
[6] Yamanaka Y., et al., 2014
External database links:  
ECOCYC:
G6789-MONOMER
ECOLIWIKI:
b1499
INTERPRO:
IPR018060
INTERPRO:
IPR020449
INTERPRO:
IPR018062
INTERPRO:
IPR009057
MODBASE:
P76135
PFAM:
PF12833
PRIDE:
P76135
PRINTS:
PR00032
PROSITE:
PS00041
PROSITE:
PS01124
REFSEQ:
NP_416016
SMART:
SM00342
SMR:
P76135
UNIPROT:
P76135


Operon      
Name: safA-ydeO         
Operon arrangement:
Transcription unit        Promoter
safA-ydeO
ydeO


Transcriptional Regulation      
Display Regulation             
Activated by: EvgA, RcsB
Repressed by: PhoP, H-NS, YdeO


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 ydeNp3 1582729 reverse Similarity to the consensus
Read more >
[ICWHO] [7]


Evidence    

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Burton NA., Johnson MD., Antczak P., Robinson A., Lund PA., 2010, Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics., J Mol Biol 401(5):726-42

 [2] Gallegos MT., Schleif R., Bairoch A., Hofmann K., Ramos JL., 1997, Arac/XylS family of transcriptional regulators., Microbiol Mol Biol Rev 61(4):393-410

 [3] Ma Z., Masuda N., Foster JW., 2004, Characterization of EvgAS-YdeO-GadE branched regulatory circuit governing glutamate-dependent acid resistance in Escherichia coli., J Bacteriol 186(21):7378-89

 [4] Masuda N., Church GM., 2002, Escherichia coli gene expression responsive to levels of the response regulator EvgA., J Bacteriol 184(22):6225-34

 [5] Masuda N., Church GM., 2003, Regulatory network of acid resistance genes in Escherichia coli., Mol Microbiol 48(3):699-712

 [6] Yamanaka Y., Oshima T., Ishihama A., Yamamoto K., 2014, Characterization of the YdeO regulon in Escherichia coli., PLoS One 9(11):e111962

 [7] 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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