RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: putP
Gene(s): putP   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under NlpE outer membrane lipoprotein overexpression, the transcription of the putP gene is decreased Raivio TL,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Nakao T., et al., 1987
[2] Nakao T., et al., 1987
Promoter
Name: putPp1
+1: 1079168
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 137
Sequence: gagtgcaacctgatgaaaaatagtgtcgctgagcactaaaatttaatgtaaatggtgtgtTaaatcgattgtgaataacca
                       -35                  -10             +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[2] Nakao T., et al., 1987
Terminator(s)
Type: rho-independent
Sequence: gctccgccgtCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTttggcttcag
Reference(s): [1] Nakao T., et al., 1987
TF binding sites (TFBSs)
[PutA,-] 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 PutA repressor putPp1 1079084 1079089 -81.5 atttttgaaaGGTGCAaccgcaaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]
proximal PutA repressor putPp1 1079111 1079116 -54.5 tgtgagagagTGCAACctgatgaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]


Transcription unit       
Name: putP
Gene(s): putP   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Nakao T., et al., 1987
[2] Nakao T., et al., 1987
Promoter
Name: putPp2
+1: 1079179
Distance from start of the gene: 126
Sequence: gatgaaaaatagtgtcgctgagcactaaaatttaatgtaaatggtgtgttaaatcgattgTgaataaccagcgcttccggc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Nakao T., et al., 1987
Terminator(s)
Type: rho-independent
Sequence: gctccgccgtCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTttggcttcag
Reference(s): [1] Nakao T., et al., 1987


Transcription unit       
Name: putP
Gene(s): putP   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Nakao T., et al., 1987
[2] Nakao T., et al., 1987
Promoter
Name: putPp3
+1: 1079185
Distance from start of the gene: 120
Sequence: aaatagtgtcgctgagcactaaaatttaatgtaaatggtgtgttaaatcgattgtgaataAccagcgcttccggcaggata
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Nakao T., et al., 1987
Terminator(s)
Type: rho-independent
Sequence: gctccgccgtCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTttggcttcag
Reference(s): [1] Nakao T., et al., 1987


Transcription unit          
Name: putP
Gene(s): putP   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Nakao T., et al., 1987
[2] Nakao T., et al., 1987
Promoter
Name: putPp4
+1: 1079210
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 95
Sequence: ttaatgtaaatggtgtgttaaatcgattgtgaataaccagcgcttccggcaggatacggtCgccctggtaaaacataaact
                           -35                    -10       +1                   
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Nakao T., et al., 1987
[2] Nakao T., et al., 1987
Terminator(s)
Type: rho-independent
Sequence: gctccgccgtCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTttggcttcag
Reference(s): [1] Nakao T., et al., 1987
TF binding sites (TFBSs)
[CRP,-] 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
remote CRP-cyclic-AMP repressor putPp4 1079093 1079114 -106.0 aggtgcaaccGCAAAAAATGTGAGAGAGTGCAacctgatgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1]
proximal CRP-cyclic-AMP repressor putPp4 1079123 1079144 -76.5 caacctgatgAAAAATAGTGTCGCTGAGCACTaaaatttaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1]
proximal CRP-cyclic-AMP repressor putPp4 1079155 1079176 -44.5 aaaatttaatGTAAATGGTGTGTTAAATCGATtgtgaataac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1]


Transcription unit       
Name: putP
Gene(s): putP   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Nakao T., et al., 1987
[2] Nakao T., et al., 1987
Promoter
Name: putPp5
+1: 1079291
Distance from start of the gene: 14
Sequence: ctgttaccccgttccggtggcagatataacggcaagtttcgacattgccgataataatttTttggagactttagatggcta
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Nakao T., et al., 1987
[5] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gctccgccgtCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTttggcttcag
Reference(s): [1] Nakao T., et al., 1987


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -7.5 1079260 1079280 cagatataacGGCAAGTTTCGACATTGCCGataataattt
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-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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

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

 [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.

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


Reference(s)    

 [1] Nakao T., Yamato I., Anraku Y., 1987, Nucleotide sequence of putP, the proline carrier gene of Escherichia coli K12., Mol Gen Genet 208(1-2):70-5

 [2] Nakao T., Yamato I., Anraku Y., 1987, Nucleotide sequence of putC, the regulatory region for the put regulon of Escherichia coli K12., Mol Gen Genet 210(2):364-8

 [3] 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

 [4] Zhou Y., Larson JD., Bottoms CA., Arturo EC., Henzl MT., Jenkins JL., Nix JC., Becker DF., Tanner JJ., 2008, Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA., J Mol Biol 381(1):174-88

 [5] 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.

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