RegulonDB RegulonDB 10.9: Gene Form
   

aidB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

aidB yjfC yjfN AidB Ada TSS_5053 TSS_5053 aidBp aidBp

Gene      
Name: aidB    Texpresso search in the literature
Synonym(s): ECK4183, EG11811, b4187
Genome position(nucleotides): 4414275 --> 4415900 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.31
External database links:  
ASAP:
ABE-0013701
CGSC:
18553
ECHOBASE:
EB1759
ECOLIHUB:
aidB
OU-MICROARRAY:
b4187
STRING:
511145.b4187
COLOMBOS: aidB


Product      
Name: putative acyl-CoA dehydrogenase AidB
Synonym(s): AidB, isovaleryl-CoA dehydrogenase and DNA-binding transcriptional repressor
Sequence: Get amino acid sequence Fasta Format
Regulator Family: AidB_like
Cellular location: cytosol
Molecular weight: 60.59
Isoelectric point: 7.892
Motif(s):
 
Type Positions Sequence
181 -> 275 GMGMTEKQGGSDVMSNTTRAERLEDGSYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFFVPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQD
285 -> 439 GEGIRLILKMGGMTRFDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLARAWDRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMPVNSIWEGSGNIMCLDVLRVL
423 -> 433 IWEGSGNIMCL
440 -> 541 NKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLRKPAEELGREITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGGVRLSEQIQNDLLLRATGGVCV
2 -> 439 HWQTHTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANVNPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFMLHAQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGMTEKQGGSDVMSNTTRAERLEDGSYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFFVPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTRFDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLARAWDRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMPVNSIWEGSGNIMCLDVLRVL

 

Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0016491 - oxidoreductase activity
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors
GO:0003995 - acyl-CoA dehydrogenase activity
GO:0008470 - isovaleryl-CoA dehydrogenase activity
GO:0043565 - sequence-specific DNA binding
GO:0042802 - identical protein binding
biological_process GO:0006974 - cellular response to DNA damage stimulus
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
Reference(s): [1] Vasil'eva SV., et al., 2005
External database links:  
DIP:
DIP-9078N
ECOCYC:
EG11811-MONOMER
ECOLIWIKI:
b4187
INTERPRO:
IPR036250
INTERPRO:
IPR034184
INTERPRO:
IPR009100
INTERPRO:
IPR041504
INTERPRO:
IPR006089
INTERPRO:
IPR006091
INTERPRO:
IPR009075
MODBASE:
P33224
PDB:
3DJL
PDB:
3U33
PFAM:
PF18158
PFAM:
PF00441
PFAM:
PF02770
PRIDE:
P33224
PRODB:
PRO_000022072
PROSITE:
PS00073
PROSITE:
PS00072
REFSEQ:
NP_418608
SMR:
P33224
UNIPROT:
P33224


Operon      
Name: aidB         
Operon arrangement:
Transcription unit        Promoter
aidB
aidB


Transcriptional Regulation      
Display Regulation             
Activated by: Ada
Repressed by: AidB, Lrp
Growth Conditions:

[1] 

C: Escherichia coli| minimal medium| casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL| oxygen atom
E: Escherichia coli| minimal medium| casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL

[2] 

C: Escherichia coli| minimal medium| casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL| oxygen atom
E: Escherichia coli| minimal medium| acetate 50 mM; casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL| pH 6.5| oxygen atom

[3] 

C: Escherichia coli| rpoS knockout mutant| minimal medium| acetate 50 mM; casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL| pH 6.5| oxygen atom
E: Escherichia coli| rpoS knockout mutant; plasmid pUBAD::rpoS (arabinose-induced rpoS) mutant| minimal medium| acetate 50 mM; casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL| pH 6.5| oxygen atom

[4] 

C: Escherichia coli| minimal medium| casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL| oxygen atom
E: Escherichia coli| minimal medium| methyl methanesulfonate 0.05%; casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL| oxygen atom

[5] 

C: Escherichia coli| minimal medium| casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL
E: Escherichia coli| rpoS knockout mutant| minimal medium| casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL

[6] 

C: Escherichia coli| minimal medium| acetate 50 mM; casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL| pH 6.5| oxygen atom
E: Escherichia coli| rpoS knockout mutant| minimal medium| acetate 50 mM; casamino acids 0.2%; glucose 0.4%; thiamine 0.2 µg/mL| pH 6.5| oxygen atom



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_5053 4415541 forward nd [RS-EPT-CBR] [2]


Evidence    

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



Reference(s)    

 [1] Vasil'eva SV., Moshkovskaia EIu., 2005, [Quasi-adaptive response to alkylating agents in Escherichia coli: a new phenomenon], Genetika 41(5):607-13

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muńiz-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.


RegulonDB