RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: ykgMO
Gene(s): ykgO, ykgM   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Hemm MR., et al., 2010
Promoter
Name: ykgMp
+1: 312805
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: ccacaaagagtcacagggattgagtgttgaaatgatccggatgagcatgtatctttatggTtatgttataacataacaggt
                                -35                    -10  +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
Reference(s): [1] Hemm MR., et al., 2010
[2] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[Zur,-] 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 Zur-Zn2+ repressor ykgMp 312784 312807 11.0 gtatctttatGGTTATGTTATAACATAACAGGTAaaaatgatga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [3], [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

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

 [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] Hemm MR., Paul BJ., Miranda-Rios J., Zhang A., Soltanzad N., Storz G., 2010, Small stress response proteins in Escherichia coli: proteins missed by classical proteomic studies., J Bacteriol 192(1):46-58

 [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] Aseev LV., Koledinskaya LS., Boni IV., 2020, Autogenous regulation in vivo of the rpmE gene encoding ribosomal protein L31 (bL31), a key component of the protein-protein intersubunit bridge B1b., RNA 26(7):814-826

 [4] Panina EM., Mironov AA., Gelfand MS., 2003, Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins., Proc Natl Acad Sci U S A 100(17):9912-7

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