dppA:Gene: Difference between revisions

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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=602 Genobase]
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=602 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:1D1|1D1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=603 Genobase]
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PMID:3038334  
PMID:3038334  
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
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[[:Category:Kohara_Phage:1D1|1D1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=603 Genobase]
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PMID:3038334


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!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10248 EcoCyc:EG10248]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0244 EchoBASE:EB0244]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3544 EcoliGenExpDB:b3544]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C4361 ECOL199310CYC:C4361]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG10248 EcoGene:EG10248]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=DPPA ECOO157CYC:DPPA]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/35111 CGSC:35111]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0011576&formSubmitReturn=1 ASAP:ABE-0011576]
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Revision as of 19:56, 21 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

dppA

Mnemonic

Dipeptide permease system

Synonyms

ECK3531, b3544, JW3513, alu, dpp, fpp[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

79.84 minutes 

MG1655: 3705728..3704121
<gbrowseImage> name=NC_000913:3704121..3705728 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3638163..3636556
<gbrowseImage> name=NC_012967:3636556..3638163 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3592615..3594222
<gbrowseImage> name=NC_012759:3592615..3594222 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3932710..3934317
<gbrowseImage> name=AC_000091:3932710..3934317 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3803473..3801866
<gbrowseImage> name=NC_010473:3801866..3803473 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

3704124

Edman degradation

PMID:1956284[2]
PMID:9298646[3]
PMID:9600841[4]
PMID:9740056[5]
PMID:10972807[6]


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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

ΔdppA (Keio:JW3513)

deletion

deletion

PMID:16738554[7]

Shigen
CGSC10599[8]

dppA::Tn5KAN-I-SceI (FB21271)

Insertion at nt 837 in Minus orientation

PMID:15262929[9]

E. coli Genome Project:FB21271

does not contain pKD46

ΔdppA728::kan

PMID:16738554[7]

CGSC:100636


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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

JW3513

Plasmid clone

Shigen

PMID:16769691[10]

Status:Clone OK

Primer 1:GCCCGTATTTCCTTGAAAAAGTC

Primer 2:CCTTCGATAGAGACGTTTTCGAA

9F6

Kohara Phage

Genobase

PMID:3038334[11]

1D1

Kohara Phage

Genobase

PMID:3038334[11]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[8]

est. P1 cotransduction: % [12]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[8]

est. P1 cotransduction: % [12]

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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
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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. ↑ Abouhamad, WN et al. (1991) Peptide transport and chemotaxis in Escherichia coli and Salmonella typhimurium: characterization of the dipeptide permease (Dpp) and the dipeptide-binding protein. Mol. Microbiol. 5 1035-47 PubMed
  3. ↑ 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
  4. ↑ Wilkins, MR et al. (1998) Protein identification with N and C-terminal sequence tags in proteome projects. J. Mol. Biol. 278 599-608 PubMed
  5. ↑ Tonella, L et al. (1998) '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 19 1960-71 PubMed
  6. ↑ Urbanowski, ML et al. (2000) The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. Mol. Microbiol. 37 856-68 PubMed
  7. ↑ 7.0 7.1 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
  8. ↑ 8.0 8.1 8.2 CGSC: The Coli Genetics Stock Center
  9. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 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 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
  12. ↑ 12.0 12.1 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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