RegulonDB RegulonDB 10.9: Operon Form

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

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

Transcription unit          
Name: ydbD
Gene(s): ydbD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Name: ydbDp
+1: 1475066
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 78
Sequence: ggagaatatggctgctgaaaaattgcatctttctgaggaagtgttgtctacgttggatggTatttcgcgagaataacgaat
                          -35               -10             +1                   
Note(s): Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity.
Evidence: [AIPP]
Reference(s): [1] Gama-Castro S., et al., 2008
[2] Huerta AM., et al., 2003
[3] Zaslaver A., et al., 2006
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NsrR repressor ydbDp 1475099 1475110 39.0 acaaaagggaAAGATGCATTTCcctttttttc nd [APIORCISFBSCS], [GEA] [4]

RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.5 1474928 1474969 accaatgcagGTGGCGCTGGCGTGGCTGTTACAGCGTTCACCGAATATTTTgctgatccca
  anti-terminator -16.9 1474898 1474940 ttccgatgttGCTGCGAGCCTGGGTGCAACACCAATGCAGGTGGCGCTGGCGtggctgttac
  anti-anti-terminator -15.3 1474859 1474909 cccgctcgggGGCTTTACACCGCTGCAATCGTCCACACTTTCCGATGTTGCTGCGAGCCTgggtgcaaca
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"