RegulonDB RegulonDB 11.1: Operon Form
   

ydcSTUV-patD operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ydcSTUV-patD
Gene(s): ydcS, ydcT, ydcU, ydcV, patD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the ydcSTUV-patD operon is induced under nitrogen-limited growth Schneider BL,2013 It also was demonstrated by in vitro transcription analysis and gene expression analysis that this operon is activated by the protein Nac and by σ38. Two putative -10 boxes for σ38 and two DNA-binding sites similar to the consensus recognized by Nac were found, but it has not been demonstrated which of these sequences are functional; therefore, we linked to the operon only the -10 box, which is more conserved relative to the consensus σ38 and the DNA-binding site that is located closer to this promoter Schneider BL,2013
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Schneider BL., et al., 2013
[2] Zimmer DP., et al., 2000
Promoter
Name: ydcSp1
+1: 1511599
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 55
Sequence: gaataaattttctcaggggcgaaggtgtgcctgcaagccgccgtctatggttaaacaaggAgatatttttacggcacggcg
                                            -10             +1                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
Reference(s): [1] Schneider BL., et al., 2013
TF binding sites (TFBSs)
[Nac,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Nac activator ydcSp1 1511541 1511555 -51.0 cacaacctgaATAAATTTTCTCAGGggcgaaggtg nd [EXP-IDA], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA] W [1]


Transcription unit       
Name: patD
Gene(s): patD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


Evidence    

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA] Inferred from direct assay

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


Reference(s)    

 [1] Schneider BL., Hernandez VJ., Reitzer L., 2013, Putrescine catabolism is a metabolic response to several stresses in Escherichia coli., Mol Microbiol 88(3):537-50

 [2] Zimmer DP., Soupene E., Lee HL., Wendisch VF., Khodursky AB., Peter BJ., Bender RA., Kustu S., 2000, Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation., Proc Natl Acad Sci U S A 97(26):14674-9

RegulonDB