aspA:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
edited by 127.0.0.1 via TableEdit
touch
 
(53 intermediate revisions by 4 users not shown)
Line 14: 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 21: Line 23:
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
Line 28: Line 29:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|{{Prettytable}}
{|   id="I46aa081765d58"  class=" tableEdit Gene_nomenclature_table" 
|-
 
!{{table_heading_style}} |Standard name
|
''aspA''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Standard name
|
||
Aspartate<ref name='LIB:EcoGene'/>
''aspA''
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Mnemonic
|
||
''ECK4133, b4139, JW4099''<ref name='LIB:Riley_2006'/>
Aspartate
|-
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.18839.I46aa081765d58&page=18839&pagename={{FULLPAGENAMEE}} edit table]
!align=left {{table_heading_style}} |Synonyms
||
''ECK4133, b4139, JW4099''<ref name='LIB:Riley_2006'/>, JW4099''
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18839.I46aa081765d58&page=18839&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.I46aa081765d58-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.I46aa081765d58-->
{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
Line 58: Line 61:
<protect>
<protect>
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.G46aa0817e934a-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.G46aa0817e934a-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='149728'
******************************************************************************************
*
*  ** 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="G46aa0817e934a"  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 68: Line 76:
94.08 minutes, 94.08 minutes&nbsp;
94.08 minutes, 94.08 minutes&nbsp;
|
|
MG1655: 4366350..4364914<br />{{GBrowseFigureByCoord|4363914|4367350|ecoli|MG1655}}
MG1655: 4366350..4364914<br /><gbrowseImage>
name=NC_000913:4364914..4366350
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10095 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10095 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4363914..4367350 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4363914|4367350|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4364914..4366350&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4364914|4366350|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10095 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10095 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4347048..4345612<br /><gbrowseImage>
name=NC_012967:4345612..4347048
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4345612|4347048|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4345612|4347048|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 4303649..4305085<br /><gbrowseImage>
name=NC_012759:4303649..4305085
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|4303649|4305085|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|4303649|4305085|FASTA Dump}}
|-  
|
|
W3110
W3110
Line 82: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 4373007..4371571<br />{{GBrowseFigureByCoord|4370571|4374007|ecoli_W3110|W3110}}  
W3110: 4373007..4371571<br /><gbrowseImage>
name=NC_007779:4371571..4373007
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|4370571|4374007|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|4371571|4373007|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 4466712..4465276<br /><gbrowseImage>
name=NC_010473:4465276..4466712
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4370571..4374007 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|4462404|4469584|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4371571..4373007&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|4462404|4469584|FASTA Dump}}
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.18839.G46aa0817e934a&page=18839&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18839.G46aa0817e934a&page=18839&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.G46aa0817e934a-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.G46aa0817e934a-->
{{Gene_location_help}}
 
<!--Location_notes--></protect>
<!--Location_notes--></protect>
===Notes===
===Notes===
Line 99: Line 166:
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.M46aa0818b1171-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.M46aa0818b1171-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='149729'
******************************************************************************************
*
*  ** 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="M46aa0818b1171"  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=421aa90e079fa326b6494f812ad13e79.18839.M46aa0818b1171&page=18839&pagename={{FULLPAGENAMEE}} edit table] || ||
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
4364917
|
Edman degradation
|
PMID:2987841<br />
|
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18839.M46aa0818b1171&page=18839&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.M46aa0818b1171-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.M46aa0818b1171-->
{{Gene_sequence_features_help}}
 
<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====Notes====
====Notes====
Line 115: Line 201:
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.Z46aa08190866b-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.Z46aa08190866b-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='149730'
******************************************************************************************
*
*  ** 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="Z46aa08190866b"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!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
|-
|-
|
aspAK327R
|
 
|
K327R
|
Auxotrophies
|
Reduces activity by 99.7%. Increases KM for aspartic acid 5-fold
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC38 UniProt:P0AC38]
|-
|
aspAR29A
|
 
|
R29A
|
Auxotrophies
|
No effect on Kcat. Increases KM for aspartic acid 40-fold
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC38 UniProt:P0AC38]
|-
|
aspAK55R
|
 
|
K55R
|
Auxotrophies
|
Loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC38 UniProt:P0AC38]
|-
|
aspAH124L
|
 
|
H124L
|
Auxotrophies
|
Reduces activity by 30%
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC38 UniProt:P0AC38]
|-
|
aspAS143G
|
 
|
S143G
|
Auxotrophies
|
Reduces Kcat by 90%. Increases KM for aspartic acid 4-fold
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC38 UniProt:P0AC38]
|-
|
aspAS143T
|
 
|
S143T
|
Auxotrophies
|
Reduces Kcat by 98.5%. Increases KM for aspartic acid 2-fold
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC38 UniProt:P0AC38]
|-
|
aspAD10A
|
 
|
D10A
|
Auxotrophies
|
Loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC38 UniProt:P0AC38]
|-
|
aspAD10N
|
 
|
D10N
|
Auxotrophies
|
Reduces Kcal by 80%. Increases KM for aspartic acid 3-fold
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC38 UniProt:P0AC38]
|-
|
aspAR15A
|
 
|
R15A
|
Auxotrophies
|
No effect on Kcat. Increases KM for aspartic acid 2.5-fold
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC38 UniProt:P0AC38]
|-
|
aspAH26N
|
 
|
H26N
|
Auxotrophies
|
No effect on Kcat. Increases KM for aspartic acid 3-fold
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AC38 UniProt:P0AC38]
|-  
|
|
&Delta;aspA (Keio:JW4099)
ΔaspA (Keio:JW4099)
|
|
deletion
deletion
|
|
deletion
deletion
|
Auxotrophies
|
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://cgsc2.biology.yale.edu/Strain.php?ID=106587 CGSC8324]<ref name='LIB:cgsc'/>
|
|-
|
''aspA22''
|
|
|
Auxotrophies
|
|
|
[[cgscmutation:5112|CGSC:5112]]
|
|-
|
''aspA23''
|
|
|
Auxotrophies
|
|
|


|
[[cgscmutation:5113|CGSC:5113]]
|
|-
|
''ΔaspA765::kan''
|
deletion
|
deletion
|
Auxotrophies
|
|


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[[cgscmutation:100110|CGSC:100110]]
|
|
   
   
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.18839.Z46aa08190866b&page=18839&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18839.Z46aa08190866b&page=18839&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.Z46aa08190866b-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.Z46aa08190866b-->
{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18839.P4e04b7e14ea6b-->
<!--
******************************************************************************************
*
*  ** 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="P4e04b7e14ea6b"  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.18839.P4e04b7e14ea6b&page=18839&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18839.P4e04b7e14ea6b--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.C46aa0819c4a91-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.C46aa0819c4a91-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='149731'
******************************************************************************************
*
*  ** 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="C46aa0819c4a91"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
|-  
|
|
JW4099
JW4099
Line 160: Line 502:
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
Line 167: Line 509:


Primer 2:CCtTGTTCGCTTTCATCAGTATA  
Primer 2:CCtTGTTCGCTTTCATCAGTATA  
|-
|-
|
[[:Category:Kohara_Phage:5G7|5G7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=648 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:9B1|9B1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=649 Genobase]
|
PMID:3038334
|-  
|
|
[[cadB:Gene|cadB2231::Tn10]]
[[cadB:Gene|cadB2231::Tn10]]
Line 175: Line 535:
CAG18488 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40596 CGSC7479]<ref name='LIB:cgsc'/>
CAG18488 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40596 CGSC7479]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 76% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 76% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zjd-2231::Tn10  
Synonyms:zjd-2231::Tn10  
|-
|-  
|
|
[[cycA:Gene|cycA30::Tn10]]
[[cycA:Gene|cycA30::Tn10]]
Line 187: Line 546:
|
|
est. P1 cotransduction: 4% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 4% <ref name='LIB:Nichols_linked_Tn'/>  
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.18839.C46aa0819c4a91&page=18839&pagename={{FULLPAGENAMEE}} edit table] || || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18839.C46aa0819c4a91&page=18839&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.C46aa0819c4a91-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.C46aa0819c4a91-->
{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
Line 199: Line 559:
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.R46aa081a73af4-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.R46aa081a73af4-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='149732'
******************************************************************************************
*
*  ** 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="R46aa081a73af4"  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=EG10095 EcoCyc:EG10095] 
EcoCyc:EG10095
|
|
''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=EB0093 EchoBASE:EB0093] 
EcoGene:EG10095
|
|
''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=b4139 EcoliGenExpDB:b4139] 
RegulonDB:ECK120000091
|
|
''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=C5222 ECOL199310CYC:C5222]
[http://www.ncbi.nlm.nih.gov/gene?term=948658 GeneID:948658]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10095 EcoGene:EG10095] 
EchoBASE:EB0093
|
|
''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=ASPA ECOO157CYC:ASPA] 
ASAP:ABE-0013551
|
|
''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=421aa90e079fa326b6494f812ad13e79.18839.R46aa081a73af4&page=18839&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/991 CGSC:991] 
|
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.18839.R46aa081a73af4&page=18839&pagename={{FULLPAGENAMEE}} edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.R46aa081a73af4-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.R46aa081a73af4-->
{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
===Notes===
===Notes===
Line 264: Line 623:
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.B46a7210fa0c62-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.B46a7210fa0c62-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
<!--
{|class = 'sortable' {{Prettytable}} id='100240'
******************************************************************************************
*
*  ** 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="B46a7210fa0c62"  class=" tableEdit Links_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Name!!URL!!Comments
!|Name!!URL!!Comments
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.18839.B46a7210fa0c62&page=18839&pagename={{FULLPAGENAMEE}} edit table] || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18839.B46a7210fa0c62&page=18839&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.B46a7210fa0c62-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18839.B46a7210fa0c62-->
{{Links_help}}
 


<noinclude><protect>
<noinclude><protect>
Line 278: Line 643:
{{BacktoTop}}
{{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:asp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:51, 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

aspA

Mnemonic

Aspartate

Synonyms

ECK4133, b4139, JW4099[1], JW4099

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

94.08 minutes, 94.08 minutes 

MG1655: 4366350..4364914
<gbrowseImage> name=NC_000913:4364914..4366350 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4347048..4345612
<gbrowseImage> name=NC_012967:4345612..4347048 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4303649..4305085
<gbrowseImage> name=NC_012759:4303649..4305085 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4373007..4371571
<gbrowseImage> name=NC_007779:4371571..4373007 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4466712..4465276
<gbrowseImage> name=NC_010473:4465276..4466712 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

4364917

Edman degradation

PMID:2987841[2]


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

aspAK327R

K327R

Auxotrophies

Reduces activity by 99.7%. Increases KM for aspartic acid 5-fold

seeded from UniProt:P0AC38

aspAR29A

R29A

Auxotrophies

No effect on Kcat. Increases KM for aspartic acid 40-fold

seeded from UniProt:P0AC38

aspAK55R

K55R

Auxotrophies

Loss of activity

seeded from UniProt:P0AC38

aspAH124L

H124L

Auxotrophies

Reduces activity by 30%

seeded from UniProt:P0AC38

aspAS143G

S143G

Auxotrophies

Reduces Kcat by 90%. Increases KM for aspartic acid 4-fold

seeded from UniProt:P0AC38

aspAS143T

S143T

Auxotrophies

Reduces Kcat by 98.5%. Increases KM for aspartic acid 2-fold

seeded from UniProt:P0AC38

aspAD10A

D10A

Auxotrophies

Loss of activity

seeded from UniProt:P0AC38

aspAD10N

D10N

Auxotrophies

Reduces Kcal by 80%. Increases KM for aspartic acid 3-fold

seeded from UniProt:P0AC38

aspAR15A

R15A

Auxotrophies

No effect on Kcat. Increases KM for aspartic acid 2.5-fold

seeded from UniProt:P0AC38

aspAH26N

H26N

Auxotrophies

No effect on Kcat. Increases KM for aspartic acid 3-fold

seeded from UniProt:P0AC38

ΔaspA (Keio:JW4099)

deletion

deletion

Auxotrophies

PMID:16738554[3]

Shigen

CGSC8324[4]

aspA22

Auxotrophies

CGSC:5112

aspA23

Auxotrophies

CGSC:5113

ΔaspA765::kan

deletion

deletion

Auxotrophies

PMID:16738554[3]

CGSC:100110


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

JW4099

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTCAAACAACATTCGTATCGA

Primer 2:CCtTGTTCGCTTTCATCAGTATA

5G7

Kohara Phage

Genobase

PMID:3038334[6]

9B1

Kohara Phage

Genobase

PMID:3038334[6]

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[4]

est. P1 cotransduction: 76% [7]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[4]

est. P1 cotransduction: 4% [7]

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:EG10095

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10095

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000091

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948658

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0093

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013551

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. ↑ Takagi, JS et al. (1985) Cloning and nucleotide sequence of the aspartase gene of Escherichia coli W. Nucleic Acids Res. 13 2063-74 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  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 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
  7. ↑ 7.0 7.1 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=aspA:Gene&oldid=1480589"