gatD:Gene

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Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

gatD

Mnemonic

Galactitol

Synonyms

ECK2084, b2091, JW2075[1], JW2075

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

46.77 minutes 

MG1655: 2170897..2169857
<gbrowseImage> name=NC_000913:2169857..2170897 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2126235..2125195
<gbrowseImage> name=NC_012967:2125195..2126235 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2062340..2063380
<gbrowseImage> name=NC_012759:2062340..2063380 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2175010..2173970
<gbrowseImage> name=NC_007779:2173970..2175010 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2261905..2260865
<gbrowseImage> name=NC_010473:2260865..2261905 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔgatD (Keio:JW2075)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9695[3]

gatD::Tn5KAN-2 (FB20609)

Insertion at nt 479 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20609

contains pKD46

gatD::Tn5KAN-2 (FB20610)

Insertion at nt 479 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20610

does not contain pKD46

ΔgatD786::kan

PMID:16738554[2]

CGSC:101106


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes

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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW2075

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAATCAGTGGTGAATGATAC

Primer 2:CCGGGAATGAGCAACACTTTGCC

1H4

Kohara Phage

Genobase

PMID:3038334[6]

10H4

Kohara Phage

Genobase

PMID:3038334[6]

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[3]

est. P1 cotransduction: % [7]
Synonyms:zee-3129::Tn10

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[3]

est. P1 cotransduction: 81% [7]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG12417

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12417

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002277

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946598

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2316

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006924

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.0 2.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  3. 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  6. 6.0 6.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  7. 7.0 7.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

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