cfa:Gene: Difference between revisions

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Fixing Blattner deletion strains in alleles table.
Adding section & Genetic interactions table to Gene pages.
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|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
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|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==

Revision as of 16:17, 24 June 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

cfa

Mnemonic

Cyclopropane fatty acid

Synonyms

ECK1657, b1661, JW1653, cdfA[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

37.49 minutes 

MG1655: 1739437..1740585
<gbrowseImage> name=NC_000913:1739437..1740585 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1718680..1719828
<gbrowseImage> name=NC_012967:1718680..1719828 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1631496..1632644
<gbrowseImage> name=NC_012759:1631496..1632644 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1743127..1744275
<gbrowseImage> name=AC_000091:1743127..1744275 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1830008..1831156
<gbrowseImage> name=NC_010473:1830008..1831156 source=ecoli_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

1739440

Edman degradation

PMID:1445840[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

Δcfa (Keio:JW1653)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9407[4]

cfa::Tn5KAN-2 (FB20416)

Insertion at nt 635 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20416

does not contain pKD46

cfa::Tn5KAN-2 (FB20417)

Insertion at nt 635 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20417

contains pKD46

cfa-1

CGSC:10811

cfa-2

PMID:6092874[6] PMID:3519583[7]

CGSC:17027

cfa-3

PMID:3519583[7] PMID:6092874[6]

CGSC:17030

cfa-4

PMID:3519583[7] PMID:6092874[6]

CGSC:17032

cfa-5::kan

PMID:10411742[8] PMID:3038679[9]

CGSC:64828

cfa-0

CGSC:73935

Δcfa-739::kan

PMID:16738554[3]

CGSC:100276


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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

JW1653

Plasmid clone

Shigen

PMID:16769691[10]

Status:Clone OK

Primer 1:GCCAGTTCATCGTGTATAGAAGA

Primer 2:CCGCGAGCCACTCGAAGGCCGTT

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[4]

est. P1 cotransduction: % [11]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[4]

est. P1 cotransduction: 21% [11]
Synonyms:zdh-925::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 (EcoliWiki Page)

EcoCyc:EG11531

EchoBASE (EcoliWiki Page)

EchoBASE:EB1493

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1661

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2055

EcoGene (EcoliWiki Page)

EcoGene:EG11531

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:CFA

CGSC (EcoliWiki Page)

CGSC:10810

ASAP (EcoliWikiPage)

ASAP:ABE-0005555


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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, AY et al. (1992) Cyclopropane fatty acid synthase of Escherichia coli: deduced amino acid sequence, purification, and studies of the enzyme active site. Biochemistry 31 11020-8 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. ↑ 5.0 5.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ 6.0 6.1 6.2 Grogan, DW & Cronan, JE Jr (1984) Genetic characterization of the Escherichia coli cyclopropane fatty acid (cfa) locus and neighboring loci. Mol. Gen. Genet. 196 367-72 PubMed
  7. ↑ 7.0 7.1 7.2 Grogan, DW & Cronan, JE Jr (1986) Characterization of Escherichia coli mutants completely defective in synthesis of cyclopropane fatty acids. J. Bacteriol. 166 872-7 PubMed
  8. ↑ Chang, YY & Cronan, JE Jr (1999) Membrane cyclopropane fatty acid content is a major factor in acid resistance of Escherichia coli. Mol. Microbiol. 33 249-59 PubMed
  9. ↑ Fellay, R et al. (1987) Interposon mutagenesis of soil and water bacteria: a family of DNA fragments designed for in vitro insertional mutagenesis of gram-negative bacteria. Gene 52 147-54 PubMed
  10. ↑ 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
  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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