degP: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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{| id="J46a9a9ce2d307"  class=" tableEdit Gene_nomenclature_table"   
{|   id="J46a9a9ce2d307"  class=" tableEdit Gene_nomenclature_table"   


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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK0160, b0161, JW0157, htrA, ptd''<ref name='LIB:Riley_2006'/>
''ECK0160, b0161, JW0157, htrA, ptd''<ref name='LIB:Riley_2006'/>, ptd''


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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="V46a9a9cea659c"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9a9cea659c"  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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3.9 minutes&nbsp;
3.9 minutes&nbsp;
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|
MG1655: 180884..182308<br />{{GBrowseFigureByCoord|180884|182308|ecoli|MG1655}}
MG1655: 180884..182308<br /><gbrowseImage>
name=NC_000913:180884..182308
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10463 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10463 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|179884|183308|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|179884|183308|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|180884|182308|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|180884|182308|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10463 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10463 EcoCyc Sequence Dump]  
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NC_012967: 183726..185150<br />{{GBrowseFigureByCoord|183726|185150|REL606|NC_012967}}
NC_012967: 183726..185150<br /><gbrowseImage>
name=NC_012967:183726..185150
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|183726|185150|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|183726|185150|GBrowse (REL606)}}
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NC_012759: 180883..182307<br />{{GBrowseFigureByCoord|180883|182307|BW2952|NC_012759}}
NC_012759: 180883..182307<br /><gbrowseImage>
name=NC_012759:180883..182307
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|BW2952|012759|180883|NC_182307|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|180883|182307|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|180883|NC_182307|FASTA Dump}}  
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&nbsp;
&nbsp;
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W3110: 180884..182308<br />{{GBrowseFigureByCoord|180884|182308|ecoli_W3110|W3110}}
W3110: 180884..182308<br /><gbrowseImage>
name=NC_007779:180884..182308
source=W3110
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|179884|183308|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|179884|183308|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|180884|182308|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|180884|182308|FASTA Dump}}  
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DH10B: 154988..156412<br />{{GBrowseFigureByCoord|154988|156412|ecoli_DH10B|DH10B}}
DH10B: 154988..156412<br /><gbrowseImage>
name=NC_010473:154988..156412
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_DH10B|NC_010473|152140|159260|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|152140|159260|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|152140|159260|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|152140|159260|FASTA Dump}}  


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*  
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|   id="G46a9a9cf4f327"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a9a9cf4f327"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
180962
|
Edman degradation
|
PMID:2180903<br />PMID:9600841<br />
|


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{| {{Prettytable}} id="S46a9a9cf8fd2b"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="S46a9a9cf8fd2b"  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;degP (Keio:JW0157)
''degP(del)'' (Keio:JW0157)
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deletion
deletion
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PMID:16738554
PMID:16738554
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106705 CGSC8424]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106705 CGSC8424]<ref name='LIB:cgsc'/>  
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&Delta;htrA::kan
''htrA(del)''::kan
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deletion
deletion
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''degP41(&#916;(PstI))::kan''
''degP41(del(PstI))::kan''
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''&#916;degP775::kan''
''degP775(del)::kan''
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[[cgscmutation:100570|CGSC:100570]]
[[cgscmutation:100570|CGSC:100570]]
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degP
|
deletion
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Sensitivity to
|
increases sensitivity to bicyclomycin
|
PMID:21357484
|
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fig 2
|-
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degP4::Tn5
|
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Growth Phenotype
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at 37 and 42 C colonies are smaller; has pleiotropic effects and reduces six unstable periplasmic or inner membrane proteins' degradation
|
PMID:3278319
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|
|
   
   
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.10897.T4e04b9b418481-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T4e04b9b418481"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{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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{|   id="T46a9a9d03857f"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9a9d03857f"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCCTGCATTAACAGGTAGATGGT  
Primer 2:CCCTGCATTAACAGGTAGATGGT  
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[[:Category:Kohara_Phage:9H2|9H2]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=117 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:4E4|4E4]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=118 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:21C8|21C8]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=119 Genobase]
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PMID:3038334
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{|   id="A46a9a9d0c2297"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46a9a9d0c2297"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10463 EcoCyc:EG10463]
EcoCyc:EG10463
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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]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0458 EchoBASE:EB0458]
EcoGene:EG10463
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0161 EcoliGenExpDB:b0161]
[http://www.ncbi.nlm.nih.gov/gene?term=947139 GeneID:947139]
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Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C0197 ECOL199310CYC:C0197]
RegulonDB:ECK120000456
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10463 EcoGene:EG10463]
EchoBASE:EB0458
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=HTRA ECOO157CYC:HTRA]
ASAP:ABE-0000551
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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]])
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/30554 CGSC:30554]
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|-
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000551&formSubmitReturn=1 ASAP:ABE-0000551]
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a677093b9e0"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
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Latest revision as of 20:19, 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

degP

Mnemonic

Degradative protease

Synonyms

ECK0160, b0161, JW0157, htrA, ptd[1], ptd

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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

3.9 minutes 

MG1655: 180884..182308
<gbrowseImage> name=NC_000913:180884..182308 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 183726..185150
<gbrowseImage> name=NC_012967:183726..185150 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 180883..182307
<gbrowseImage> name=NC_012759:180883..182307 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 180884..182308
<gbrowseImage> name=NC_007779:180884..182308 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 154988..156412
<gbrowseImage> name=NC_010473:154988..156412 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


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

180962

Edman degradation

PMID:2180903[2]
PMID:9600841[3]


edit table


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

degP(del) (Keio:JW0157)

deletion

deletion

PMID:16738554[4]

Shigen

CGSC8424[5]

htrA(del)::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[6]

degP41(del(PstI))::kan

CGSC:92707

degP775(del)::kan

PMID:16738554[4]

CGSC:100570

degP

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[7]

fig 2

degP4::Tn5

Growth Phenotype

at 37 and 42 C colonies are smaller; has pleiotropic effects and reduces six unstable periplasmic or inner membrane proteins' degradation

PMID:3278319[8]


edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0157

Plasmid clone

Shigen

PMID:16769691[9]

Status:Clone OK

Primer 1:GCCAAAAAAACCACATTAGCACT

Primer 2:CCCTGCATTAACAGGTAGATGGT

9H2

Kohara Phage

Genobase

PMID:3038334[10]

4E4

Kohara Phage

Genobase

PMID:3038334[10]

21C8

Kohara Phage

Genobase

PMID:3038334[10]

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[5]

est. P1 cotransduction: 28% [11]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[5]

est. P1 cotransduction: 9% [11]
Synonyms:zae-502::Tn10

edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10463

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10463

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947139

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000456

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0458

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000551

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

[back to top]



<protect>

References

[back to top]


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. ↑ Lipinska, B et al. (1990) The HtrA (DegP) protein, essential for Escherichia coli survival at high temperatures, is an endopeptidase. J. Bacteriol. 172 1791-7 PubMed
  3. ↑ Wilkins, MR et al. (1998) Protein identification with N and C-terminal sequence tags in proteome projects. J. Mol. Biol. 278 599-608 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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
  7. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  8. ↑ Strauch, KL & Beckwith, J (1988) An Escherichia coli mutation preventing degradation of abnormal periplasmic proteins. Proc. Natl. Acad. Sci. U.S.A. 85 1576-80 PubMed
  9. ↑ 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
  10. ↑ 10.0 10.1 10.2 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
  11. ↑ 11.0 11.1 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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