lipB:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Data loaded by TableEdit_Loader.
touch
 
(23 intermediate revisions by 3 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 31: Line 33:
*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="W46a9b55f2bfd1" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''lipB''  
''lipB''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Lipoate
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
Line 46: Line 48:
''ECK0623, b0630, JW5089, lip, cde, cde4''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK0623, b0630, JW5089, lip, cde, cde4''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.W46a9b55f2bfd1&page=11823&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.W46a9b55f2bfd1&page=11823&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.W46a9b55f2bfd1-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.W46a9b55f2bfd1-->
Line 65: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a9b55fa3ef8"  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
Line 74: Line 76:
14.24 minutes&nbsp;
14.24 minutes&nbsp;
|
|
MG1655: 661501..660860<br />{{GBrowseFigureByCoord|660860|661501|ecoli|MG1655}}
MG1655: 661501..660860<br /><gbrowseImage>
name=NC_000913:660860..661501
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11591 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11591 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|659860|662501|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|659860|662501|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|660860|661501|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|660860|661501|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11591 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11591 EcoCyc Sequence Dump]  
|-  
|-  
|
|
W3110
[[REL606]]
|
|
&nbsp;
 
|
|
W3110: 662700..662059<br />{{GBrowseFigureByCoord|662059|662700|ecoli_W3110|W3110}}
NC_012967: 644861..644220<br /><gbrowseImage>
name=NC_012967:644220..644861
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|661059|663700|GBrowse(W3110)}}  
{{GBrowseLink|REL606|NC_012967|644220|644861|GBrowse (REL606)}}
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|662059|662700|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|644220|644861|FASTA Dump}}  
|-  
|-  
|
|
[[DH10B]]
[[BW2952]]
|
|


|
|
DH10B: 600833..600192<br />{{GBrowseFigureByCoord|600192|600833|ecoli_DH10B|DH10B}}
NC_012759: 563620..564261<br /><gbrowseImage>
name=NC_012759:563620..564261
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|598910|602115|GBrowse(DH10B)}}
{{GBrowseLink|BW2952|NC_012759|563620|564261|GBrowse (BW2952)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|598910|602115|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|563620|564261|FASTA Dump}}
|-
|
W3110
|
&nbsp;
|
W3110: 662700..662059<br /><gbrowseImage>
name=NC_007779:662059..662700
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|661059|663700|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|662059|662700|FASTA Dump}}  
|-  
|-  
|
|
Line 110: Line 143:


|
|
DH10B: 714093..713452<br />{{GBrowseFigureByCoord|713452|714093|ecoli_DH10B|DH10B}}
DH10B: 600833..600192<br /><gbrowseImage>
name=NC_010473:600192..600833
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|712170|715375|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|598910|602115|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|712170|715375|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|598910|602115|FASTA Dump}}  
|-  
|-  
|
|
[[REL606]]
[[DH10B]]
|
|


|
|
NC_012967: 644220..644861<br />{{GBrowseFigureByCoord|644220|644861|REL606|NC_012967}}
DH10B: 714093..713452<br /><gbrowseImage>
name=NC_010473:713452..714093
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|644220|644861|GBrowse (REL606)}}
{{GBrowseLink|DH10B|NC_010473|712170|715375|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|REL606|NC_012967|644220|644861|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|712170|715375|FASTA Dump}}  


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.D46a9b55fa3ef8&page=11823&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.D46a9b55fa3ef8&page=11823&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.D46a9b55fa3ef8-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.D46a9b55fa3ef8-->
Line 145: Line 188:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9b5604bafe"  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'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.N46a9b5604bafe&page=11823&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.N46a9b5604bafe&page=11823&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.N46a9b5604bafe-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.N46a9b5604bafe-->
Line 167: Line 210:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="H46a9b5608b07e"  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
|-  
|-  
|
|
&Delta;lipB (Keio:JW5089)
''lipB(del)'' (Keio:JW5089)
|
|
deletion
deletion
Line 187: Line 230:
|
|
   
   
|-
|
lipBC169S
|
|
C169S
|
|
Loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P60720 UniProt:P60720]
|-
|
lipBC169A
|
|
C169A
|
|
1% of wild-type activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P60720 UniProt:P60720]
|-
|
lipBC137A
|
|
C137A
|
|
No effect on activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P60720 UniProt:P60720]
|-
|
lipBC147A
|
|
C147A
|
|
No effect on activity
|
|


|-class='sortbottom'
|
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.H46a9b5608b07e&page=11823&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
seeded from [http://www.uniprot.org/uniprot/P60720 UniProt:P60720]
|-
|
CAG45114 ''lipB769(del)''::FRTKanFRT
|
Deletion
|
 
|
Sigma<sup>E</sup> activity
|
Decrease in sigma<sup>E</sup> activity
|
PMID:23224554
|
Parental Strain: CAG45114
Experimental Strain: SMR15295
|
See table S11 for full experimental calculations
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.H46a9b5608b07e&page=11823&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.H46a9b5608b07e-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.H46a9b5608b07e-->
Line 196: Line 325:
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11823.I4e04be6968a81-->
<!--
******************************************************************************************
*
*  ** 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="I4e04be6968a81"  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.11823.I4e04be6968a81&page=11823&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11823.I4e04be6968a81--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
Line 206: Line 357:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9b56132456"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 224: Line 375:


Primer 2:CCAGCGGTAATATATTCGAAGTC  
Primer 2:CCAGCGGTAATATATTCGAAGTC  
|-
|
[[:Category:Kohara_Phage:1G6|1G6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=168 Genobase]
|
PMID:3038334
|-  
|-  
|
|
Line 245: Line 405:
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.  
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.  


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.Q46a9b56132456&page=11823&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table] || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.Q46a9b56132456&page=11823&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.Q46a9b56132456-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.Q46a9b56132456-->
Line 263: Line 423:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9b561b9d5c"  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=EG11591 EcoCyc:EG11591]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1549 EchoBASE:EB1549]
EcoCyc:EG11591
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0630 EcoliGenExpDB:b0630]
EcoGene:EG11591
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0720 ECOL199310CYC:C0720]
RegulonDB:ECK120001540
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11591 EcoGene:EG11591]
[http://www.ncbi.nlm.nih.gov/gene?term=945217 GeneID:945217]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=LIPB ECOO157CYC:LIPB]
EchoBASE:EB1549
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/555 CGSC:555]
|
|
ASAP:ABE-0002160
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0002160&formSubmitReturn=1 ASAP:ABE-0002160]
|


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.T46a9b561b9d5c&page=11823&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.T46a9b561b9d5c&page=11823&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.T46a9b561b9d5c-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.T46a9b561b9d5c-->
Line 341: Line 487:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46a6d2886b7f8"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.I46a6d2886b7f8&page=11823&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11823.I46a6d2886b7f8&page=11823&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.I46a6d2886b7f8-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.11823.I46a6d2886b7f8-->
Line 363: Line 509:
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:lip genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:lip genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:34, 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

lipB

Mnemonic

Lipoate

Synonyms

ECK0623, b0630, JW5089, lip, cde, cde4[1][2]

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

14.24 minutes 

MG1655: 661501..660860
<gbrowseImage> name=NC_000913:660860..661501 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 644861..644220
<gbrowseImage> name=NC_012967:644220..644861 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 563620..564261
<gbrowseImage> name=NC_012759:563620..564261 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 662700..662059
<gbrowseImage> name=NC_007779:662059..662700 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 600833..600192
<gbrowseImage> name=NC_010473:600192..600833 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 714093..713452
<gbrowseImage> name=NC_010473:713452..714093 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
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

lipB(del) (Keio:JW5089)

deletion

deletion

PMID:16738554[3]

Shigen

lipBC169S

C169S

Loss of activity

seeded from UniProt:P60720

lipBC169A

C169A

1% of wild-type activity

seeded from UniProt:P60720

lipBC137A

C137A

No effect on activity

seeded from UniProt:P60720

lipBC147A

C147A

No effect on activity

seeded from UniProt:P60720

CAG45114 lipB769(del)::FRTKanFRT

Deletion

SigmaE activity

Decrease in sigmaE activity

PMID:23224554[4]

Parental Strain: CAG45114 Experimental Strain: SMR15295

See table S11 for full experimental calculations

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

JW5089

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTATCAGGATAAAATTCTTGT

Primer 2:CCAGCGGTAATATATTCGAAGTC

1G6

Kohara Phage

Genobase

PMID:3038334[6]

crcA280::Tn10

Linked marker

CAG12077 = CGSC7347[7]

est. P1 cotransduction: 80% [8]
Synonyms:zbe-280::Tn10

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[7]

est. P1 cotransduction: 19% [8]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

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:EG11591

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11591

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001540

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945217

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1549

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002160

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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. ↑ Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  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. ↑ 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 CGSC: The Coli Genetics Stock Center
  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).

Categories

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=lipB:Gene&oldid=1477256"