dcd:Gene: Difference between revisions

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est. P1 cotransduction: 23% <ref name='LIB:Nichols_linked_Tn'/> <br />  
est. P1 cotransduction: 23% <ref name='LIB:Nichols_linked_Tn'/> <br />  
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10  
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10  
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[[:Category:Kohara_Phage:2E1|2E1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=355 Genobase]
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PMID:3038334


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Revision as of 20:54, 2 September 2011

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

dcd

Mnemonic

dCTP deaminase

Synonyms

ECK2059, b2065, JW2050, paxA, dus[1]

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Notes

Location(s) and DNA Sequence

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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

46.12 minutes 

MG1655: 2140239..2139658
<gbrowseImage> name=NC_000913:2139658..2140239 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2075421..2074840
<gbrowseImage> name=NC_012967:2074840..2075421 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2032141..2032722
<gbrowseImage> name=NC_012759:2032141..2032722 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2144352..2143771
<gbrowseImage> name=AC_000091:2143771..2144352 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2231247..2230666
<gbrowseImage> name=NC_010473:2230666..2231247 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

Coding Start (SO:0000323)

MG1655

2139658

Edman degradation

PMID:1324907[2]


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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

Δdcd (Keio:JW2050)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9684[4]

dcd-1

CGSC:9217

Δdcd-763::kan

PMID:16738554[3]

CGSC:100534


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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

JW2050

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCCGTCTGTGTGACCGAGATAT

Primer 2:CCGTCTTTATCGATTCGGCTGGC

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[4]

est. P1 cotransduction: 6% [6]
Synonyms:zee-3129::Tn10

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[4]

est. P1 cotransduction: 23% [6]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

2E1

Kohara Phage

Genobase

PMID:3038334[7]

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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 (EcoliWiki Page)

EcoCyc:EG11418

EchoBASE (EcoliWiki Page)

EchoBASE:EB1389

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2065

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2592

EcoGene (EcoliWiki Page)

EcoGene:EG11418

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:DCD

CGSC (EcoliWiki Page)

CGSC:875

ASAP (EcoliWikiPage)

ASAP:ABE-0006835


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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. ↑ Wang, L & Weiss, B (1992) dcd (dCTP deaminase) gene of Escherichia coli: mapping, cloning, sequencing, and identification as a locus of suppressors of lethal dut (dUTPase) mutations. J. Bacteriol. 174 5647-53 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  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 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).
  7. ↑ 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

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