RegulonDB RegulonDB 10.8: Operon Form
   

pdxH-tyrS-pdxY operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: pdxH-tyrS-pdxY
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: tyrS-pdxY
Gene(s): pdxY, tyrS   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Yang Y., et al., 1998
Promoter
Name: tyrSp1
+1: 1717269
Distance from start of the gene: 47
Sequence: taatcgctggtactcctgattctggcactttattctatgtctctttcgcatctggcgaaaAgtcgtgtaccggcaaaggtg
Evidence: [TIM]
Reference(s): [2] Lam HM., et al., 1992
[1] Yang Y., et al., 1998


Transcription unit       
Name: tyrS-pdxY
Gene(s): pdxY, tyrS   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC] Inferred by curator
Promoter
Name: tyrSp2
+1: 1717283
Distance from start of the gene: 61
Sequence: caaaaatcttgctttaatcgctggtactcctgattctggcactttattctatgtctctttCgcatctggcgaaaagtcgtg
Evidence: [HTIM]
Reference(s): [3] Mendoza-Vargas A., et al., 2009


Transcription unit       
Name: pdxH-tyrS-pdxY
Gene(s): pdxY, tyrS, pdxH   Genome Browser M3D Gene expression COLOMBOS
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[CV(PM)] cross validation(PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Yang Y., et al., 1998
Promoter
Name: pdxHp
+1: 1718034
Distance from start of the gene: 27
Sequence: actgtcagttacaaaatccacagcgttgagatttttccaggggcggcgcacaatagcgtcAcccactgacaatccgtaaag
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[IEP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Lam HM., et al., 1992
[4] Salgado H, et al., 2012
[1] Yang Y., et al., 1998
[5] Zaslaver A., et al., 2006


Transcription unit       
Name: pdxY
Gene(s): pdxY   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [5] Zaslaver A., et al., 2006
Promoter
Name: pdxYp
+1: Unknown
Evidence: [IEP]
Reference(s): [5] Zaslaver A., et al., 2006


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -23.5 1715899 1715933 ttaagtggaaAGGGGGAGTGAGAAATCACTCCCCCTGGTTTTTAtacagggaac
  terminator -7.4 1717247 1717264 cgaaaagtcgTGTACCGGCAAAGGTGCagtcgttata
  terminator -12.9 1718031 1718054 atttttccagGGGCGGCGCACAATAGCGTCACCcactgacaat
  anti-terminator -8.16 1715923 1715972 gtaaaaagaaTTACTGTCTGATTTGCTGGAAATAATGCATTAAGTGGAAAGGGGGAGTGagaaatcact
  anti-anti-terminator -6.6 1715953 1715987 ccttactgcgTCGCGGTAAAAAGAATTACTGTCTGATTTGCTGGaaataatgca
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"




Reference(s)    

 [1] Yang Y., Tsui HC., Man TK., Winkler ME., 1998, Identification and function of the pdxY gene, which encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate biosynthesis in Escherichia coli K-12., J Bacteriol 180(7):1814-21

 [2] Lam HM., Winkler ME., 1992, Characterization of the complex pdxH-tyrS operon of Escherichia coli K-12 and pleiotropic phenotypes caused by pdxH insertion mutations., J Bacteriol 174(19):6033-45

 [3] 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

 [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] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8


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