ydfA:Gene: Difference between revisions

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Refreshing information from GenBank record NC_000913
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9c9e6c2a6e"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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W3110: 1650222..1650377<br /><gbrowseImage>
W3110: 1650222..1650377<br /><gbrowseImage>
name=AC_000091:1650222..1650377
name=NC_007779:1650222..1650377
source=W3110
source=W3110
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|1649222|1651377|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1649222|1651377|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|1650222|1650377|FASTA Dump}}  
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{|   id="Y46a9c9e772eb9"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a9c9e772eb9"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="A46a9c9e7b578c"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="A46a9c9e7b578c"  class=" tableEdit Gene_allele_table dataTable"   
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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{|   id="G4e04c7c2e2cca"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G4e04c7c2e2cca"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="T46a9c9e865d79"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9c9e865d79"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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{|   id="Z46a9c9e900d01"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9c9e900d01"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11300 ECOCYC:EG11300]
EcoCyc:EG11300
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG11300
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG11300 EcoGene:EG11300]
RegulonDB:ECK120001273
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[EchoBASE]]
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EchoBASE:EB1277
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0005251
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:28, 19 September 2013

{{#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

ydfA

Mnemonic

Systematic nomenclature

Synonyms

ECK1565, b1571, JW1563[1], JW1563

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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

35.49 minutes 

MG1655: 1646532..1646687
<gbrowseImage> name=NC_000913:1646532..1646687 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1538591..1538746
<gbrowseImage> name=NC_012759:1538591..1538746 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1650222..1650377
<gbrowseImage> name=NC_007779:1650222..1650377 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1736157..1736312
<gbrowseImage> name=NC_010473:1736157..1736312 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

ΔydfA (Keio:JW1563)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9337[3]

ΔydfA::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[4]

ΔydfA::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[4]

ΔydfA721::kan

PMID:16738554[2]

CGSC:104238

ydfA

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[5]

fig 2

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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

JW1563

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGATACTATCGATCTTGGCAA

Primer 2:CCtTCACCTGAGTTTCTTTCCAG

12E2

Kohara Phage

Genobase

PMID:3038334[7]

7B6

Kohara Phage

Genobase

PMID:3038334[7]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[3]

est. P1 cotransduction: % [8]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[3]

est. P1 cotransduction: % [8]
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

EcoCyc:EG11300

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11300

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001273

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946082

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1277

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005251

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  5. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 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 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
  8. ↑ 8.0 8.1 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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