dppB:Gene: Difference between revisions

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Fixing Blattner deletion strains in alleles table.
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011572 dppB::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011572 dppB::Tn5KAN-I-SceI] (FB21269)
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Insertion at nt 731 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:FB21269]
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At position 731 in Plus orientation, contains plasmid  [[pKD46]].<br />ASAP strain name: FB21269
contains [[pKD46]]  
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011572 dppB::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011572 dppB::Tn5KAN-I-SceI] (FB21270)
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Insertion at nt 731 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:FB21270]
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At position 731 in Plus orientation, does not contain plasmid  [[pKD46]].<br />ASAP strain name: FB21270
does not contain [[pKD46]]  
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Revision as of 21:31, 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

dppB

Mnemonic

Dipeptide permease system

Synonyms

ECK3530, b3543, JW3512[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

79.81 minutes 

MG1655: 3703813..3702794
<gbrowseImage> name=NC_000913:3702794..3703813 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3636248..3635229
<gbrowseImage> name=NC_012967:3635229..3636248 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3591288..3592307
<gbrowseImage> name=NC_012759:3591288..3592307 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3934625..3935644
<gbrowseImage> name=AC_000091:3934625..3935644 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3801558..3800539
<gbrowseImage> name=NC_010473:3800539..3801558 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

ΔdppB (Keio:JW3512)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10598[3]

dppB::Tn5KAN-I-SceI (FB21269)

Insertion at nt 731 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB21269

contains pKD46

dppB::Tn5KAN-I-SceI (FB21270)

Insertion at nt 731 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB21270

does not contain pKD46

ΔdppB726::kan

PMID:16738554[2]

CGSC:100638


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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

JW3512

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTTGCAGTTTATTCTCCGACG

Primer 2:CCtTTCTTATGACGAATACGCGG

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[3]

est. P1 cotransduction: % [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[3]

est. P1 cotransduction: % [6]

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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:EG12625

EchoBASE (EcoliWiki Page)

EchoBASE:EB2509

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3543

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4358

EcoGene (EcoliWiki Page)

EcoGene:EG12625

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:DPPB

CGSC (EcoliWiki Page)

CGSC:33771

ASAP (EcoliWikiPage)

ASAP:ABE-0011572


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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. ↑ 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
  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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