RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: gpmA
Gene(s): gpmA   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: gpmAp4
+1: 787632
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 37
Sequence: tattttcgctatggttatgcgtaagcattgctgttgcttcgtcgcggcaatataatgagaAttattatcattaaaagatga
                                   -35                   -10+1                   
Evidence: [COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[RS-EPT-CBR]
Reference(s): [1] Olvera L., et al., 2009
[2] Salgado H, et al., 2012
[3] Vassinova N., et al., 2000
TF binding sites (TFBSs)
[Fur,-] 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 Fur-Fe2+ repressor gpmAp4 787618 787636 6.0 gcaatataatGAGAATTATTATCATTAAAagatgatttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]
proximal Fur-Fe2+ repressor gpmAp4 787621 787639 3.0 gcggcaatatAATGAGAATTATTATCATTaaaagatgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [5]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA FnrS gpmA repressor 787592 787608 CCAUAUACUUACUCCUC nd [EXP-IEP], [EXP-IMP-SITE-MUTATION] [4]


Transcription unit          
Name: gpmA
Gene(s): gpmA   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: gpmAp
+1: 787632
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 37
Sequence: tattttcgctatggttatgcgtaagcattgctgttgcttcgtcgcggcaatataatgagaAttattatcattaaaagatga
                                   -35                   -10+1                   
Evidence: [COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[RS-EPT-CBR]
Reference(s): [1] Olvera L., et al., 2009
[2] Salgado H, et al., 2012
[3] Vassinova N., et al., 2000
TF binding sites (TFBSs)
[Fur,-] 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 Fur-Fe2+ repressor gpmAp 787618 787636 6.0 gcaatataatGAGAATTATTATCATTAAAagatgatttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]
proximal Fur-Fe2+ repressor gpmAp 787621 787639 3.0 gcggcaatatAATGAGAATTATTATCATTaaaagatgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [5]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA FnrS gpmA repressor 787592 787608 CCAUAUACUUACUCCUC nd [EXP-IEP], [EXP-IMP-SITE-MUTATION] [4]


Transcription unit       
Name: gpmA
Gene(s): gpmA   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: gpmAp3
+1: 787670
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 75
Sequence: tgcaactcaatattcacaacaaccttacactgcgccactattttcgctatggttatgcgtAagcattgctgttgcttcgtc
                                                      -10   +1                   
Evidence: [COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[RS-EPT-CBR]
Reference(s): [1] Olvera L., et al., 2009
[2] Salgado H, et al., 2012


Transcription unit       
Name: gpmA
Gene(s): gpmA   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: gpmAp2
+1: 787670
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 75
Sequence: tgcaactcaatattcacaacaaccttacactgcgccactattttcgctatggttatgcgtAagcattgctgttgcttcgtc
                                                      -10   +1                   
Evidence: [COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[RS-EPT-CBR]
Reference(s): [1] Olvera L., et al., 2009
[2] Salgado H, et al., 2012


Evidence    

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

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

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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

 [EXP-IEP] Inferred from expression pattern

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Olvera L., Mendoza-Vargas A., Flores N., Olvera M., Sigala JC., Gosset G., Morett E., Bolivar F., 2009, Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation., PLoS One 4(10):e7466

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [3] Vassinova N., Kozyrev D., 2000, A method for direct cloning of fur-regulated genes: identification of seven new fur-regulated loci in Escherichia coli., Microbiology 146 Pt 12:3171-3182

 [4] Durand S., Storz G., 2010, Reprogramming of anaerobic metabolism by the FnrS small RNA., Mol Microbiol 75(5):1215-31

 [5] Chen Z., Lewis KA., Shultzaberger RK., Lyakhov IG., Zheng M., Doan B., Storz G., Schneider TD., 2007, Discovery of Fur binding site clusters in Escherichia coli by information theory models., Nucleic Acids Res 35(20):6762-77

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