proC: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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*  
*  
****************************************************************************************** -->{{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="G46a9aece2acb8" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''proC''  
''proC''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Proline
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK0381, b0386, JW0377, pro2, pro3, pro(3)''<ref name='LIB:Riley_2006'/>
''ECK0381, b0386, JW0377, pro2, pro3, pro(3)''<ref name='LIB:Riley_2006'/>, pro, Pro2''


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*  
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****************************************************************************************** -->{{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="R46a9aeced71da"  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
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8.71 minutes&nbsp;
8.71 minutes&nbsp;
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MG1655: 404868..404059<br />{{GBrowseFigureByCoord|403059|405868|ecoli|MG1655}}
MG1655: 404868..404059<br /><gbrowseImage>
name=NC_000913:404059..404868
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10769 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10769 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|403059|405868|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|403059|405868|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|404059|404868|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|404059|404868|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10769 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10769 EcoCyc Sequence Dump]  
|-
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[[REL606]]
|
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NC_012967: 373290..372481<br /><gbrowseImage>
name=NC_012967:372481..373290
source=REL606
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|REL606|NC_012967|372481|373290|GBrowse (REL606)}}
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[[BW2952]]
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NC_012759: 306818..307627<br /><gbrowseImage>
name=NC_012759:306818..307627
source=BW2952
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|BW2952|NC_012759|306818|307627|GBrowse (BW2952)}}
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&nbsp;
&nbsp;
|
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W3110: 404868..404059<br />{{GBrowseFigureByCoord|403059|405868|ecoli_W3110|W3110}}  
W3110: 404868..404059<br /><gbrowseImage>
name=NC_007779:404059..404868
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|403059|405868|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|404059|404868|FASTA Dump}}  
|-
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[[DH10B]]
|
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{{GBrowseLink|ecoli_W3110|AC_000091|403059|405868|GBrowse(W3110)}}
 
|
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|404059|404868|FASTA Dump}}
DH10B: 344199..343390<br /><gbrowseImage>
name=NC_010473:343390..344199
source=DH10B
preset=GeneLocation
</gbrowseImage>


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*  
*  
****************************************************************************************** -->{{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="T46a9aecfc5a25"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
404059
|
Edman degradation
|
PMID:6089111<br />
|


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*  
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****************************************************************************************** -->{{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="C46a9aed0427d8"  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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&Delta;proC (Keio:JW0377)
ΔproC (Keio:JW0377)
|
|
deletion
deletion
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deletion
deletion
|
|
 
Auxotrophies
|
Requires proline for growth
|
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]


|[[PMID:16738554]]<ref name=PMID:16738554/>
[http://cgsc2.biology.yale.edu/Strain.php?ID=106835 CGSC8554]<ref name='LIB:cgsc'/>  
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106835 CGSC8554]<ref name='LIB:cgsc'/>  
|
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Auxotrophies
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Requires proline for growth
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Requires proline for growth
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Requires proline for growth
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Requires proline for growth
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Auxotrophies
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Requires proline for growth
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Auxotrophies
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Requires proline for growth
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Auxotrophies
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Requires proline for growth
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Auxotrophies
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Requires proline for growth
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Auxotrophies
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Requires proline for growth
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Auxotrophies
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Requires proline for growth
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|-  
|-  
|
|
''&#916;proC751::kan''
''ΔproC751::kan''
|
deletion
|
|
 
deletion
|
|
 
Auxotrophies
|
|
 
Requires proline for growth
|
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PMID:16738554
|[[PMID:16738554]]<ref name=PMID:16738554/>
|
|
[[cgscmutation:102470|CGSC:102470]]
[[cgscmutation:102470|CGSC:102470]]
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11339.L4e04c181c19dd-->
<!--
******************************************************************************************
*
*  ** 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="L4e04c181c19dd"  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.11339.L4e04c181c19dd&page=11339&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11339.L4e04c181c19dd--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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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:CCGGATTTGCTGAGTTTTTCTGA  
Primer 2:CCGGATTTGCTGAGTTTTTCTGA  
|-
|
[[:Category:Kohara_Phage:1A10|1A10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=142 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6A12|6A12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=143 Genobase]
|
PMID:3038334
|-  
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est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>  


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*  
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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;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9aed232fbb"  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=EG10769 EcoCyc:EG10769]
EcoCyc:EG10769
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0762 EchoBASE:EB0762]
EcoGene:EG10769
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0386 EcoliGenExpDB:b0386]
RegulonDB:ECK120000760
|
|
''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=C0493 ECOL199310CYC:C0493]
[http://www.ncbi.nlm.nih.gov/gene?term=945034 GeneID:945034]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10769 EcoGene:EG10769]
EchoBASE:EB0762
|
|
''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=PROC ECOO157CYC:PROC]
|
|
ASAP:ABE-0001338
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/362 CGSC:362]
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0001338&formSubmitReturn=1 ASAP:ABE-0001338]
|


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!|Name!!URL!!Comments
!|Name!!URL!!Comments


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===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:pro genes]]
[[Category:pro genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:28, 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

proC

Mnemonic

Proline

Synonyms

ECK0381, b0386, JW0377, pro2, pro3, pro(3)[1], pro, Pro2

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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

8.71 minutes 

MG1655: 404868..404059
<gbrowseImage> name=NC_000913:404059..404868 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 373290..372481
<gbrowseImage> name=NC_012967:372481..373290 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 306818..307627
<gbrowseImage> name=NC_012759:306818..307627 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 404868..404059
<gbrowseImage> name=NC_007779:404059..404868 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 344199..343390
<gbrowseImage> name=NC_010473:343390..344199 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

404059

Edman degradation

PMID:6089111[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

ΔproC (Keio:JW0377)

deletion

deletion

Auxotrophies

Requires proline for growth

PMID:16738554[3]

Shigen

CGSC8554[4]

proC14

Auxotrophies

Requires proline for growth

CGSC:4929

proC32

Auxotrophies

Requires proline for growth

CGSC:5085

proC47

Auxotrophies

Requires proline for growth

CGSC:5514

proC34

Auxotrophies

Requires proline for growth

CGSC:5702

proC24

Auxotrophies

Requires proline for growth

CGSC:5825

proC55

Auxotrophies

Requires proline for growth

CGSC:6485

proC83

Auxotrophies

Requires proline for growth

CGSC:10340

proC43

Auxotrophies

Requires proline for growth

CGSC:11027

proC29

Auxotrophies

Requires proline for growth

CGSC:11502

proC9999

Auxotrophies

Requires proline for growth

CGSC:39363

proC677(tetR)::Tn5-132

Auxotrophies

Requires proline for growth

CGSC:75247

proC471::Tn5

Auxotrophies

Requires proline for growth

CGSC:90706

ΔproC751::kan

deletion

deletion

Auxotrophies

Requires proline for growth

PMID:16738554[3]

CGSC:102470


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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

JW0377

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGAAAAGAAAATCGGTTTTAT

Primer 2:CCGGATTTGCTGAGTTTTTCTGA

1A10

Kohara Phage

Genobase

PMID:3038334[6]

6A12

Kohara Phage

Genobase

PMID:3038334[6]

zai-3053::Tn10

Linked marker

CAG18091 = CGSC7336[4]

est. P1 cotransduction: 72% [7]
Synonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).

tsx-247::Tn10

Linked marker

CAG12148 = CGSC7337[4]

est. P1 cotransduction: 35% [7]

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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:EG10769

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10769

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000760

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945034

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0762

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001338

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. ↑ Deutch, AH et al. (1984) Analysis of the Escherichia coli proBA locus by DNA and protein sequencing. Nucleic Acids Res. 12 6337-55 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. ↑ 6.0 6.1 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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