sfmD: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

sfmD

Mnemonic

Salmonella fimbriae

Synonyms

ECK0525, b0532, JW0521[1], fimD, JW0521

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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

12.05 minutes 

MG1655: 558920..561523
<gbrowseImage> name=NC_000913:558920..561523 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 531805..534414
<gbrowseImage> name=NC_012967:531805..534414 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 461680..464283
<gbrowseImage> name=NC_012759:461680..464283 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 558920..561523
<gbrowseImage> name=NC_007779:558920..561523 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 498252..500855
<gbrowseImage> name=NC_010473:498252..500855 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

ΔsfmD (Keio:JW0521)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8661[3]

ΔsfmD742::kan

PMID:16738554[2]

CGSC:102930


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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

JW0521

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAAAATACCCACTACTACGGA

Primer 2:CCTGAGCCAGGATGTGTGCAAAC

2C4

Kohara Phage

Genobase

PMID:3038334[5]

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 80% [6]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[3]

est. P1 cotransduction: 1% [6]
Synonyms:zbd-601::Tn10, zbe-601::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:G6292

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13883

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002900

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945160

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3642

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001830

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. 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
  5. 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
  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).

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