sufB: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="D46a9cc78de0a4"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''sufB''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''sufB''
Sulfur
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1679, b1683, JW5273, ynhE''<ref name='LIB:Riley_2006'/>, ynhE''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13933.D46a9cc78de0a4&page=13933&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK1679, b1683, JW5273, ynhE''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='135000'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9cc79651f5"  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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37.95 minutes&nbsp;
37.95 minutes&nbsp;
|
|
MG1655: 1762033..1760546<br />{{GBrowseFigureByCoord|1759546|1763033|ecoli|MG1655}}
MG1655: 1762033..1760546<br /><gbrowseImage>
name=NC_000913:1760546..1762033
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6909 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6909 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1759546..1763033 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1759546|1763033|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1760546..1762033&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1760546|1762033|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6909 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6909 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1741276..1739789<br /><gbrowseImage>
name=NC_012967:1739789..1741276
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1739789|1741276|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1739789|1741276|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 1652605..1654092<br /><gbrowseImage>
name=NC_012759:1652605..1654092
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1652605|1654092|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1652605|1654092|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1765723..1764236<br />{{GBrowseFigureByCoord|1763236|1766723|ecoli_W3110|W3110}}  
W3110: 1765723..1764236<br /><gbrowseImage>
name=NC_007779:1764236..1765723
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1763236|1766723|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1764236|1765723|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 1852604..1851117<br /><gbrowseImage>
name=NC_010473:1851117..1852604
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1763236..1766723 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|1848143|1855578|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1764236..1765723&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|1848143|1855578|FASTA Dump}}
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='135001'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9cc7a16882"  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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====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="B46a9cc7a59b79"  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
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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=109566 CGSC11285]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109566 CGSC11285]<ref name='LIB:cgsc'/>  
|
|-
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&Delta;ynhE::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-D-Glucose-1-phosphate]]
|
PMID:16095938
|
|
|-
|
&Delta;ynhE::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-D-Glucose-6-phosphate]]
|
PMID:16095938
|
|
|-
|
&Delta;ynhE::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketobutyrate]]
|
PMID:16095938
|
|
|
   
   
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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:103058|CGSC:103058]]
[[cgscmutation:103058|CGSC:103058]]
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13933.B46a9cc7a59b79&page=13933&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13933.C4e04c44985905-->
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|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW5273
JW5273
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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:CCTCCGACGCTGTGTTCAAGACT  
Primer 2:CCTCCGACGCTGTGTTCAAGACT  
|-
|-
|
[[:Category:Kohara_Phage:15G10|15G10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=320 Genobase]
|
PMID:3038334
|-  
|
|
[[yddE:Gene|zdd-235::Tn10]]
[[yddE:Gene|zdd-235::Tn10]]
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CAG18461 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39848 CGSC7378]<ref name='LIB:cgsc'/>
CAG18461 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39848 CGSC7378]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zdc-235::Tn10  
Synonyms:zdc-235::Tn10  
|-
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|
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zdi-925::Tn10
zdi-925::Tn10
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CAG12151 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39862 CGSC7385]<ref name='LIB:cgsc'/>
CAG12151 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39862 CGSC7385]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 56% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 56% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zdh-925::Tn10


Synonyms:zdh-925::Tn10
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===Notes===
===Notes===
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6909 EcoCyc:G6909]
EcoCyc:G6909
|
|
''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=EB3723 EchoBASE:EB3723]
EcoGene:EG13965
|
|
''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=b1683 EcoliGenExpDB:b1683]
RegulonDB:ECK120003498
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C2078 ECOL199310CYC:C2078]
|
|-  
|-  
|
|
[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=EG13965 EcoGene:EG13965]
[http://www.ncbi.nlm.nih.gov/gene?term=945753 GeneID:945753]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YNHE ECOO157CYC:YNHE]
EchoBASE:EB3723
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0005621&formSubmitReturn=1 ASAP:ABE-0005621] 
ASAP:ABE-0005621
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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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:suf genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:38, 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

sufB

Mnemonic

Sulfur

Synonyms

ECK1679, b1683, JW5273, ynhE[1], ynhE

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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

37.95 minutes 

MG1655: 1762033..1760546
<gbrowseImage> name=NC_000913:1760546..1762033 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1741276..1739789
<gbrowseImage> name=NC_012967:1739789..1741276 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1652605..1654092
<gbrowseImage> name=NC_012759:1652605..1654092 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1765723..1764236
<gbrowseImage> name=NC_007779:1764236..1765723 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1852604..1851117
<gbrowseImage> name=NC_010473:1851117..1852604 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
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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

ΔsufB (Keio:JW5273)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11285[3]

ΔynhE::kan

deletion

Biolog:respiration

unable to respire a-D-Glucose-1-phosphate

PMID:16095938[4]

ΔynhE::kan

deletion

Biolog:respiration

unable to respire a-D-Glucose-6-phosphate

PMID:16095938[4]

ΔynhE::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[4]

ΔsufB758::kan

PMID:16738554[2]

CGSC:103058


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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

JW5273

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTCTCGTAATACTGAAGCAAC

Primer 2:CCTCCGACGCTGTGTTCAAGACT

15G10

Kohara Phage

Genobase

PMID:3038334[6]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[3]

est. P1 cotransduction: % [7]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[3]

est. P1 cotransduction: 56% [7]
Synonyms:zdh-925::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:G6909

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13965

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003498

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945753

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3723

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005621

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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 4.2 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 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 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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