secA: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="T46a9a86e61eda"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''secA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''secA''
Secretory
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0099, b0098, JW0096, azi, pea, prlD''<ref name='LIB:Riley_2006'/>, prlD''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10775.T46a9a86e61eda&page=10775&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0099, b0098, JW0096, azi, pea, prlD''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='125523'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a9a86edad85"  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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2.33 minutes&nbsp;
2.33 minutes&nbsp;
|
|
MG1655: 108279..110984<br />{{GBrowseFigureByCoord|107279|111984|ecoli|MG1655}}
MG1655: 108279..110984<br /><gbrowseImage>
name=NC_000913:108279..110984
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10936 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10936 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:107279..111984 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|107279|111984|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:108279..110984&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|108279|110984|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10936 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10936 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 111083..113788<br /><gbrowseImage>
name=NC_012967:111083..113788
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|111083|113788|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|111083|113788|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 108278..110983<br /><gbrowseImage>
name=NC_012759:108278..110983
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|108278|110983|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|108278|110983|FASTA Dump}}
|-  
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|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 108279..110984<br />{{GBrowseFigureByCoord|107279|111984|ecoli_W3110|W3110}}
W3110: 108279..110984<br /><gbrowseImage>
name=NC_007779:108279..110984
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:107279..111984 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|107279|111984|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:108279..110984&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|108279|110984|FASTA Dump}}
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|
[[DH10B]]
|
 
|
DH10B: 82383..85088<br /><gbrowseImage>
name=NC_010473:82383..85088
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|76973|90498|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|76973|90498|FASTA Dump}}
 
|- class="tableEdit_footer"
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='125524'
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|- {{table_heading_style}}
|- {{table_heading_style}}
!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
|-
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Coding Start (SO:0000323)
|
[[MG1655]]
|
108279
|
Edman degradation
|
PMID:2841285<br />
|
 
|- class="tableEdit_footer"
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====Notes====
====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="X46a9a86fc341c"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!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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''secA207''(aziR)
|
 
|
 
|
 
|
azide resistant
|
 
|
[[cgscmutation:6430|CGSC:6430]]
|
|-
|
''secA206''(aziR)
|
 
|
 
|
 
|
azide resistant
|
 
|
[[cgscmutation:4928|CGSC:4928]]
|
|-
|
''secA214''(aziR)
|
 
|
 
|
 
|
azide resistant
|
 
|
[[cgscmutation:6432|CGSC:6432]]
|
|-
|
''secA215''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:6917|CGSC:6917]]
|
|-
|
''secA204''(aziR)
|
 
|
 
|
 
|
azide resistant
|
 
|
[[cgscmutation:8372|CGSC:8372]]
|
|-
|
''secA209''(aziR)
|
 
|
 
|
 
|
azide resistant
|
 
|
[[cgscmutation:8422|CGSC:8422]]
|
|-
|
''secA216''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:9825|CGSC:9825]]
|
|-
|
''secA201''(aziR)
|
 
|
 
|
 
|
azide resistant
|
 
|
[[cgscmutation:13121|CGSC:13121]]
|
|-
|
''secA202''(aziR)
|
 
|
 
|
 
|
azide resistant
|
 
|
[[cgscmutation:13339|CGSC:13339]]
|
|-
|
''secA203''(aziR)
|
 
|
 
|
 
|
azide resistant
|
 
|
[[cgscmutation:13341|CGSC:13341]]
|
|-
|
''secA205''(aziR)
|
 
|
 
|
 
|
azide resistant
|
 
|
|
&Delta;secA (Keio:)
[[cgscmutation:13953|CGSC:13953]]
|
|
deletion
|-
|
|
deletion
''secA51''(ts)
|
|


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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
 
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
temperature sensitive
|
PMID:7665473
|
[[cgscmutation:38546|CGSC:38546]]
|
|
   
   
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10775.X46a9a86fc341c&page=10775&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===
SecA mutants were first identified by Oliver and Beckwith<ref name='PMID:7026050'/> by looking for suppressors of the Lac<sup>-</sup> phenotype of a maE-lacZ fusion.  The original secA alleles were ts lethals.
==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.10775.I4e04c3a19cb72-->
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes


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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW0096
JW0096
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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]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTTGCAGGCGGCCATGGCACTG  
Primer 2:CCTTGCAGGCGGCCATGGCACTG  
|-
|-
|
[[:Category:Kohara_Phage:15B8|15B8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=111 Genobase]
|
PMID:3038334
|-  
|
|
leuO3051::Tn10
leuO3051::Tn10
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CAG12095 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37901 CGSC7324]<ref name='LIB:cgsc'/>
CAG12095 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37901 CGSC7324]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 39% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 39% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).  
Synonyms:zab-3051::Tn10  
|-  
 
 
The start of leuO was reannotated by Riley et al. (2006).  
|-
|
|
[[yadC:Gene|zad-220::Tn10]]
[[yadC:Gene|zad-220::Tn10]]
Line 209: Line 501:
|
|
est. P1 cotransduction: 18% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 18% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10936 EcoCyc:EG10936] 
|
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0929 EchoBASE:EB0929] 
EcoCyc:EG10936
|
|
''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=b0098 EcoliGenExpDB:b0098] 
EcoGene:EG10936
|
|
''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=C0116 ECOL199310CYC:C0116] 
RegulonDB:ECK120000925
|
|
''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=EG10936 EcoGene:EG10936]
[http://www.ncbi.nlm.nih.gov/gene?term=944821 GeneID:944821]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=SECA ECOO157CYC:SECA] 
EchoBASE:EB0929
|
|
''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/176 CGSC:176] 
ASAP:ABE-0000343
|
|
''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]]
[[Category:Gene List:W3110]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:sec genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:37, 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

secA

Mnemonic

Secretory

Synonyms

ECK0099, b0098, JW0096, azi, pea, prlD[1], prlD

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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

2.33 minutes 

MG1655: 108279..110984
<gbrowseImage> name=NC_000913:108279..110984 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 111083..113788
<gbrowseImage> name=NC_012967:111083..113788 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 108278..110983
<gbrowseImage> name=NC_012759:108278..110983 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 108279..110984
<gbrowseImage> name=NC_007779:108279..110984 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 82383..85088
<gbrowseImage> name=NC_010473:82383..85088 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

108279

Edman degradation

PMID:2841285[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

secA207(aziR)

azide resistant

CGSC:6430

secA206(aziR)

azide resistant

CGSC:4928

secA214(aziR)

azide resistant

CGSC:6432

secA215

CGSC:6917

secA204(aziR)

azide resistant

CGSC:8372

secA209(aziR)

azide resistant

CGSC:8422

secA216

CGSC:9825

secA201(aziR)

azide resistant

CGSC:13121

secA202(aziR)

azide resistant

CGSC:13339

secA203(aziR)

azide resistant

CGSC:13341

secA205(aziR)

azide resistant

CGSC:13953

secA51(ts)

temperature sensitive

PMID:7665473[3]

CGSC:38546


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Notes

SecA mutants were first identified by Oliver and Beckwith[4] by looking for suppressors of the Lac- phenotype of a maE-lacZ fusion. The original secA alleles were ts lethals.


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

JW0096

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCCTAATCAAATTGTTAACTAA

Primer 2:CCTTGCAGGCGGCCATGGCACTG

15B8

Kohara Phage

Genobase

PMID:3038334[6]

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[7]

est. P1 cotransduction: 39% [8]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[7]

est. P1 cotransduction: 18% [8]

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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:EG10936

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10936

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000925

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944821

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0929

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000343

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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. ↑ Schmidt, MG et al. (1988) Nucleotide sequence of the secA gene and secA(Ts) mutations preventing protein export in Escherichia coli. J. Bacteriol. 170 3404-14 PubMed
  3. ↑ Danese, PN et al. (1995) Multicopy suppression of cold-sensitive sec mutations in Escherichia coli. J. Bacteriol. 177 4969-73 PubMed
  4. ↑ Oliver, DB & Beckwith, J (1981) E. coli mutant pleiotropically defective in the export of secreted proteins. Cell 25 765-72 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

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