RegulonDB RegulonDB 10.9: 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
ECOLIHUB:
ydaS
OU-MICROARRAY:
b1357
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
1 -> 22 MKKENYSFKQACAVVGGQSAMA
9 -> 72 KQACAVVGGQSAMARLLGVSPPSVNQWIKGVRQLPAERCPAIERATRGEVLCEELRPDIDWSYL
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:
IPR010982
INTERPRO:
IPR031856
PFAM:
PF15943
PRIDE:
P76063
REFSEQ:
NP_415875
SMR:
P76063
UNIPROT:
P76063


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


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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