proW:Gene: Difference between revisions

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Convert to gbrowse_img.php extension.
Fixing Blattner deletion strains in alleles table.
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0008816 proW::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0008816 proW::Tn5KAN-I-SceI] (FB20878)
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Insertion at nt 835 in Plus orientation
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PMID:12519969
PMID:15262929
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[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20878]
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At position 835 in Plus orientation, does not contain plasmid  [[pKD46]].<br />ASAP strain name: FB20878
does not contain [[pKD46]]  
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0008816 proW::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0008816 proW::Tn5KAN-I-SceI] (FB20879)
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Insertion at nt 835 in Plus orientation
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PMID:12519969
PMID:15262929
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[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20879]
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At position 835 in Plus orientation, contains plasmid  [[pKD46]].<br />ASAP strain name: FB20879
contains [[pKD46]]  
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Revision as of 22:02, 9 March 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 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

proW

Mnemonic

Proline

Synonyms

ECK2672, b2678, JW2653, osrA, proU, G7982[1][2]

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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

60.44 minutes, 60.44 minutes 

MG1655: 2804032..2805096
<gbrowseImage> name=NC_000913:2804032..2805096 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2700762..2701826
<gbrowseImage> name=NC_012967:2700762..2701826 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2689844..2690908
<gbrowseImage> name=NC_012759:2689844..2690908 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2804666..2805730
<gbrowseImage> name=AC_000091:2804666..2805730 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2896574..2897638
<gbrowseImage> name=NC_010473:2896574..2897638 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
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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

ΔproW (Keio:JW2653)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10092[4]

proW::Tn5KAN-I-SceI (FB20878)

Insertion at nt 835 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20878

does not contain pKD46

proW::Tn5KAN-I-SceI (FB20879)

Insertion at nt 835 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20879

contains pKD46

ΔproW759::kan

PMID:16738554[3]

CGSC:102478


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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

JW2653

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGCTGATCAAAATAATCCGTG

Primer 2:CCtTTAATGAATGGGCGGGTCAG

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[4]

est. P1 cotransduction: 2% [7]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[4]

est. P1 cotransduction: 45% [7]
Synonyms:zfh-3131::Tn10, zfi-3131::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:EG10772

EchoBASE (EcoliWiki Page)

EchoBASE:EB0765

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2678

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3231

EcoGene (EcoliWiki Page)

EcoGene:EG10772

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:PROW

ASAP (EcoliWikiPage)

ASAP:ABE-0008816


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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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  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. ↑ 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
  7. ↑ 7.0 7.1 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).

Categories

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