RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: ydhYVWXUT
Gene(s): ydhT, ydhU, ydhX, ydhW, ydhV, ydhY   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Partridge JD., et al., 2008
Promoter
Name: ydhYp
+1: 1754642
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 165
Sequence: tgtaattttaattgataacgatcaatgttaagggctcagaataatcacattattttttctCctaaccataaaggattagtt
                                 -35                    -10 +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[3] Maciag A., et al., 2011
[1] Partridge JD., et al., 2008
TF binding sites (TFBSs)
[FNR,+] 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 FNR activator ydhYp 1754678 1754691 -42.5 gtaattttaaTTGATAACGATCAAtgttaagggc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [4]
[NarL,-] 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 NarL-phosphorylated repressor ydhYp 1754625 1754631 15.0 ctaaccataaAGGATTAgtttatcggc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
proximal NarL-phosphorylated repressor ydhYp 1754634 1754640 6.0 ttttttctccTAACCATaaaggattag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
proximal NarL-phosphorylated repressor ydhYp 1754655 1754661 -16.0 gggctcagaaTAATCACattatttttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
proximal NarL-phosphorylated repressor ydhYp 1754681 1754687 -42.0 ttttaattgaTAACGATcaatgttaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1]
[NarP,-] 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 NarP-phosphorylated repressor ydhYp 1754625 1754632 15.0 cctaaccataAAGGATTAgtttatcggc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
proximal NarP-phosphorylated repressor ydhYp 1754634 1754641 6.0 attttttctcCTAACCATaaaggattag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]


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


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


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP] Inferred from expression pattern

 [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.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Partridge JD., Browning DF., Xu M., Newnham LJ., Scott C., Roberts RE., Poole RK., Green J., 2008, Characterization of the Escherichia coli K-12 ydhYVWXUT operon: regulation by FNR, NarL and NarP., Microbiology 154(Pt 2):608-18

 [2] 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

 [3] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [4] Kang Y., Weber KD., Qiu Y., Kiley PJ., Blattner FR., 2005, Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function., J Bacteriol 187(3):1135-60

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