RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: nlpA
Gene(s): nlpA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: nlpAp
+1: 3840017
Distance from start of the gene: 24
Sequence: tattcttatcgatagcgtttcgttttttaaaccgcagcgaccttaccgctatagtcaggtAatcattaataaaaggataaa
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Bodero MD., et al., 2007
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
[CsgD,+] 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 CsgD activator nlpAp 3840087 3840101 -76.5 gtgccagactTTATATTCCACTTTTattccttttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal CsgD activator nlpAp 3840102 3840116 -91.5 cgtggtcagtAAGAAGTGCCAGACTttatattcca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA GcvB nlpA repressor 3839961 3839970 CCCUGUCCGU MRNA-DEGRADATION [EXP-IEP], [EXP-NUC-ACID-BINDING] [3]


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-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IEP] Inferred from expression pattern

 [EXP-NUC-ACID-BINDING] Nucleic acid binding evidence


Reference(s)    

 [1] Bodero MD., Pilonieta MC., Munson GP., 2007, Repression of the inner membrane lipoprotein NlpA by Rns in enterotoxigenic Escherichia coli., J Bacteriol 189(5):1627-32

 [2] 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.

 [3] Lalaouna D., Eyraud A., Devinck A., Prevost K., Masse E., 2019, GcvB small RNA uses two distinct seed regions to regulate an extensive targetome., Mol Microbiol 111(2):473-486

 [4] Ogasawara H., Yamamoto K., Ishihama A., 2011, Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis., J Bacteriol 193(10):2587-97

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