fbaB:Gene: Difference between revisions

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|{{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]]
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{|{{Prettytable}}
{|   id="I46a9d5f4818b2"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''fbaB''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''fbaB''
Fructose bis-P aldolase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2090, b2097, JW5344, dhnA''<ref name='LIB:Riley_2006'/>, dhnA''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14755.I46a9d5f4818b2&page=14755&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2090, b2097, JW5344, dhnA''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='137461'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46a9d5f50a2d6"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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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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MG1655
MG1655
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46.89 minutes&nbsp;
46.89 minutes&nbsp;
|
|
MG1655: 2176586..2175534<br />{{GBrowseFigureByCoord|2174534|2177586|ecoli|MG1655}}
MG1655: 2176586..2175534<br /><gbrowseImage>
name=NC_000913:2175534..2176586
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7129 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7129 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2174534|2177586|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2174534|2177586|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2175534..2176586&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2175534|2176586|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7129 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7129 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2132693..2131641<br /><gbrowseImage>
name=NC_012967:2131641..2132693
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2131641|2132693|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2131641|2132693|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2068017..2069069<br /><gbrowseImage>
name=NC_012759:2068017..2069069
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2068017|2069069|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2068017|2069069|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2181898..2180846<br />{{GBrowseFigureByCoord|2179846|2182898|ecoli_W3110|W3110}}  
W3110: 2181898..2180846<br /><gbrowseImage>
name=NC_007779:2180846..2181898
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2179846|2182898|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|2180846|2181898|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 2267594..2266542<br /><gbrowseImage>
name=NC_010473:2266542..2267594
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2179846..2182898 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|2264438|2269698|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2180846..2181898&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|2264438|2269698|FASTA Dump}}
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|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14755.A46a9d5f50a2d6&page=14755&pagename={{FULLPAGENAMEE}} edit table] || || || ||
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='137462'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a9d5f5b3a64"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
2175537
|
Edman degradation
|
PMID:9531482<br />
|
 
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====Notes====
====Notes====
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{|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="C46a9d5f604075"  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
|-
|
fbaBK237A
|
|
K237A
|
|
Loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A991 UniProt:P0A991]
|-
|
fbaBK239A
|
|
K239A
|
|
No change in activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A991 UniProt:P0A991]
|-  
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109611 CGSC11330]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109611 CGSC11330]<ref name='LIB:cgsc'/>  
Line 162: Line 273:


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:100790|CGSC:100790]]
[[cgscmutation:100790|CGSC:100790]]
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14755.C46a9d5f604075&page=14755&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14755.O4e04babb994cd-->
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|- {{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.14755.O4e04babb994cd&page=14755&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW5344
JW5344
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[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]
|
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCGGCGATAGTAATTTTGCTATC  
Primer 2:CCGGCGATAGTAATTTTGCTATC  
|-
|-
|
[[:Category:Kohara_Phage:8F4|8F4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=359 Genobase]
|
PMID:3038334
|-  
|
|
zef-3129::Tn10
zef-3129::Tn10
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CAG12099 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39996 CGSC7397]<ref name='LIB:cgsc'/>
CAG12099 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39996 CGSC7397]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zee-3129::Tn10  
Synonyms:zee-3129::Tn10  
|-
|-  
|
|
[[gatY:Gene|zbd-3104::Tn10]]
[[gatY:Gene|zbd-3104::Tn10]]
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CAG12021 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39386 CGSC7344]<ref name='LIB:cgsc'/>
CAG12021 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39386 CGSC7344]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 98% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 98% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10


Synonyms:zbc-3105::Tn10, zbd-3105::Tn10
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===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9d5f74bbb0"  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=G7129 EcoCyc:G7129]
EcoCyc:G7129
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''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=EB3815 EchoBASE:EB3815]
EcoGene:EG14062
|
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''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=b2097 EcoliGenExpDB:b2097]
RegulonDB:ECK120003712
|
|
''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=C2623 ECOL199310CYC:C2623]
[http://www.ncbi.nlm.nih.gov/gene?term=946632 GeneID:946632]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14062 EcoGene:EG14062]
EchoBASE:EB3815
|
|
''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=Z3260 ECOO157CYC:Z3260]
ASAP:ABE-0006941
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0006941&formSubmitReturn=1 ASAP:ABE-0006941] 
|


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===Notes===
===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:fba genes]]
[[Category:fba genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:40, 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

fbaB

Mnemonic

Fructose bis-P aldolase

Synonyms

ECK2090, b2097, JW5344, dhnA[1], dhnA

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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

46.89 minutes 

MG1655: 2176586..2175534
<gbrowseImage> name=NC_000913:2175534..2176586 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2132693..2131641
<gbrowseImage> name=NC_012967:2131641..2132693 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2068017..2069069
<gbrowseImage> name=NC_012759:2068017..2069069 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2181898..2180846
<gbrowseImage> name=NC_007779:2180846..2181898 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2267594..2266542
<gbrowseImage> name=NC_010473:2266542..2267594 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

2175537

Edman degradation

PMID:9531482[2]


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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

fbaBK237A

K237A

Loss of activity

seeded from UniProt:P0A991

fbaBK239A

K239A

No change in activity

seeded from UniProt:P0A991

ΔfbaB (Keio:JW5344)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC11330[4]

ΔfbaB722::kan

PMID:16738554[3]

CGSC:100790


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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

JW5344

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCACAGATATTGCGCAGTTGCT

Primer 2:CCGGCGATAGTAATTTTGCTATC

8F4

Kohara Phage

Genobase

PMID:3038334[6]

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[4]

est. P1 cotransduction: % [7]
Synonyms:zee-3129::Tn10

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[4]

est. P1 cotransduction: 98% [7]
Synonyms:zbc-3105::Tn10, zbd-3105::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:G7129

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14062

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003712

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946632

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3815

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006941

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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. ↑ Thomson, GJ et al. (1998) The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase. Biochem. J. 331 ( Pt 2) 437-45 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. ↑ 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

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