RegulonDB RegulonDB 11.1: Gene Form
   

garD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

garD garP prlF Fur sohAp sohAp TSS_3408 TSS_3408 garPp garPp

Gene      
Name: garD    Texpresso search in the literature
Synonym(s): ECK3116, EG12522, b3128, yhaG
Genome position(nucleotides): 3275282 --> 3276853
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.86
Reference(s): [1] Monterrubio R., et al., 2000
External database links:  
ASAP:
 ABE-0010284
ECHOBASE:
 EB2413
ECOLIHUB:
 garD
OU-MICROARRAY:
 b3128
STRING:
 511145.b3128
COLOMBOS: garD


Product      
Synonym(s): GarD, YhaG
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 56.402
Isoelectric point: 5.334
Motif(s):
 
Type Positions Sequence Comment
22 -> 91 DNVAIIVNDNGLKAGTRFPDGLELIEHIPQGHKVALLDIPANGEIIRYGEVIGYAVRAIPRGSWIDESMV
119 -> 520 TFEGYRNADGSVGTKNLLGITTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCGVAINAPAAVVPIRTIHNISLNPNFGGEVMVIGLGCEKLQPERLLTGTDDVQAIPVESASIVSLQDEKHVGFQSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASDLLVRCGATVMFSEVTEVRDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGKTDRSANPSPGNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDFVCGTQQVASGITVQVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEETIEEVGWKLFHFILDVASGKKKTFSDQWGLHNQLAVFNPA

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.1 - carbon compounds
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0016829 - lyase activity
GO:0046872 - metal ion binding
GO:0008867 - galactarate dehydratase activity
GO:0008198 - ferrous iron binding
GO:0042803 - protein homodimerization activity
biological_process GO:0046392 - galactarate catabolic process
GO:0019698 - D-galacturonate catabolic process
External database links:  
ALPHAFOLD:
 P39829
ECOCYC:
 GALACTARDEHYDRA-MONOMER
ECOLIWIKI:
 b3128
INTERPRO:
 IPR044144
INTERPRO:
 IPR032893
INTERPRO:
 IPR017654
INTERPRO:
 IPR013974
INTERPRO:
 IPR007392
PDB:
 3LAZ
PDB:
 6U7L
PFAM:
 PF08666
PFAM:
 PF04295
PRIDE:
 P39829
PRODB:
 PRO_000022750
REFSEQ:
 NP_417597
SMART:
 SM00858
SMR:
 P39829
UNIPROT:
 P39829


Operon      
Name: garD         
Operon arrangement:
Transcription unit        Promoter
garD


Transcriptional Regulation      
Display Regulation             
Activated by: CdaR


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_3408 3276940 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] Monterrubio R., Baldoma L., Obradors N., Aguilar J., Badia J., 2000, A common regulator for the operons encoding the enzymes involved in D-galactarate, D-glucarate, and D-glycerate utilization in Escherichia coli., J Bacteriol 182(9):2672-4

 [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.

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