RegulonDB RegulonDB 10.9: Gene Form
   

slyA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

slyB slyA ydhI slyAp10 slyAp10 ydhIp ydhIp TSS_1928 TSS_1928 TSS_1927 (cluster) TSS_1927 (cluster) slyAp14 slyAp14 slyAp13 slyAp13 TSS_1926 TSS_1926

Gene      
Name: slyA    Texpresso search in the literature
Synonym(s): ECK1638, G6882, b1642
Genome position(nucleotides): 1720390 <-- 1720824 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 48.28
External database links:  
ASAP:
 ABE-0005495
ECHOBASE:
 EB3184
ECOLIHUB:
 slyA
OU-MICROARRAY:
 b1642
STRING:
 511145.b1642
COLOMBOS: slyA


Shine dalgarno      
Sequence: gcaagctaatTATAAGgagatgaaATT


Product      
Name: SlyA
Sequence: Get amino acid sequence Fasta Format
Regulator Family: MarR
Cellular location: cytosol
Molecular weight: 16.353
Isoelectric point: 7.161
Motif(s):
 
Type Positions Sequence
29 -> 87 LTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRA
121 -> 121 E
49 -> 72 QIQLAKAIGIEQPSLVRTLDQLEE
2 -> 135 ESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEMEAVINKTRAEILHGISAEELEQLITLIAKLEH

 
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 --> 3.3.1 - operon
  5 - cell processes --> 5.6 - protection --> 5.6.3 - cell killing
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0000976 - transcription regulatory region sequence-specific DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0009405 - pathogenesis
GO:2000143 - negative regulation of DNA-templated transcription, initiation
GO:2000144 - positive regulation of DNA-templated transcription, initiation
External database links:  
ECOCYC:
 G6882-MONOMER
ECOLIWIKI:
 b1642
INTERPRO:
 IPR023071
INTERPRO:
 IPR036390
INTERPRO:
 IPR036388
INTERPRO:
 IPR023187
INTERPRO:
 IPR000835
MODBASE:
 P0A8W2
PFAM:
 PF01047
PRIDE:
 P0A8W2
PRINTS:
 PR00598
PRODB:
 PRO_000023957
PROSITE:
 PS01117
PROSITE:
 PS50995
REFSEQ:
 NP_416159
SMART:
 SM00347
SMR:
 P0A8W2
SWISSMODEL:
 P0A8W2
UNIPROT:
 P0A8W2


Operon      
Name: slyA         
Operon arrangement:
Transcription unit        Promoter
slyA


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_1926 1720091 forward nd [RS-EPT-CBR] [1]
  promoter slyAp13 1720849 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter slyAp14 1720865 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter TSS_1927 (cluster) 1720870 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [1]
  promoter TSS_1928 1720879 reverse nd [RS-EPT-CBR] [1]
  promoter slyAp10 1721014 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]


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] 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.

 [2] 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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