RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: add
Gene(s): add   Genome Browser M3D Gene expression COLOMBOS
Note(s): The site for the RbsR transcriptional regulator in the add operon was identified based on genomic Selex analysis Shimada T,2013
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: addp6
+1: 1702202
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 31
Sequence: aacgtaaaaaatcgttgcgcaatcgtggatttttaccctgctttgtttttataatggtgcGcacttttatatccagaaaaa
                         -35                      -10       +1                   
Evidence: [ICWHO]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[RbsR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RbsR-D-ribose activator addp6 1702145 1702164 -47.5 attgcgcaacGTAAAAAATCGTTGCGCAATcgtggatttt nd [GEA], [AIBSCS], [BPP] [2]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [3] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -18.4 1702132 1702176 tcgttaacccCAATTGCGCAACGTAAAAAATCGTTGCGCAATCGTGGATTTTTAccctgctttg
  anti-terminator -4.07 1702116 1702141 acgccatccgCGCTGTTCGTTAACCCCAATTGCGCaacgtaaaaa
  anti-anti-terminator -11.7 1702088 1702120 ctggaaaaagGTGTGGCTGGATTAATTAACGCCATCCGCGCTgttcgttaac
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins


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., Kori A., Ishihama A., 2013, Involvement of the ribose operon repressor RbsR in regulation of purine nucleotide synthesis in Escherichia coli., FEMS Microbiol Lett 344(2):159-65

 [3] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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