secY:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|secY}}{{Tab On|Gene|secY}}{{Tab|Gene Product(s)|secY}}{{Tab|Expression|secY}}{{Tab|Evolution|secY}}{{Tab|On One Page|secY}}{{TabsBottom}}
{{Tab|Quickview|secY}}{{Tab On|Gene|secY}}{{Tab|Gene Product(s)|secY}}{{Tab|Expression|secY}}{{Tab|Evolution|secY}}{{Tab|On One Page|secY}}{{TabsBottom}}
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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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</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''secY''  
''secY''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Secretory
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3287, b3300, JW3262, prlA''<ref name='LIB:Riley_2006'/>, prlA''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17149.D46a9f27a0ab33&page=17149&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3287, b3300, JW3262, prlA''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a9f27a8b20f"  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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74.16 minutes&nbsp;
74.16 minutes&nbsp;
|
|
MG1655: 3442119..3440788<br />{{GBrowseFigureByCoord|3439788|3443119|ecoli|MG1655}}
MG1655: 3442119..3440788<br /><gbrowseImage>
name=NC_000913:3440788..3442119
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10766 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10766 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3439788..3443119 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3439788|3443119|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3440788..3442119&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3440788|3442119|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10766 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10766 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3370671..3372002<br /><gbrowseImage>
name=NC_012967:3370671..3372002
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3370671|3372002|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3370671|3372002|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 3327945..3329276<br /><gbrowseImage>
name=NC_012759:3327945..3329276
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3327945|3329276|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3327945|3329276|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 4196319..4197650<br />{{GBrowseFigureByCoord|4195319|4198650|ecoli_W3110|W3110}}
W3110: 4196319..4197650<br /><gbrowseImage>
name=NC_007779:4196319..4197650
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4195319..4198650 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|4195319|4198650|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4196319..4197650&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|4196319|4197650|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 3539864..3538533<br /><gbrowseImage>
name=NC_010473:3538533..3539864
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3535871|3542526|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3535871|3542526|FASTA Dump}}
 
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a9f27b4cf1b"  class=" tableEdit Gene_sequence_features_table" 
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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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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9f27b9688f"  class=" tableEdit Gene_allele_table dataTable" 
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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secYI290T
|
 
|
I290T
|
 
|
In secY121; alterated signal sequence interaction
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AGA2 UniProt:P0AGA2]
|-
|
secYP40S
|
 
|
P40S
|
 
|
In secY100; temperature-sensitive
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AGA2 UniProt:P0AGA2]
|-
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secYR357H
|
 
|
R357H
|
 
|
In secY39; cold-sensitive
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AGA2 UniProt:P0AGA2]
|-
|
secYF67C
|
 
|
F67C
|
 
|
In prlA3; alterated signal sequence interaction
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AGA2 UniProt:P0AGA2]
|-
|
secYG167E
|
 
|
G167E
|
 
|
In secY100; temperature-sensitive
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AGA2 UniProt:P0AGA2]
|-
|
secYG240D
|
 
|
G240D
|
 
|
In secY24; temperature-sensitive
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AGA2 UniProt:P0AGA2]
|-
|
secYS282R
|
 
|
S282R
|
 
|
In prlA401; alterated signal sequence interaction
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AGA2 UniProt:P0AGA2]
|-
|
secYF286Y
|
 
|
F286Y
|
 
|
In prlA4-1; alterated signal sequence interaction
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AGA2 UniProt:P0AGA2]
|-
|
secYP287L
|
 
|
P287L
|
 
|
In secY161; alterated signal sequence interaction
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AGA2 UniProt:P0AGA2]
|-
|
secYA363S
|
 
|
A363S
|
 
|
In secY40; cold-sensitive
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AGA2 UniProt:P0AGA2]
|-
|
secYI408N
|
 
|
I408N
|
 
|
In prlA4-2; alterated signal sequence interaction
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0AGA2 UniProt:P0AGA2]
|-
|
secY*
|
 
|
 
|
 
|
 
|
 
|
 
|
|-
|
''secY24''(ts)
|
 
|
 
|
 
|
temperature sensitive
|
PMID:7665473 PMID:8650200
|
[[cgscmutation:19326|CGSC:19326]]
|
|-
|
secY125
|
 
|
 
|
Growth Phenotype
|
cold-sensitive
|
PMID:10852867
PMID:8190079
 
|
 
|
|-
|
secY215 (ts)
|
 
|
 
|
Growth Phenotype
|
growth stops at 42C and sensitivity to temperature becomes more pronounced with increase in salt concentration
|
PMID:6339072
|
 
|
previously known as ts215
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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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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|
JW3262
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCGCTAAACAACCGGGATTAGA
 
Primer 2:CCTCGGCCGTAGCCTTTCAGGTT
|-
|
[[:Category:Kohara_Phage:E1H9|E1H9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=628 Genobase]
|
PMID:3038334
|-
|
[[smg:Gene|smg-3082::Tn10]]
|
Linked marker
|
CAG12071 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40240 CGSC7444]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 66% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10
|-
|
[[yhfT:Gene|zhf-3084::Tn10]]
|
Linked marker
|
CAG18456 = [http://cgsc2.biology.yale.edu/Strain.php?ID=61450 CGSC7576]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 4% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10766 EcoCyc:EG10766] 
|
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0759 EchoBASE:EB0759] 
EcoCyc:EG10766
|
|
''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=b3300 EcoliGenExpDB:b3300] 
EcoGene:EG10766
|
|
''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=C4061 ECOL199310CYC:C4061] 
RegulonDB:ECK120000757
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG10766 EcoGene:EG10766]
[http://www.ncbi.nlm.nih.gov/gene?term=947799 GeneID:947799]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=PRLA ECOO157CYC:PRLA] 
EchoBASE:EB0759
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/18037 CGSC:18037] 
ASAP:ABE-0010814
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout 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 20:47, 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

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

secY

Mnemonic

Secretory

Synonyms

ECK3287, b3300, JW3262, prlA[1], prlA

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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

74.16 minutes 

MG1655: 3442119..3440788
<gbrowseImage> name=NC_000913:3440788..3442119 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3370671..3372002
<gbrowseImage> name=NC_012967:3370671..3372002 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3327945..3329276
<gbrowseImage> name=NC_012759:3327945..3329276 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4196319..4197650
<gbrowseImage> name=NC_007779:4196319..4197650 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3539864..3538533
<gbrowseImage> name=NC_010473:3538533..3539864 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

secYI290T

I290T

In secY121; alterated signal sequence interaction

seeded from UniProt:P0AGA2

secYP40S

P40S

In secY100; temperature-sensitive

seeded from UniProt:P0AGA2

secYR357H

R357H

In secY39; cold-sensitive

seeded from UniProt:P0AGA2

secYF67C

F67C

In prlA3; alterated signal sequence interaction

seeded from UniProt:P0AGA2

secYG167E

G167E

In secY100; temperature-sensitive

seeded from UniProt:P0AGA2

secYG240D

G240D

In secY24; temperature-sensitive

seeded from UniProt:P0AGA2

secYS282R

S282R

In prlA401; alterated signal sequence interaction

seeded from UniProt:P0AGA2

secYF286Y

F286Y

In prlA4-1; alterated signal sequence interaction

seeded from UniProt:P0AGA2

secYP287L

P287L

In secY161; alterated signal sequence interaction

seeded from UniProt:P0AGA2

secYA363S

A363S

In secY40; cold-sensitive

seeded from UniProt:P0AGA2

secYI408N

I408N

In prlA4-2; alterated signal sequence interaction

seeded from UniProt:P0AGA2

secY*

secY24(ts)

temperature sensitive

PMID:7665473[2] PMID:8650200[3]

CGSC:19326

secY125

Growth Phenotype

cold-sensitive

PMID:10852867[4] PMID:8190079[5]

secY215 (ts)

Growth Phenotype

growth stops at 42C and sensitivity to temperature becomes more pronounced with increase in salt concentration

PMID:6339072[6]

previously known as ts215

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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

JW3262

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCGCTAAACAACCGGGATTAGA

Primer 2:CCTCGGCCGTAGCCTTTCAGGTT

E1H9

Kohara Phage

Genobase

PMID:3038334[8]

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[9]

est. P1 cotransduction: 66% [10]
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[9]

est. P1 cotransduction: 4% [10]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

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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:EG10766

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10766

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000757

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947799

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0759

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010814

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. ↑ Danese, PN et al. (1995) Multicopy suppression of cold-sensitive sec mutations in Escherichia coli. J. Bacteriol. 177 4969-73 PubMed
  3. ↑ Nouwen, N et al. (1996) prlA suppressors in Escherichia coli relieve the proton electrochemical gradient dependency of translocation of wild-type precursors. Proc. Natl. Acad. Sci. U.S.A. 93 5953-7 PubMed
  4. ↑ Matsumoto, G et al. (2000) A mutation in secY that causes enhanced SecA insertion and impaired late functions in protein translocation. J. Bacteriol. 182 3377-82 PubMed
  5. ↑ Taura, T et al. (1994) Genetic analysis of SecY: additional export-defective mutations and factors affecting their phenotypes. Mol. Gen. Genet. 243 261-9 PubMed
  6. ↑ Ito, K et al. (1983) A temperature-sensitive mutant of E. coli exhibiting slow processing of exported proteins. Cell 32 789-97 PubMed
  7. ↑ 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
  8. ↑ 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
  9. ↑ 9.0 9.1 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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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