RegulonDB RegulonDB 11.1: Gene Form
   

ratA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

smpB ratA bamE yfjF anti-anti-terminator anti-terminator terminator smpBp5 smpBp5 TSS_2970 TSS_2970

Gene      
Name: ratA    Texpresso search in the literature
Synonym(s): ECK2615, G7358, b2619, yfjG
Genome position(nucleotides): 2754288 <-- 2754764
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 47.17
External database links:  
ASAP:
 ABE-0008618
ECHOBASE:
 EB2985
ECOLIHUB:
 yfjG
OU-MICROARRAY:
 b2619
STRING:
 511145.b2619
COLOMBOS: ratA


Product      
Name: ribosome association toxin RatA
Synonym(s): 50S ribosomal subunit-binding toxin of a putative toxin-antitoxin pair, RatA, YfjG
Sequence: Get amino acid sequence Fasta Format
Cellular location: membrane
Molecular weight: 17.727
Isoelectric point: 8.697
Motif(s):
 
Type Positions Sequence Comment
23 -> 148 VPYSAEQMYQLVNDVQSYPQFLPGCTGSRILESTPGQMTAAVDVSKAGISKTFTTRNQLTSNQSILMNLVDGPFKKLIGGWKFTPLSQEACRIEFHLDFEFTNKLIELAFGRVFKELAANMVQAFT

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.6 - protection --> 5.6.3 - cell killing
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
molecular_function GO:0048039 - ubiquinone binding
GO:0043023 - ribosomal large subunit binding
biological_process GO:0006744 - ubiquinone biosynthetic process
GO:0045333 - cellular respiration
GO:0045947 - negative regulation of translational initiation
Note(s): Note(s): ...[more].
Evidence: [EXP] Inferred from experiment
Reference(s): [1] Fino C., et al., 2020
[2] Zhang Y., et al., 2011
External database links:  
ALPHAFOLD:
 P0AGL5
ECOCYC:
 G7358-MONOMER
ECOLIWIKI:
 b2619
INTERPRO:
 IPR005031
INTERPRO:
 IPR023393
PFAM:
 PF03364
PRIDE:
 P0AGL5
REFSEQ:
 NP_417109
UNIPROT:
 P0AGL5


Operon      
Name: ratA-yfjF         
Operon arrangement:
Transcription unit        Promoter
ratA-yfjF


RNA cis-regulatory element    
Attenuation: Transcriptional


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_2970 2753605 forward nd [RS-EPT-CBR] [3]
  promoter smpBp5 2754767 forward nd [COMP-AINF] [4]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Fino C., Vestergaard M., Ingmer H., Pierrel F., Gerdes K., Harms A., 2020, PasT of Escherichia coli sustains antibiotic tolerance and aerobic respiration as a bacterial homolog of mitochondrial Coq10., Microbiologyopen 9(8):e1064

 [2] Zhang Y., Inouye M., 2011, RatA (YfjG), an Escherichia coli toxin, inhibits 70S ribosome association to block translation initiation., Mol Microbiol 79(6):1418-29

 [3] 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.

 [4] 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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