RegulonDB RegulonDB 10.8: Operon Form
   

ydeI operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ydeI
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: ydeI
Gene(s): ydeI   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene ydeI is increased when colicin (at 30 ng/ml) is added to the medium 23421615.
Evidence: [IC] Inferred by curator
Promoter
Name: ydeIp5
+1: 1624559
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 62
Sequence: tatttgacagctagttggctgattttaaatgccttataacaattggcaatattcttatttGgcaattataaaaatagcaac
                        -35                       -10       +1                   
Note(s): Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.234. P-value: 1.921e-5
Evidence: [ICWHO]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[RcdA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd RcdA activator ydeIp5 nd nd nd nd nd [BPP], [GEA] [2]


Transcription unit       
Gene(s): ydeI   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene ydeI is increased when colicin (at 30 ng/ml) is added to the medium 23421615.
Evidence: [ICWHO] Inferred computationally without human oversight


Transcription unit       
Gene(s): ydeI   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene ydeI is increased when colicin (at 30 ng/ml) is added to the medium 23421615.
Evidence: [IC] Inferred by curator


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis


Reference(s)    

 [1] 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

 [2] Shimada T., Katayama Y., Kawakita S., Ogasawara H., Nakano M., Yamamoto K., Ishihama A., 2012, A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli., Microbiologyopen 1(4):381-94

RegulonDB