U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    ttdR DNA-binding transcriptional activator Dan [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947562, updated on 23-Nov-2023

    Summary

    Go to the top of the page Help
    Gene symbol
    ttdR
    Gene description
    DNA-binding transcriptional activator Dan
    Primary source
    ASAP:ABE-0010045
    Locus tag
    b3060
    See related
    ECOCYC:EG12694
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
    Lineage
    Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
    Also known as
    dan; ECK3050; ygiP
    Summary
    LysR family. [More information is available at EcoGene: EG12694].
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Sequence:
    NC_000913.3 (3205324..3206256, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene dihydroneopterin aldolase Neighboring gene putative glycerol-3-phosphate acyltransferase Neighboring gene L(+)-tartrate dehydratase subunit alpha Neighboring gene L(+)-tartrate dehydratase subunit beta Neighboring gene L-tartrate:succinate antiporter

    Genomic regions, transcripts, and products

    Go to the top of the page Help
    Genomic Sequence:
    NC_000913.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. The nucleoid-associated protein Dan organizes chromosomal DNA through rigid nucleoprotein filament formation in E. coli during anoxia. Lim CJ, et al. Nucleic Acids Res, 2013 Jan. PMID 23180762, Free PMC Article
    2. A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions. Teramoto J, et al. Nucleic Acids Res, 2010 Jun. PMID 20156994, Free PMC Article
    3. Identification of the L-tartrate dehydratase genes (ttdA and ttdB) of Escherichia coli and evolutionary relationship with the class I fumarase genes. Reaney SK, et al. J Gen Microbiol, 1993 Jul. PMID 8371115
    4. Possible new genes as revealed by molecular analysis of a 5-kb Escherichia coli chromosomal region 5' to the rpsU-dnaG-rpoD macromolecular-synthesis operon. Nesin M, et al. Gene, 1987. PMID 3297921
    5. Regulation of tartrate metabolism by TtdR and relation to the DcuS-DcuR-regulated C4-dicarboxylate metabolism of Escherichia coli. Kim OB, et al. Microbiology (Reading), 2009 Nov. PMID 19661178

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Dan binds cooperatively along DNA, resulting in formation of a rigid periodic nucleoprotein filament that strongly restricts accessibility to DNA.
      Title: The nucleoid-associated protein Dan organizes chromosomal DNA through rigid nucleoprotein filament formation in E. coli during anoxia.
    2. High abundance and large number of binding sites together indicate that YgiP is a nucleoid-associated protein with both architectural and regulatory roles as the nucleoid proteins Fis and IHF.
      Title: A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions.
    3. Induction of L-tartrate fermentation is regulated by TtdR and L- or meso-tartrate. Expression was repressed by O(2), nitrate and glucose, and positively regulated by TtdR and DcuS.
      Title: Regulation of tartrate metabolism by TtdR and relation to the DcuS-DcuR-regulated C4-dicarboxylate metabolism of Escherichia coli.
    Submit: New GeneRIF Correction

    General gene information

    Go to the top of the page Help

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription activator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    DNA-binding transcriptional activator Dan

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_000913.3 Reference assembly

      Range
      3205324..3206256 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417532.1 DNA-binding transcriptional activator Dan [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417532.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      W1WSB4
      Conserved Domains (1) summary
      PRK09801
      Location:1 → 310
      PRK09801; LysR family transcriptional regulator
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.