RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: glk
Gene(s): glk   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[IC] Inferred by curator
Reference(s): [1] Meyer D., et al., 1997
Promoter
Name: glkp3
+1: 2509447
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 21
Sequence: cctttccggcgttgttgttatgcccccaggtatttacagtgtgagaaagaattattttgaCtttagcggagcagttgaaga
                                                     -10    +1                   
Evidence: [COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[RS-EPT-CBR]
Reference(s): [2] Mendoza-Vargas A., et al., 2009
[3] Olvera L., et al., 2009
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: tttaaaagatTATCGGGAGAGTTACCTCCCGATAtaaaaggaag
Reference(s): [1] Meyer D., et al., 1997


Transcription unit       
Name: glk
Gene(s): glk   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[IC] Inferred by curator
Reference(s): [1] Meyer D., et al., 1997
Promoter
Name: glkp1
+1: 2509447
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 21
Sequence: cctttccggcgttgttgttatgcccccaggtatttacagtgtgagaaagaattattttgaCtttagcggagcagttgaaga
                                                     -10    +1                   
Evidence: [COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[RS-EPT-CBR]
Reference(s): [2] Mendoza-Vargas A., et al., 2009
[3] Olvera L., et al., 2009
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: tttaaaagatTATCGGGAGAGTTACCTCCCGATAtaaaaggaag
Reference(s): [1] Meyer D., et al., 1997


Transcription unit          
Name: glk
Gene(s): glk   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Meyer D., et al., 1997
Promoter
Name: glkp4
+1: 2509461
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 35
Sequence: ttacagggagcctgcctttccggcgttgttgttatgcccccaggtatttacagtgtgagaAagaattattttgactttagc
                                                       -10  +1                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [1] Meyer D., et al., 1997
[3] Olvera L., et al., 2009
Terminator(s)
Type: rho-independent
Sequence: tttaaaagatTATCGGGAGAGTTACCTCCCGATAtaaaaggaag
Reference(s): [1] Meyer D., et al., 1997
TF binding sites (TFBSs)
[Cra,-] 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 Cra repressor glkp4 2509544 2509561 -91.5 ctgcaattggTGCTGAAACGATAAAGTAattgtgtgac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [5]


Transcription unit          
Name: glk
Gene(s): glk   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Meyer D., et al., 1997
Promoter
Name: glkp2
+1: 2509461
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 35
Sequence: ttacagggagcctgcctttccggcgttgttgttatgcccccaggtatttacagtgtgagaAagaattattttgactttagc
                                                       -10  +1                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [1] Meyer D., et al., 1997
[3] Olvera L., et al., 2009
Terminator(s)
Type: rho-independent
Sequence: tttaaaagatTATCGGGAGAGTTACCTCCCGATAtaaaaggaag
Reference(s): [1] Meyer D., et al., 1997
TF binding sites (TFBSs)
[Cra,-] 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 Cra repressor glkp2 2509544 2509561 -91.5 ctgcaattggTGCTGAAACGATAAAGTAattgtgtgac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [5]


Evidence    

 [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

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

 [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.


Reference(s)    

 [1] Meyer D., Schneider-Fresenius C., Horlacher R., Peist R., Boos W., 1997, Molecular characterization of glucokinase from Escherichia coli K-12., J Bacteriol 179(4):1298-306

 [2] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [3] 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

 [4] 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.

 [5] Shimada T., Yamamoto K., Ishihama A., 2011, Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli., J Bacteriol 193(3):649-59

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