RegulonDB RegulonDB 11.1: Gene Form
   

appY gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ompT appY tfaX ArcA TSS_694 TSS_694 TSS_693 TSS_693 TSS_692 TSS_692 TSS_691 TSS_691 TSS_690 (cluster) TSS_690 (cluster) TSS_689 TSS_689 TSS_688 TSS_688 TSS_687 TSS_687 appYp2 appYp2 appYp3 appYp3 appYp1 appYp1

Gene      
Name: appY    Texpresso search in the literature
Synonym(s): ECK0556, EG10050, b0564
Genome position(nucleotides): 583681 --> 584430
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 31.73
External database links:  
ASAP:
 ABE-0001929
CGSC:
 31146
ECHOBASE:
 EB0048
ECOLIHUB:
 appY
ECOO157CYC:
 Z2104
ECOO157CYC:
 Z0321
ECOO157CYC:
 Z1789
OU-MICROARRAY:
 b0564
STRING:
 511145.b0564
COLOMBOS: appY


Product      
Name: DLP12 prophage; DNA-binding transcriptional activator AppY
Synonym(s): AppY
Sequence: Get amino acid sequence Fasta Format
Regulator Family: AraC/XylS
Cellular location: cytosol
Molecular weight: 28.763
Isoelectric point: 8.858
Motif(s):
 
Type Positions Sequence Comment
26 -> 31 KKNSLF UniProt: In Ref. 2..
139 -> 236 CKITGIISFNIERQWHLKDIAELIYTSESLIKKRLRDEGTSFTEILRDTRMRYAKKLITSNSYSINVVAQKCGYNSTSYFICAFKDYYGVTPSHYFEK UniProt: HTH araC/xylS-type.
156 -> 177 KDIAELIYTSESLIKKRLRDEG UniProt: H-T-H motif.
162 -> 235 IYTSESLIKKRLRDEGTSFTEILRDTRMRYAKKLITSNSYSINVVAQKCGYNSTSYFICAFKDYYGVTPSHYFE
203 -> 226 INVVAQKCGYNSTSYFICAFKDYY UniProt: H-T-H motif.

 
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 --> 3.3 - genetic unit regulated --> 3.3.3 - stimulon
  5 - cell processes --> 5.5 - adaptations --> 5.5.3 - starvation
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
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
biological_process GO:0010165 - response to X-ray
GO:0006355 - regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0016036 - cellular response to phosphate starvation
Note(s): Note(s): ...[more].
Evidence: [EXP] Inferred from experiment
Reference(s): [1] Atlung T., et al., 1994
[2] Atlung T., et al., 1989
[3] Kemp EH., et al., 1987
[4] Sargentini NJ., et al., 2016
External database links:  
ALPHAFOLD:
 P05052
ECOCYC:
 PD00967
ECOLIWIKI:
 b0564
ECOO157CYC:
 Z0321-MONOMER
ECOO157CYC:
 Z1789-MONOMER
ECOO157CYC:
 Z2104-MONOMER
INTERPRO:
 IPR020449
INTERPRO:
 IPR009057
INTERPRO:
 IPR018060
INTERPRO:
 IPR018062
MODBASE:
 P05052
PFAM:
 PF12833
PRIDE:
 P05052
PRINTS:
 PR00032
PRODB:
 PRO_000022112
PROSITE:
 PS01124
PROSITE:
 PS00041
REFSEQ:
 NP_415096
SMART:
 SM00342
SMR:
 P05052
UNIPROT:
 P05052


Operon      
Name: appY         
Operon arrangement:
Transcription unit        Promoter
appY
appY
appY


Transcriptional Regulation      
Display Regulation             
Activated by: ArcA
Repressed by: DpiA, 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_687 584165 forward nd [RS-EPT-CBR] [5]
  promoter TSS_688 585378 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_689 585380 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_690 (cluster) 585383 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_691 585398 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_692 585408 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_693 585420 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_694 585594 reverse nd [RS-EPT-CBR] [5]


Evidence    

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


Reference(s)    

 [1] Atlung T., Brondsted L., 1994, Role of the transcriptional activator AppY in regulation of the cyx appA operon of Escherichia coli by anaerobiosis, phosphate starvation, and growth phase., J Bacteriol 176(17):5414-22

 [2] Atlung T., Nielsen A., Hansen FG., 1989, Isolation, characterization, and nucleotide sequence of appY, a regulatory gene for growth-phase-dependent gene expression in Escherichia coli., J Bacteriol 171(3):1683-91

 [3] Kemp EH., Minton NP., Mann NH., 1987, Complete nucleotide sequence and deduced amino acid sequence of the M5 polypeptide gene of Escherichia coli., Nucleic Acids Res 15(9):3924

 [4] Sargentini NJ., Gularte NP., Hudman DA., 2016, Screen for genes involved in radiation survival of Escherichia coli and construction of a reference database., Mutat Res 793-794:1-14

 [5] 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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