RegulonDB RegulonDB 10.10: Operon Form
   

yiaKLMNO-lyxK-sgbHUE operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: yiaKLMNO-lyxK-sgbHUE
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: yiaKLMNO-lyx-sgbHUE
Synonym(s): yiaKLMNO-lyxK-sgbHUE, yiaKLMNOPQRS
Gene(s): yiaK, yiaL, yiaM, yiaN, yiaO, lyxK, sgbH, sgbU, sgbE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Ibanez E., et al., 2000
[2] Ibanez E., et al., 2000
[3] Yew WS., et al., 2002
Promoter
Name: yiaKp
+1: 3742674
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 59
Sequence: tcttttgaaattcatcaatcagattgccttgttaaaaagtgatcgatatatttgaaatcaAgtttcgcatattgaaatttt
                        -35                    -10          +1                   
Evidence: [ICWHO]
[IMP]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[1] Ibanez E., et al., 2000
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP activator yiaKp 3742558 3742579 -105.5 tggtagcgcaAAGTGTGCCGTAGTTCACGATCtcgacagata nd [GEA], [APIORCISFBSCS], [BPP] [1]
[CRP,?] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP unknown yiaKp 3742725 3742746 62.5 aaaacaaggaAGCCTGGGATGAAAGTGACATTtgagcagtta nd [GEA], [APIORCISFBSCS], [BPP] [1]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF activator yiaKp 3742618 3742630 -49.5 tttatgtcttTTGAAATTCATCAatcagattgc nd [GEA], [APIORCISFBSCS], [BPP], [SM] [1]
[PlaR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PlaR repressor yiaKp 3742663 3742683 -1.0 tgatcgatatATTTGAAATCAAGTTTCGCATattgaaattt nd [GEA], [BCE] [1]


Transcription unit       
Name: yiaKLMNO-lyx-sgbHUE
Gene(s): yiaK, yiaL, yiaM, yiaN, yiaO, lyxK, sgbH, sgbU, sgbE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Ibanez E., et al., 2000
[2] Ibanez E., et al., 2000
[3] Yew WS., et al., 2002
Promoter
Name: yiaKp2
+1: 3742720
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 13
Sequence: tatatttgaaatcaagtttcgcatattgaaattttaagccaaaaaagcgatcaaaaaaacAaggaagcctgggatgaaagt
                            -35                    -10      +1                   
Evidence: [AIBSCS]
[AIPP]
[ICWHO]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Rhodius VA., et al., 2005


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [IMP] Inferred from mutant phenotype

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [SM] Site mutation

 [BCE] Binding of cellular extracts

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [AIPP] Automated inference of promoter position


Reference(s)    

 [1] Ibanez E., Campos E., Baldoma L., Aguilar J., Badia J., 2000, Regulation of expression of the yiaKLMNOPQRS operon for carbohydrate utilization in Escherichia coli: involvement of the main transcriptional factors., J Bacteriol 182(16):4617-24

 [2] Ibanez E., Gimenez R., Pedraza T., Baldoma L., Aguilar J., Badia J., 2000, Role of the yiaR and yiaS genes of Escherichia coli in metabolism of endogenously formed L-xylulose., J Bacteriol 182(16):4625-7

 [3] Yew WS., Gerlt JA., 2002, Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons., J Bacteriol 184(1):302-6

 [4] 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

 [5] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

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