araF:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
imported>WikiEntryBot
Automated import of articles
 
touch
 
(56 intermediate revisions by 3 users not shown)
Line 1: Line 1:
<!--PLEASE EDIT FROM THE SECTION OR TABLE EDIT LINKS...IF YOU SEE THIS MESSAGE, YOU'RE PROBABLY IN THE WRONG PLACE-->
<!--
***************************************************************************************************************************************************
*
*              PLEASE EDIT FROM THE SECTION OR TABLE EDIT LINKS...IF YOU SEE THIS MESSAGE,
*                            YOU'RE PROBABLY IN THE WRONG PLACE
*
*
***************************************************************************************************************************************************
-->{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|araF}}{{Tab On|Gene|araF}}{{Tab|Gene Product(s)|araF}}{{Tab|Expression|araF}}{{Tab|Evolution|araF}}{{Tab|On One Page|araF}}{{TabsBottom}}
{{Tab|Quickview|araF}}{{Tab On|Gene|araF}}{{Tab|Gene Product(s)|araF}}{{Tab|Expression|araF}}{{Tab|Evolution|araF}}{{Tab|On One Page|araF}}{{TabsBottom}}
Line 6: Line 14:
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
Line 15: Line 25:
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
<!--box uid=421aa90e079fa326b6494f812ad13e79..G469faa8270062-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.P46a9d191204a1-->
{|{{Prettytable}}
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|  id="P46a9d191204a1"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''araF''  
''araF''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Arabinose
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1899, b1901, JW1889''<ref name='LIB:Riley_2006'/>, JW1889''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14373.P46a9d191204a1&page=14373&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK1899, b1901, JW1889''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..G469faa8270062&page=&pagename={{FULLPAGENAMEE}} edit table]
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..G469faa8270062-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.P46a9d191204a1-->
{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
Line 40: Line 58:


==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
<!--box uid=421aa90e079fa326b6494f812ad13e79..N469faa82b542d-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.B46a9d1919c74d-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='15910'
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_location_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9d1919c74d"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
Line 52: Line 76:
42.74 minutes&nbsp;
42.74 minutes&nbsp;
|
|
MG1655: 1984152..1983163<br />{{GBrowseFigureByCoord|1982163|1985152|ecoli|MG1655}}
MG1655: 1984152..1983163<br /><gbrowseImage>
name=NC_000913:1983163..1984152
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10057 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10057 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1982163..1985152 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1982163|1985152|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1983163..1984152&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1983163|1984152|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10057 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10057 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1964122..1963133<br /><gbrowseImage>
name=NC_012967:1963133..1964122
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1963133|1964122|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1963133|1964122|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 1875646..1876635<br /><gbrowseImage>
name=NC_012759:1875646..1876635
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1875646|1876635|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1875646|1876635|FASTA Dump}}
|-  
|
|
W3110
W3110
Line 66: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 1988265..1987276<br />{{GBrowseFigureByCoord|1986276|1989265|ecoli_W3110|W3110}}  
W3110: 1988265..1987276<br /><gbrowseImage>
name=NC_007779:1987276..1988265
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1986276|1989265|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1987276|1988265|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 2075160..2074171<br /><gbrowseImage>
name=NC_010473:2074171..2075160
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1986276..1989265 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|2072193|2077138|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1987276..1988265&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|2072193|2077138|FASTA Dump}}
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..N469faa82b542d&page=&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14373.B46a9d1919c74d&page=14373&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..N469faa82b542d-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.B46a9d1919c74d-->
{{Gene_location_help}}
 
<!--Location_notes--></protect>
<!--Location_notes--></protect>
===Notes===
===Notes===
Line 81: Line 164:


==Sequence Features==
==Sequence Features==
<!--box uid=421aa90e079fa326b6494f812ad13e79..I469faa82cbf56-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.H46a9d1925050f-->
{|class = 'sortable' {{Prettytable}} id='15911'
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_sequence_features_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9d1925050f"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
|-
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..I469faa82cbf56&page=&pagename={{FULLPAGENAMEE}} edit table] || ||
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
1983166
|
Edman degradation
|
PMID:326784<br />PMID:9298646<br />
|
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14373.H46a9d1925050f&page=14373&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..I469faa82cbf56-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.H46a9d1925050f-->
{{Gene_sequence_features_help}}
 
<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====Notes====
====Notes====
Line 96: Line 199:


==Alleles and Phenotypes==
==Alleles and Phenotypes==
<!--box uid=421aa90e079fa326b6494f812ad13e79..K469faa82d5024-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.H46a9d1929439f-->
{|class = 'sortable' {{Prettytable}} id='15912'
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_alleles_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9d1929439f"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
|-
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..K469faa82d5024&page=&pagename={{FULLPAGENAMEE}} edit table] || || || || || ||
|
araFP277G
|
 
|
P277G
|
 
|
Improves binding to galactose
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P02924 UniProt:P02924]
|-
|
&Delta;araF (Keio:JW1889)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107852 CGSC9571]<ref name='LIB:cgsc'/>
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0006330 araF::Tn5KAN-2] (FB20510)
|
Insertion at nt 512 in Minus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20510]
|
contains [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0006330 araF::Tn5KAN-2] (FB20511)
|
Insertion at nt 512 in Minus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20511]
|
does not contain [[pKD46]]
|-
|
''araF432''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:80485|CGSC:80485]]
|
|-
|
''araF434''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:80488|CGSC:80488]]
|
|-
|
''&#916;araF751::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100026|CGSC:100026]]
|
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14373.H46a9d1929439f&page=14373&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..K469faa82d5024-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.H46a9d1929439f-->
{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14373.C4e04b770da021-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Genetic_interaction_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C4e04b770da021"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.14373.C4e04b770da021&page=14373&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14373.C4e04b770da021--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
<!--box uid=421aa90e079fa326b6494f812ad13e79..R469faa82de15b-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.O46a9d1934792b-->
{|class = 'sortable' {{Prettytable}} id='15913'
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_resources_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9d1934792b"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-class='sortbottom'
|-  
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..R469faa82de15b&page=&pagename={{FULLPAGENAMEE}} edit table] || || ||
|
JW1889
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCCACAAATTTACTAAAGCCCT
 
Primer 2:CCtTTACCGCCTAAACCTTTTTT
|-
|
[[:Category:Kohara_Phage:7F11|7F11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=339 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:18A9|18A9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=340 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:16B12|16B12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=341 Genobase]
|
PMID:3038334
|-
|
[[eda:Gene|eda-51::Tn10]]
|
Linked marker
|
CAG18486 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39983 CGSC7392]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 8% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[uvrC:Gene|uvrC279::Tn10]]
|
Linked marker
|
CAG12156 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39987 CGSC7394]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 78% <ref name='LIB:Nichols_linked_Tn'/>
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14373.O46a9d1934792b&page=14373&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..R469faa82de15b-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.O46a9d1934792b-->
{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
Line 126: Line 444:


==Accessions in Other Databases==
==Accessions in Other Databases==
<!--box uid=421aa90e079fa326b6494f812ad13e79..P469faa82e72a5-->
{{BacktoTop}}
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.V46a9d193d97d0-->
{|class = 'sortable' {{Prettytable}} id='15914'
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Gene_accessions_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9d193d97d0"  class=" tableEdit Gene_accessions_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10057 EcoCyc:EG10057] 
EcoCyc:EG10057
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0055 EchoBASE:EB0055] 
EcoGene:EG10057
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1901 EcoliGenExpDB:b1901] 
RegulonDB:ECK120000053
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2314 ECOL199310CYC:C2314]
[http://www.ncbi.nlm.nih.gov/gene?term=946409 GeneID:946409]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10057 EcoGene:EG10057] 
EchoBASE:EB0055
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=ARAF ECOO157CYC:ARAF] 
ASAP:ABE-0006330
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
|
|- class="tableEdit_footer"
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14373.V46a9d193d97d0&page=14373&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/1023 CGSC:1023] 
|
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..P469faa82e72a5&page=&pagename={{FULLPAGENAMEE}} edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..P469faa82e72a5-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.V46a9d193d97d0-->
{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
===Notes===
===Notes===
Line 190: Line 508:


==Links==
==Links==
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.G46a6eeec30967-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a6eeec30967"  class=" tableEdit Links_table" 
|- {{table_heading_style}}
!|Name!!URL!!Comments
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14373.G46a6eeec30967&page=14373&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.14373.G46a6eeec30967-->




<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:ara genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:39, 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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

araF

Mnemonic

Arabinose

Synonyms

ECK1899, b1901, JW1889[1], JW1889

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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

42.74 minutes 

MG1655: 1984152..1983163
<gbrowseImage> name=NC_000913:1983163..1984152 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1964122..1963133
<gbrowseImage> name=NC_012967:1963133..1964122 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1875646..1876635
<gbrowseImage> name=NC_012759:1875646..1876635 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1988265..1987276
<gbrowseImage> name=NC_007779:1987276..1988265 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2075160..2074171
<gbrowseImage> name=NC_010473:2074171..2075160 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


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

1983166

Edman degradation

PMID:326784[2]
PMID:9298646[3]


edit table


Notes

Alleles and Phenotypes

[back to top]


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

araFP277G

P277G

Improves binding to galactose

seeded from UniProt:P02924

ΔaraF (Keio:JW1889)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC9571[5]

araF::Tn5KAN-2 (FB20510)

Insertion at nt 512 in Minus orientation

PMID:15262929[6]

E. coli Genome Project:FB20510

contains pKD46

araF::Tn5KAN-2 (FB20511)

Insertion at nt 512 in Minus orientation

PMID:15262929[6]

E. coli Genome Project:FB20511

does not contain pKD46

araF432

CGSC:80485

araF434

CGSC:80488

ΔaraF751::kan

PMID:16738554[4]

CGSC:100026


edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW1889

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCCACAAATTTACTAAAGCCCT

Primer 2:CCtTTACCGCCTAAACCTTTTTT

7F11

Kohara Phage

Genobase

PMID:3038334[8]

18A9

Kohara Phage

Genobase

PMID:3038334[8]

16B12

Kohara Phage

Genobase

PMID:3038334[8]

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[5]

est. P1 cotransduction: 8% [9]

uvrC279::Tn10

Linked marker

CAG12156 = CGSC7394[5]

est. P1 cotransduction: 78% [9]

edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10057

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10057

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000053

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946409

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0055

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006330

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]



<protect>

References

[back to top]


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. ↑ Hogg, RW & Hermodson, MA (1977) Amino acid sequence of the L-arabinose-binding protein from Escherichia coli B/r. J. Biol. Chem. 252 5135-41 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. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 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. ↑ 8.0 8.1 8.2 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 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

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=araF:Gene&oldid=1478360"