RegulonDB RegulonDB 11.1: Gene Form
   

dmlR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dmlA dmlR leuE Lrp Lrp Lrp Lrp anti-terminator anti-anti-terminator anti-terminator terminator TSS_2129 TSS_2129 dmlRp3 dmlRp3 dmlAp4 dmlAp4 leuEp leuEp leuEp4 leuEp4

Gene      
Name: dmlR    Texpresso search in the literature
Synonym(s): ECK1797, G6985, b1799, yeaT
Genome position(nucleotides): 1880886 <-- 1881809
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.38
External database links:  
ASAP:
 ABE-0005987
ECHOBASE:
 EB3279
ECOLIHUB:
 yeaT
OU-MICROARRAY:
 b1799
STRING:
 511145.b1799
COLOMBOS: dmlR


Product      
Name: DNA-binding transcriptional regulator DmlR
Synonym(s): DmlR, YeaT
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 34.631
Isoelectric point: 6.678
Motif(s):
 
Type Positions Sequence Comment
5 -> 62 PLLNDLRVFMLVARRAGFAAVAEELGVSPAFVSKRIALLEQTLNVVLLHRTTRRVTIT UniProt: HTH lysR-type.
7 -> 66 LNDLRVFMLVARRAGFAAVAEELGVSPAFVSKRIALLEQTLNVVLLHRTTRRVTITEEGE
22 -> 41 FAAVAEELGVSPAFVSKRIA UniProt: H-T-H motif.
91 -> 295 QVPQGMLRIISSFGFGRQVVAPALLALAKAYPQLELRFDVEDRLVDLVNEGVDLDIRIGDDIAPNLIARKLATNYRILCASPEFIAQHGAPKHLTDLSALPCLVIKERDHPFGVWQLRNKEGPHAIKVTGPLSSNHGEIVHQWCLDGQGIALRSWWDVSENIASGHLVQVLPEYYQPANVWAVYVSRLATSAKVRITVEFLRQYF

 
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
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
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0006108 - malate metabolic process
GO:0045893 - positive regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [COMP-AINF-FN-FROM-SEQ] Automated inference of function from sequence
[EXP-IEP] Inferred from expression pattern
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Lukas H., et al., 2010
[2] Perez-Rueda E., et al., 2004
[3] Reed JL., et al., 2006
External database links:  
ALPHAFOLD:
 P76250
ECOCYC:
 G6985-MONOMER
ECOLIWIKI:
 b1799
INTERPRO:
 IPR000847
INTERPRO:
 IPR005119
INTERPRO:
 IPR036388
INTERPRO:
 IPR036390
MODBASE:
 P76250
PFAM:
 PF00126
PFAM:
 PF03466
PRIDE:
 P76250
PROSITE:
 PS50931
REFSEQ:
 NP_416313
SMR:
 P76250
UNIPROT:
 P76250


Operon      
Name: dmlR         
Operon arrangement:
Transcription unit        Promoter
dmlR


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 leuEp4 1880767 reverse nd [COMP-AINF] [4]
  promoter dmlAp4 1881712 forward nd [COMP-AINF] [4]
  promoter dmlRp3 1881855 reverse nd [COMP-AINF] [4]
  promoter TSS_2129 1881877 forward nd [RS-EPT-CBR] [5]


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] Lukas H., Reimann J., Kim OB., Grimpo J., Unden G., 2010, Regulation of aerobic and anaerobic D-malate metabolism of Escherichia coli by the LysR-type regulator DmlR (YeaT)., J Bacteriol 192(10):2503-11

 [2] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [3] Reed JL., Patel TR., Chen KH., Joyce AR., Applebee MK., Herring CD., Bui OT., Knight EM., Fong SS., Palsson BO., 2006, Systems approach to refining genome annotation., Proc Natl Acad Sci U S A 103(46):17480-4

 [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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