aroK:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3377, b3390, JW5947''<ref name='LIB:Riley_2006'/>
''ECK3377, b3390, JW5947''<ref name='LIB:Riley_2006'/>, JW5947''


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{|   id="I46a9f4b97c284"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46a9f4b97c284"  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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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10081 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10081 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3515565|3518086|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3515565|3518086|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3516565|3517086|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3516565|3517086|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10081 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10081 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|3403722|NC_3404243|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|3403722|3404243|GBrowse (BW2952)}}
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W3110: 4121352..4121873<br /><gbrowseImage>
W3110: 4121352..4121873<br /><gbrowseImage>
name=AC_000091:4121352..4121873
name=NC_007779:4121352..4121873
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|4120352|4122873|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|4120352|4122873|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|4121352|4121873|FASTA Dump}}  
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DH10B: 3614831..3614310<br /><gbrowseImage>
DH10B: 3614831..3614310<br /><gbrowseImage>
name=NC_010473:3614310..3614831
name=NC_010473:3614310..3614831
source=MG1655_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|3613268|3615873|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|3613268|3615873|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3613268|3615873|FASTA Dump}}  
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{|   id="S46a9f4ba3d11b"  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="S46a9f4ba3d11b"  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="M46a9f4ba86292"  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="M46a9f4ba86292"  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="Q4e04b7b3e34b6"  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="Q4e04b7b3e34b6"  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="F46a9f4bb47481"  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="F46a9f4bb47481"  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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Primer 2:  
Primer 2:  
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[[:Category:Kohara_Phage:4D4|4D4]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=622 Genobase]
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PMID:3038334
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{|   id="H46a9f4bbe4005"  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="H46a9f4bbe4005"  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=EG10081 EcoCyc:EG10081]
EcoCyc:EG10081
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0079 EchoBASE:EB0079]
EcoGene:EG10081
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3390 EcoliGenExpDB:b3390]
RegulonDB:ECK120000077
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C4160 ECOL199310CYC:C4160]
[http://www.ncbi.nlm.nih.gov/gene?term=2847759 GeneID:2847759]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10081 EcoGene:EG10081]
EchoBASE:EB0079
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=AROK ECOO157CYC:AROK]
ASAP:ABE-0011069
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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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/30224 CGSC:30224]
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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=0011069&formSubmitReturn=1 ASAP:ABE-0011069]
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!|Name!!URL!!Comments
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Latest revision as of 20:47, 19 September 2013

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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

aroK

Mnemonic

Aromatic

Synonyms

ECK3377, b3390, JW5947[1], JW5947

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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

75.79 minutes 

MG1655: 3517086..3516565
<gbrowseImage> name=NC_000913:3516565..3517086 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3447746..3447225
<gbrowseImage> name=NC_012967:3447225..3447746 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3403722..3404243
<gbrowseImage> name=NC_012759:3403722..3404243 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4121352..4121873
<gbrowseImage> name=NC_007779:4121352..4121873 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3614831..3614310
<gbrowseImage> name=NC_010473:3614310..3614831 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

3516568

Edman degradation

PMID:9298646[2]
PMID:9600841[3]
PMID:9740056[4]


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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

ΔaroK (Keio:JW5947)

deletion

deletion

PMID:16738554[5]

Shigen

aroK17::Cm

PMID:1309529[6]

CGSC:68842


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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

Plasmid clone

Shigen

PMID:16769691[7]

Status:

Primer 1:

Primer 2:

4D4

Kohara Phage

Genobase

PMID:3038334[8]

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[9]

est. P1 cotransduction: 62% [10]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[9]

est. P1 cotransduction: 12% [10]
Synonyms:zhg-3086::Tn10, zhh-21::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:EG10081

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10081

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000077

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:2847759

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0079

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011069

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. ↑ 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
  3. ↑ Wilkins, MR et al. (1998) Protein identification with N and C-terminal sequence tags in proteome projects. J. Mol. Biol. 278 599-608 PubMed
  4. ↑ Tonella, L et al. (1998) '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 19 1960-71 PubMed
  5. ↑ 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
  6. ↑ Løbner-Olesen, A & Marinus, MG (1992) Identification of the gene (aroK) encoding shikimic acid kinase I of Escherichia coli. J. Bacteriol. 174 525-9 PubMed
  7. ↑ 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
  8. ↑ 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
  9. ↑ 9.0 9.1 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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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