dsdC: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

dsdC

Mnemonic

D-Serine deaminase

Synonyms

ECK2360, b2364, JW2361[1], JW2361

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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

53.34 minutes 

MG1655: 2475651..2474716
<gbrowseImage> name=NC_000913:2474716..2475651 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2411856..2410921
<gbrowseImage> name=NC_012967:2410921..2411856 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2360521..2361456
<gbrowseImage> name=NC_012759:2360521..2361456 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2483075..2482140
<gbrowseImage> name=NC_007779:2482140..2483075 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2567416..2566481
<gbrowseImage> name=NC_010473:2566481..2567416 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

ΔdsdC (Keio:JW2361)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9885[3]

dsdC::Tn5KAN-2 (FB20776)

Insertion at nt 751 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20776

does not contain pKD46

dsdC::Tn5KAN-2 (FB20777)

Insertion at nt 751 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20777

contains pKD46

ΔdsdC::kan

deletion

Biolog:respiration

unable to respire D-Serine

PMID:16095938[5]

dsdC3

PMID:4864409[6] PMID:4574696[7] PMID:5340178[8]

CGSC:72932

dsdC4

CGSC:72933

dsdC5

CGSC:72934

dsdC9

CGSC:72935

ΔdsdC773::kan

PMID:16738554[2]

CGSC:100658


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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

JW2361

Plasmid clone

Shigen

PMID:16769691[9]

Status:Clone OK

Primer 1:GCCGAACCCCTTCGTGAAATAAG

Primer 2:CCTGAAGTGGTTTTTACCTGTTC

3A11

Kohara Phage

Genobase

PMID:3038334[10]

6B9

Kohara Phage

Genobase

PMID:3038334[10]

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[3]

est. P1 cotransduction: % [11]
Synonyms:zej-223::Tn10

zfd-1::Tn10

Linked marker

CAG18467 = CGSC7408[3]

est. P1 cotransduction: 55% [11]
Synonyms:zfb-1::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:EG13161

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13161

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002429

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948828

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2953

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007797

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. Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  6. McFall, E (1967) Dominance studies with stable merodiploids in the D-serine deaminase system of Escherichia coli K-12. J. Bacteriol. 94 1982-8 PubMed
  7. Cosloy, SD (1973) D-serine transport system in Escherichia coli K-12. J. Bacteriol. 114 679-84 PubMed
  8. McFall, E (1967) Mapping of the d-serine deaminase region in Escherichia coli K-12. Genetics 55 91-9 PubMed
  9. 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
  10. 10.0 10.1 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
  11. 11.0 11.1 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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