RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: fabB
Gene(s): fabB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Kauppinen S., et al., 1988
Promoter
Name: fabBp
+1: 2441641
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 36
Sequence: ttctctattaaatggctgatcggacttgttcggcgtacaagtgtacgctattgtgcattcGaaacttactctatgtgcgac
                               -35                    -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[1] Kauppinen S., et al., 1988
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: caatgatgtgAAAAAGGGAACCATCAGGTTCCCTTTTGcgttagtgcc
Reference(s): [1] Kauppinen S., et al., 1988
TF binding sites (TFBSs)
[FabR,-] 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 FabR repressor fabBp 2441653 2441670 -20.5 ggacttgttcGGCGTACAAGTGTACGCTattgtgcatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [6], [7]
[FadR,+] 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 FadR activator fabBp 2441672 2441688 -39.0 tctattaaatGGCTGATCGGACTTGTTcggcgtacaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4], [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [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-CELLULAR-EXTRACTS] Binding of cellular extracts

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


Reference(s)    

 [1] Kauppinen S., Siggaard-Andersen M., von Wettstein-Knowles P., 1988, beta-Ketoacyl-ACP synthase I of Escherichia coli: nucleotide sequence of the fabB gene and identification of the cerulenin binding residue., Carlsberg Res Commun 53(6):357-70

 [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] 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.

 [4] Campbell JW., Cronan JE., 2001, Escherichia coli FadR positively regulates transcription of the fabB fatty acid biosynthetic gene., J Bacteriol 183(20):5982-90

 [5] Feng Y., Cronan JE., 2011, Complex binding of the FabR repressor of bacterial unsaturated fatty acid biosynthesis to its cognate promoters., Mol Microbiol 80(1):195-218

 [6] McCue L., Thompson W., Carmack C., Ryan MP., Liu JS., Derbyshire V., Lawrence CE., 2001, Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes., Nucleic Acids Res 29(3):774-82

 [7] Zhang YM., Marrakchi H., Rock CO., 2002, The FabR (YijC) transcription factor regulates unsaturated fatty acid biosynthesis in Escherichia coli., J Biol Chem 277(18):15558-65

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