serC:Gene: Difference between revisions

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est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/>  
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[[:Category:Kohara_Phage:13E3|13E3]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=216 Genobase]
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PMID:3038334


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Revision as of 20:26, 2 September 2011

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

serC

Mnemonic

Serine

Synonyms

ECK0898, b0907, JW0890, pdxC, pdxF[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

20.62 minutes 

MG1655: 956876..957964
<gbrowseImage> name=NC_000913:956876..957964 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 974745..975833
<gbrowseImage> name=NC_012967:974745..975833 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 859844..860932
<gbrowseImage> name=NC_012759:859844..860932 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 958075..959163
<gbrowseImage> name=AC_000091:958075..959163 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1010804..1011892
<gbrowseImage> name=NC_010473:1010804..1011892 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

956879

Edman degradation

PMID:9298646[2]
PMID:9740056[3]


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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

ΔserC (Keio:JW0890)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC8913[5]

serC53

CGSC:9696

serC13

CGSC:10177

serC903

CGSC:23663

ΔserC731::kan

PMID:16738554[4]

CGSC:102918

pdxF5

Auxotrophies

Mutation in allele causes production of pyridoxine to halt and can be restored when supplemented with L-serine, Figure 1.

PMID:4321330[6]

pdxF

Strain History: WG1

SerC57

Auxotrophies

Mutation causes double requirement for pyridoxine and serine due to lack of 3-phosphoserine-2-oxoglutarate aminotransferase (POA), Figure 6.

PMID:4321330[6]

Strain History: WG1145

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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

JW0890

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCGCTCAAATCTTCAATTTTAG

Primer 2:CCACCGTGACGGCGTTCGAACTC

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[5]

est. P1 cotransduction: 70% [8]
Synonyms:zbj-1230::Tn10

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[5]

est. P1 cotransduction: 13% [8]

13E3

Kohara Phage

Genobase

PMID:3038334[9]

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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:EG10946

EchoBASE (EcoliWiki Page)

EchoBASE:EB0939

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0907

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C1045

EcoGene (EcoliWiki Page)

EcoGene:EG10946

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:SERC

CGSC (EcoliWiki Page)

CGSC:171

ASAP (EcoliWikiPage)

ASAP:ABE-0003093


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Notes

Links

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<protect>

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. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  3. ↑ Tonella, L et al. (1998) '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 19 1960-71 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 Dempsey, WB & Ito, H (1970) Characterization of pyridoxine auxotrophs of Escherichia coli: serine and pdxF mutants. J. Bacteriol. 104 658-67 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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).
  9. ↑ 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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