RegulonDB RegulonDB 10.8: Gene Form
   

gadB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pqqL gadC gadB GadX GadX GadW GadX GadW GadX GadX GadW Fis GadX GadW RcsB CRP GadE Fis GadX Fis GadX Fis terminator TSS_1835 TSS_1835 gadBp gadBp TSS_1834 TSS_1834 gadCp1 gadCp1 gadCp6 gadCp6 gadCp5 gadCp5

Gene      
Name: gadB    Texpresso search in the literature
Synonym(s): ECK1487, EG11490, b1493
Genome position(nucleotides): 1570645 <-- 1572045 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.32
External database links:  
ASAP:
 ABE-0004976
CGSC:
 32194
ECHOBASE:
 EB1453
OU-MICROARRAY:
 b1493
PortEco:
 gadB
STRING:
 511145.b1493
COLOMBOS: gadB


Product      
Name: glutamate decarboxylase B
Synonym(s): GadB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,membrane
Molecular weight: 52.668
Isoelectric point: 5.13
Motif(s):
 
Type Positions Sequence
276 -> 276 K
33 -> 383 PLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLK
126 -> 127 SS

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.5 - adaptations --> 5.5.4 - pH
Gene Ontology Terms (GO)  
cellular_component GO:0005623 - cell
GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016020 - membrane
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0016829 - lyase activity
GO:0016831 - carboxy-lyase activity
GO:0004351 - glutamate decarboxylase activity
GO:0030170 - pyridoxal phosphate binding
biological_process GO:0006538 - glutamate catabolic process
GO:0019752 - carboxylic acid metabolic process
GO:0006536 - glutamate metabolic process
GO:0051454 - intracellular pH elevation
Note(s): Note(s): ...[more].
Reference(s): [1] De Biase D., et al., 1999
[2] Lin J., et al., 1995
[3] Smith DK., et al., 1992
External database links:  
DIP:
 DIP-36202N
ECOCYC:
 GLUTDECARBOXB-MONOMER
ECOLIWIKI:
 b1493
INTERPRO:
 IPR015421
INTERPRO:
 IPR002129
INTERPRO:
 IPR010107
INTERPRO:
 IPR015424
INTERPRO:
 IPR021115
MINT:
 P69910
MODBASE:
 P69910
PANTHER:
 PTHR43321
PDB:
 3FZ8
PDB:
 3FZ6
PDB:
 2DGM
PDB:
 2DGL
PDB:
 2DGK
PDB:
 1PMO
PDB:
 1PMM
PDB:
 3FZ7
PFAM:
 PF00282
PRIDE:
 P69910
PRODB:
 PRO_000022742
PROSITE:
 PS00392
REFSEQ:
 NP_416010
SMR:
 P69910
UNIPROT:
 P69910


Operon      
Name: gadBC         
Operon arrangement:
Transcription unit        Promoter
gadBC
 


Transcriptional Regulation      
Display Regulation             
Activated by: GadX, GadW, AdiY, RcsB, GadE
Repressed by: CRP, FliZ, GadW, Fis


Regulation by small RNA    
  Display Regulation
small RNA oxyS


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 gadCp5 1570527 reverse Similarity to the consensus
Read more > 		[ICWHO] [4]
  promoter gadCp6 1570577 reverse Similarity to the consensus
Read more > 		[ICWHO] [4]
  promoter gadCp1 1570584 reverse Similarity to the consensus
Read more > 		[ICWHO] [4]
  promoter TSS_1834 1571620 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_1835 1572073 reverse nd [RS-EPT-CBR] [5]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] De Biase D., Tramonti A., Bossa F., Visca P., 1999, The response to stationary-phase stress conditions in Escherichia coli: role and regulation of the glutamic acid decarboxylase system., Mol Microbiol 32(6):1198-211

 [2] Lin J., Lee IS., Frey J., Slonczewski JL., Foster JW., 1995, Comparative analysis of extreme acid survival in Salmonella typhimurium, Shigella flexneri, and Escherichia coli., J Bacteriol 177(14):4097-104

 [3] Smith DK., Kassam T., Singh B., Elliott JF., 1992, Escherichia coli has two homologous glutamate decarboxylase genes that map to distinct loci., J Bacteriol 174(18):5820-6

 [4] 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

 [5] 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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