RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: ytfE
Gene(s): ytfE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[IC] Inferred by curator
Promoter
Name: ytfEp
+1: 4432009
Distance from start of the gene: 26
Sequence: aagcctctgctacgtaagggttatagcttttgccttaaagatgcatttaaaatacatcttAtcttattaagaatgaggtat
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Bodenmiller DM., et al., 2006
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
nd FNR repressor ytfEp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
[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 activator ytfEp 4432047 4432053 -41.0 ctgctacgtaAGGGTTAtagcttttgc nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [2]
proximal NarL-phosphorylated activator ytfEp 4432056 4432062 -50.0 aataagcctcTGCTACGtaagggttat nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [2]
[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 activator ytfEp 4432042 4432057 -41.0 gcctctgctaCGTAAGGGTTATAGCTtttgccttaa nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [2]
proximal NarP-phosphorylated activator ytfEp 4432051 4432066 -50.0 gttaaataagCCTCTGCTACGTAAGGgttatagctt nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [2]
[NsrR,-] 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 NsrR repressor ytfEp 4432012 4432030 -12.0 ttgccttaaaGATGCATTTAAAATACATCttatcttatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [1], [3], [4]


Evidence    

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

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Bodenmiller DM., Spiro S., 2006, The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator., J Bacteriol 188(3):874-81

 [2] Rodionov DA., Dubchak IL., Arkin AP., Alm EJ., Gelfand MS., 2005, Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks., PLoS Comput Biol 1(5):e55

 [3] Filenko N., Spiro S., Browning DF., Squire D., Overton TW., Cole J., Constantinidou C., 2007, The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase., J Bacteriol 189(12):4410-7

 [4] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [5] Justino MC., Almeida CC., Goncalves VL., Teixeira M., Saraiva LM., 2006, Escherichia coli YtfE is a di-iron protein with an important function in assembly of iron-sulphur clusters., FEMS Microbiol Lett 257(2):278-84

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