RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: gltX
Gene(s): gltX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Champagne N., et al., 1998
Promoter
Name: gltXp3
+1: 2520730
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 58
Sequence: gcgtaaggtagaaacccgaactacattgaggaatcaggcgggagtgatagaatatcgcccActtaatttttccaggatttg
                               -35                   -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Champagne N., et al., 1998
[2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cagcataaatAAAAAACGGCAGGATATTATCTCCTGCCGTTTATCtttttacacg
Reference(s): [4] Breton R., et al., 1986
TF binding sites (TFBSs)
[Fis,-] 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 Fis repressor gltXp3 2520803 2520817 -80.0 agaccgtgttGCGCAATTTGTCAACgaaaacaata nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
remote Fis repressor gltXp3 2520824 2520838 -101.0 taagcaagatGATCGCAAAACAGACcgtgttgcgc nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
remote Fis repressor gltXp3 2520844 2520858 -121.0 ttgttcgttcGTCGTAAATTTAAGCaagatgatcg nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]


Transcription unit       
Name: gltX
Gene(s): gltX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Champagne N., et al., 1998
Promoter
Name: gltXp2
+1: 2520776
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 104
Sequence: tcgcaaaacagaccgtgttgcgcaatttgtcaacgaaaacaataatgcgtaaggtagaaaCccgaactacattgaggaatc
                                -35                    -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Champagne N., et al., 1998
[2] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: cagcataaatAAAAAACGGCAGGATATTATCTCCTGCCGTTTATCtttttacacg
Reference(s): [4] Breton R., et al., 1986


Transcription unit       
Name: gltX
Gene(s): gltX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Champagne N., et al., 1998
Promoter
Name: gltXp1
+1: 2520784
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 112
Sequence: caagatgatcgcaaaacagaccgtgttgcgcaatttgtcaacgaaaacaataatgcgtaaGgtagaaacccgaactacatt
                               -35                    -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Champagne N., et al., 1998
[2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cagcataaatAAAAAACGGCAGGATATTATCTCCTGCCGTTTATCtttttacacg
Reference(s): [4] Breton R., et al., 1986


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -8.9 2520690 2520717 taatttttccAGGATTTGCCGGTTGTCGGCATCTTTCtaaacgtaag
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [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-CELLULAR-EXTRACTS] Binding of cellular extracts


Reference(s)    

 [1] Champagne N., Lapointe J., 1998, Influence of FIS on the transcription from closely spaced and non-overlapping divergent promoters for an aminoacyl-tRNA synthetase gene (gltX) and a tRNA operon (valU) in Escherichia coli., Mol Microbiol 27(6):1141-56

 [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] 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.

 [4] Breton R., Sanfacon H., Papayannopoulos I., Biemann K., Lapointe J., 1986, Glutamyl-tRNA synthetase of Escherichia coli. Isolation and primary structure of the gltX gene and homology with other aminoacyl-tRNA synthetases., J Biol Chem 261(23):10610-7

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