RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: metK
Gene(s): metK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: metKp
+1: 3086577
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 129
Sequence: gattcaaaaaaaagtggaaatagggtgaagaattgacctaaaatagccatccagatgttaAtccatccataccgattaaca
                                 -35                  -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Seo SW., et al., 2015
[3] Wei Y., et al., 2002
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
proximal CRP-cyclic-AMP repressor metKp 3086506 3086527 -60.5 gtttttaacaGAATGAGACACGATTCAAAAAAaagtggaaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4]
[MetJ,-] 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 MetJ-S-adenosyl-L-methionine repressor metKp 3086555 3086570 -14.5 agaattgaccTAAAATAGCCATCCAGatgttaatcc nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [5]
proximal MetJ-S-adenosyl-L-methionine repressor metKp 3086567 3086582 -2.5 aaatagccatCCAGATGTTAATCCATccataccgat nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [5]


Transcription unit          
Name: metK
Gene(s): metK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: metKp2
+1: 3086577
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 129
Sequence: gattcaaaaaaaagtggaaatagggtgaagaattgacctaaaatagccatccagatgttaAtccatccataccgattaaca
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[EXP-IPI]
Reference(s): [2] Seo SW., et al., 2015
[3] Wei Y., et al., 2002
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
proximal CRP-cyclic-AMP repressor metKp2 3086506 3086527 -60.5 gtttttaacaGAATGAGACACGATTCAAAAAAaagtggaaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4]
[MetJ,-] 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 MetJ-S-adenosyl-L-methionine repressor metKp2 3086555 3086570 -14.5 agaattgaccTAAAATAGCCATCCAGatgttaatcc nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [5]
proximal MetJ-S-adenosyl-L-methionine repressor metKp2 3086567 3086582 -2.5 aaatagccatCCAGATGTTAATCCATccataccgat nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [5]


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

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

 [EXP-IEP] Inferred from expression pattern

 [EXP-IPI] Inferred from physical interaction


Reference(s)    

 [1] 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

 [2] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970

 [3] Wei Y., Newman EB., 2002, Studies on the role of the metK gene product of Escherichia coli K-12., Mol Microbiol 43(6):1651-6

 [4] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [5] Liu R., Blackwell TW., States DJ., 2001, Conformational model for binding site recognition by the E.coli MetJ transcription factor., Bioinformatics 17(7):622-33

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