RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: yhiM
Gene(s): yhiM   Genome Browser M3D Gene expression COLOMBOS
Note(s): Microarray analyses have shown that the yhiM gene is activated by the transcriptional regulator GadX, but it is not known if the effect of the regulator on the operon is direct or indirect. The positive regulation of the yhiM gene by GadX is positively influenced by the transcriptional regulator GadW Tucker DL,2003.
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: yhiMp
+1: 3634743
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 98
Sequence: tggccttttgaacgctgaaaagtagcgctctgcaaagtaaaccccgctatagttatgctaTgcatttgtctttaatgatat
                       -35                 -10              +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
[EXP-IEP]
[EXP-IPI]
Reference(s): [1] Gama-Castro S., et al., 2008
[2] Huerta AM., et al., 2003
[3] Seo SW., et al., 2015
TF binding sites (TFBSs)
[GadE,+] 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 GadE activator yhiMp 3634655 3634674 -78.5 gcataagaatTAATCTTAGGATAAATTTTTatttatcatg nd [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] S [3]
[GadE-RcsB,+] 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
nd GadE-RcsB activator yhiMp nd nd nd nd nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
[H-NS,-] 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
nd H-NS repressor yhiMp nd nd nd nd nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [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] Inferred from expression pattern

 [EXP-IPI] Inferred from physical interaction

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion

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


Reference(s)    

 [1] Gama-Castro S., Jimenez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., Penaloza-Spinola MI., Contreras-Moreira B., Segura-Salazar J., Muniz-Rascado L., Martinez-Flores I., Salgado H., Bonavides-Martinez C., Abreu-Goodger C., Rodriguez-Penagos C., Miranda-Rios J., Morett E., Merino E., Huerta AM., Trevino-Quintanilla L., Collado-Vides J., 2008, RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation., Nucleic Acids Res 36(Database issue):D120-4

 [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] 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

 [4] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273

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