RegulonDB RegulonDB 11.1: Operon Form
   

ibaG-murA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: ibaG-murA
Gene(s): murA, ibaG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Guinote IB., et al., 2012
Promoter
Name: ibaGp1
+1: 3336833
Distance from start of the gene: 30
Sequence: atttatcagcgaggctttttgcttatttatgccagcgcaactttgctctaagatgtttcgCtggtttattaactgatgatt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Guinote IB., et al., 2012


Transcription unit          
Name: ibaG
Gene(s): ibaG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ibaGp2
+1: 3336886
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 83
Sequence: tatggcgttaaccgcctgtccggcaaacctgcctgcaagtcgagccttgtctgatttatcAgcgaggctttttgcttattt
                               -35                    -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [2] Gama-Castro S., et al., 2008
[3] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[MlrA,+] 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 MlrA activator ibaGp2 3336987 3337021 -117.5 ggggtaaacgACAAAGTGTATACCCTGGCGAAATTGTATAATTTGcctgctgatg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]


Transcription unit       
Name: murA
Gene(s): murA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -8.4 3336513 3336541 tgagctatggGCGATTCGCCGGTAGCGGATATGAATTGttaactgaga
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    

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

 [COMP-AINF] Inferred computationally without human oversight

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

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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


Reference(s)    

 [1] Guinote IB., Moreira RN., Freire P., Arraiano CM., 2012, Characterization of the BolA Homolog IbaG: A New Gene Involved in Acid Resistance., J Microbiol Biotechnol 22(4):484-93

 [2] 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

 [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] Ogasawara H., Yamamoto K., Ishihama A., 2010, Regulatory role of MlrA in transcription activation of csgD, the master regulator of biofilm formation in Escherichia coli., FEMS Microbiol Lett 312(2):160-8

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