RegulonDB RegulonDB 11.1: Gene Form
   

glaR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

gabP glaR kbp csiRp5 csiRp5 TSS_2986 TSS_2986 csiRp3 csiRp3

Gene      
Name: glaR    Texpresso search in the literature
Synonym(s): ECK2658, EG12386, b2664, csiR, gabC, ygaE
Genome position(nucleotides): 2795674 --> 2796336
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.54
External database links:  
ASAP:
 ABE-0008765
ECHOBASE:
 EB2287
ECOLIHUB:
 csiR
OU-MICROARRAY:
 b2664
STRING:
 511145.b2664
COLOMBOS: glaR


Product      
Name: DNA-binding transcriptional repressor GlaR
Synonym(s): CsiR, GabC, GlaR, YgaE
Sequence: Get amino acid sequence Fasta Format
Regulator Family: GntR
Cellular location: cytosol
Molecular weight: 24.991
Isoelectric point: 6.634
Motif(s):
 
Type Positions Sequence Comment
1 -> 69 MTITSLDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASM UniProt: HTH gntR-type.
10 -> 66 RWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRV
29 -> 48 MSLLTSRYALGVGPLREALS UniProt: H-T-H motif.
76 -> 207 DIFDARANMEAMLVSLAIARGGDEWEADVLAKAHLLSKLEACDASEKMLDEWDLRHQAFHTAIVAGCGSHYLLQMRERLFDLAARYRFIWLRRTVLSVEMLEDKHDQHQTLTAAVLARDTARASELMRQHLL

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.32 - putrescine catabolism
  1 - metabolism --> 1.8 - metabolism of other compounds --> 1.8.3 - nitrogen metabolism
  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
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:2000143 - negative regulation of DNA-templated transcription, initiation
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
[IDA-PURIFIED-PROTEIN-NH] Assay of protein purified to homogeneity from its native host
Reference(s): [1] Aquino P., et al., 2017
[2] Knorr S., et al., 2018
[3] Metzer E., et al., 1990
[4] Schneider BL., et al., 2002
[5] Zaboura M., et al., 1978
External database links:  
ALPHAFOLD:
 P37338
DIP:
 DIP-12095N
ECOCYC:
 EG12386-MONOMER
ECOLIWIKI:
 b2664
INTERPRO:
 IPR036390
INTERPRO:
 IPR036388
INTERPRO:
 IPR008920
INTERPRO:
 IPR000524
INTERPRO:
 IPR011711
MODBASE:
 P37338
PFAM:
 PF00392
PFAM:
 PF07729
PRIDE:
 P37338
PROSITE:
 PS50949
REFSEQ:
 NP_417150
SMART:
 SM00895
SMART:
 SM00345
SMR:
 P37338
UNIPROT:
 P37338


Operon      
Name: glaR         
Operon arrangement:
Transcription unit        Promoter
CsiR


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 csiRp3 2795471 forward nd [COMP-AINF] [6]
  promoter TSS_2986 2795625 forward nd [RS-EPT-CBR] [7]
  promoter csiRp5 2795643 forward nd [COMP-AINF] [6]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Aquino P., Honda B., Jaini S., Lyubetskaya A., Hosur K., Chiu JG., Ekladious I., Hu D., Jin L., Sayeg MK., Stettner AI., Wang J., Wong BG., Wong WS., Alexander SL., Ba C., Bensussen SI., Bernstein DB., Braff D., Cha S., Cheng DI., Cho JH., Chou K., Chuang J., Gastler DE., Grasso DJ., Greifenberger JS., Guo C., Hawes AK., Israni DV., Jain SR., Kim J., Lei J., Li H., Li D., Li Q., Mancuso CP., Mao N., Masud SF., Meisel CL., Mi J., Nykyforchyn CS., Park M., Peterson HM., Ramirez AK., Reynolds DS., Rim NG., Saffie JC., Su H., Su WR., Su Y., Sun M., Thommes MM., Tu T., Varongchayakul N., Wagner TE., Weinberg BH., Yang R., Yaroslavsky A., Yoon C., Zhao Y., Zollinger AJ., Stringer AM., Foster JW., Wade J., Raman S., Broude N., Wong WW., Galagan JE., 2017, Coordinated regulation of acid resistance in Escherichia coli., BMC Syst Biol 11(1):1

 [2] Knorr S., Sinn M., Galetskiy D., Williams RM., Wang C., Muller N., Mayans O., Schleheck D., Hartig JS., 2018, Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate., Nat Commun 9(1):5071

 [3] Metzer E., Halpern YS., 1990, In vivo cloning and characterization of the gabCTDP gene cluster of Escherichia coli K-12., J Bacteriol 172(6):3250-6

 [4] Schneider BL., Ruback S., Kiupakis AK., Kasbarian H., Pybus C., Reitzer L., 2002, The Escherichia coli gabDTPC operon: specific gamma-aminobutyrate catabolism and nonspecific induction., J Bacteriol 184(24):6976-86

 [5] Zaboura M., Halpern YS., 1978, Regulation of gamma-aminobutyric acid degradation in Escherichia coli by nitrogen metabolism enzymes., J Bacteriol 133(2):447-51

 [6] 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

 [7] 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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