RegulonDB RegulonDB 10.8: Gene Form
   

ydaS gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

racR ydaT ydaS racRp4 racRp4 ydaSp6 ydaSp6 ydaSp2 ydaSp2 ydaSp4 ydaSp4 racRp3 racRp3 racRp5 racRp5 ydaSp3 ydaSp3 TSS_1775 TSS_1775

Gene      
Name: ydaS    Texpresso search in the literature
Synonym(s): ECK1355, G6681, b1357
Genome position(nucleotides): 1420365 --> 1420661 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
43.43
External database links:  
ASAP:
ABE-0004552
ECHOBASE:
EB3144
OU-MICROARRAY:
b1357
PortEco:
ydaS
STRING:
511145.b1357
COLOMBOS: ydaS


Product      
Name: Rac prophage; toxin YdaS
Synonym(s): Rac prophage; putative DNA-binding transcriptional regulator YdaS, YdaS
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 10.976
Isoelectric point: 8.77
Motif(s):
 
Type Positions Sequence
8 -> 72 FKQACAVVGGQSAMARLLGVSPPSVNQWIKGVRQLPAERCPAIERATRGEVLCEELRPDIDWSYL
1 -> 22 MKKENYSFKQACAVVGGQSAMA
23 -> 98 RLLGVSPPSVNQWIKGVRQLPAERCPAIERATRGEVLCEELRPDIDWSYLRRSACCSQNMSVKQLNDSNKSSFDHT

 

Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
molecular_function GO:0003677 - DNA binding
biological_process GO:0008219 - cell death
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Krishnamurthi R., et al., 2017
External database links:  
ECOCYC:
G6681-MONOMER
ECOLIWIKI:
b1357
INTERPRO:
IPR001387
INTERPRO:
IPR031856
INTERPRO:
IPR010982
PFAM:
PF15943
PRIDE:
P76063
REFSEQ:
NP_415875
SMR:
P76063
UNIPROT:
P76063


Operon      
Name: ydaSTUVW-rzpR         
Operon arrangement:
Transcription unit        Promoter
 


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_1775 1419829 reverse nd [RS-EPT-CBR] [2]
  promoter ydaSp3 1420170 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter racRp5 1420242 reverse Similarity to the consensus
Read more >
[ICWHO], [RS-EPT-CBR] [2], [3]
  promoter racRp3 1420244 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter ydaSp4 1420260 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter ydaSp2 1420277 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter ydaSp6 1420343 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter racRp4 1420449 reverse Similarity to the consensus
Read more >
[ICWHO] [3]


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] Krishnamurthi R., Ghosh S., Khedkar S., Seshasayee ASN., 2017, Repression of YdaS Toxin Is Mediated by Transcriptional Repressor RacR in the Cryptic rac Prophage of Escherichia coli K-12., mSphere 2(6)

 [2] 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.

 [3] 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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