RegulonDB RegulonDB 10.8: Gene Form
   

lrhA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

alaA lrhA nuoA Fis Fis Fis NarL ArcA IHF IHF IHF FNR anti-anti-terminator anti-terminator terminator terminator alaAp7 alaAp7 alaAp9 alaAp9 TSS_2569 TSS_2569 lrhAp lrhAp TSS_2568 TSS_2568 TSS_2567 (cluster) TSS_2567 (cluster) TSS_2566 (cluster) TSS_2566 (cluster) nuoAp1 nuoAp1 nuoAp2 nuoAp2 TSS_2565 TSS_2565 TSS_2564 TSS_2564

Gene      
Name: lrhA    Texpresso search in the literature
Synonym(s): ECK2283, EG12123, b2289, genR
Genome position(nucleotides): 2405703 <-- 2406641 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
49.73
External database links:  
ASAP:
ABE-0007555
CGSC:
32685
ECHOBASE:
EB2044
OU-MICROARRAY:
b2289
PortEco:
lrhA
STRING:
511145.b2289
COLOMBOS: lrhA


Shine dalgarno      
Sequence: tgagccgccaGTAAGTgataataTAT


Product      
Name: DNA-binding transcriptional dual regulator LrhA
Synonym(s): GenR, LrhA
Sequence: Get amino acid sequence Fasta Format
Regulator Family: LysR
Cellular location: cytosol
Molecular weight: 34.594
Isoelectric point: 5.029
Motif(s):
 
Type Positions Sequence
291 -> 312 WQYSPMSAPEGDDSLLIERDIE
13 -> 71 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHG
11 -> 68 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLT
28 -> 47 FAAAAAAVCRTQSAVSQQMQ
97 -> 281 LQGVLTIGASDESADTILPFLLNRVSSVYPKLALDVRVKRNAYMAEMLESQEVDLMVTTHRPSAFKALNLRTSPTHWYCAAEYILQKGEPIPLVLLDDPSPFRDMVLATLNKADIPWRLAYVASTLPAVRAAVKAGLGVTARPVEMMSPDLRVLSGVDGLPPLPDTEYLLCYDPSSNNELAQVIY

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0043565 - sequence-specific DNA binding
GO:0000986 - bacterial-type cis-regulatory region sequence-specific DNA binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
[HIFS] Human inference of function from sequence
Reference(s): [1] Bongaerts J., et al., 1995
[2] Gibson KE., et al., 1999
[3] Lehnen D., et al., 2002
External database links:  
ECOCYC:
EG12123-MONOMER
ECOLIWIKI:
b2289
INTERPRO:
IPR036388
INTERPRO:
IPR036390
INTERPRO:
IPR005119
INTERPRO:
IPR000847
MODBASE:
P36771
PFAM:
PF00126
PFAM:
PF03466
PRIDE:
P36771
PRINTS:
PR00039
PROSITE:
PS50931
REFSEQ:
NP_416792
SMR:
P36771
UNIPROT:
P36771


Operon      
Name: lrhA         
Operon arrangement:
Transcription unit        Promoter
lrhA


Transcriptional Regulation      
Display Regulation             
Activated by: LrhA


RNA cis-regulatory element    
Attenuation: Transcriptional


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_2564 2404729 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2565 2405136 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2566 (cluster) 2405828 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [4]
  promoter TSS_2567 (cluster) 2406635 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [4]
  promoter TSS_2568 2406641 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2569 2407012 reverse nd [RS-EPT-CBR] [4]
  promoter alaAp7 2407414 forward Similarity to the consensus
Read more >
[ICWHO] [5]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Bongaerts J., Zoske S., Weidner U., Unden G., 1995, Transcriptional regulation of the proton translocating NADH dehydrogenase genes (nuoA-N) of Escherichia coli by electron acceptors, electron donors and gene regulators., Mol Microbiol 16(3):521-34

 [2] Gibson KE., Silhavy TJ., 1999, The LysR homolog LrhA promotes RpoS degradation by modulating activity of the response regulator sprE., J Bacteriol 181(2):563-71

 [3] Lehnen D., Blumer C., Polen T., Wackwitz B., Wendisch VF., Unden G., 2002, LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli., Mol Microbiol 45(2):521-32

 [4] 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.

 [5] 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


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