ompT: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}}
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{|   id="J46a9b395bf746" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''ompT''  
''ompT''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Outer membrane protein
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK0557, b0565, JW0554''<ref name='LIB:Riley_2006'/>
''ECK0557, b0565, JW0554''<ref name='LIB:Riley_2006'/>, JW0554''


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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="T46a9b39643165"  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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12.58 minutes&nbsp;
12.58 minutes&nbsp;
|
|
MG1655: 584856..583903<br />{{GBrowseFigureByCoord|583903|584856|ecoli|MG1655}}
MG1655: 584856..583903<br /><gbrowseImage>
name=NC_000913:583903..584856
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10673 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10673 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|582903|585856|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|582903|585856|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|583903|584856|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|583903|584856|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10673 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10673 EcoCyc Sequence Dump]  
|-  
|-  
|
|
W3110
[[REL606]]
|
|
&nbsp;
 
|
|
W3110: 584856..583903<br />{{GBrowseFigureByCoord|583903|584856|ecoli_W3110|W3110}}
NC_012967: 560984..560031<br /><gbrowseImage>
name=NC_012967:560031..560984
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|582903|585856|GBrowse(W3110)}}  
{{GBrowseLink|REL606|NC_012967|560031|560984|GBrowse (REL606)}}
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|583903|584856|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|560031|560984|FASTA Dump}}  
|-  
|-  
|
|
[[DH10B]]
[[BW2952]]
|
 
|
|
NC_012759: 486663..487616<br /><gbrowseImage>
name=NC_012759:486663..487616
source=BW2952
preset=GeneLocation
</gbrowseImage>


|
|
DH10B: 524188..523235<br />{{GBrowseFigureByCoord|523235|524188|ecoli_DH10B|DH10B}}
{{GBrowseLink|BW2952|NC_012759|486663|487616|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|486663|487616|FASTA Dump}}  
|-
|
W3110
|
&nbsp;
|
W3110: 584856..583903<br /><gbrowseImage>
name=NC_007779:583903..584856
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|521329|526094|GBrowse(DH10B)}}
{{GBrowseLink|W3110|NC_007779|582903|585856|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|521329|526094|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|583903|584856|FASTA Dump}}  
|-  
|-  
|
|
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|
|
DH10B: 637448..636495<br />{{GBrowseFigureByCoord|636495|637448|ecoli_DH10B|DH10B}}
DH10B: 524188..523235<br /><gbrowseImage>
name=NC_010473:523235..524188
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|634589|639354|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|521329|526094|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|634589|639354|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|521329|526094|FASTA Dump}}  
|-  
|-  
|
|
[[REL606]]
[[DH10B]]
|
|


|
|
NC_012967: 560031..560984<br />{{GBrowseFigureByCoord|560031|560984|REL606|NC_012967}}
DH10B: 637448..636495<br /><gbrowseImage>
name=NC_010473:636495..637448
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|560031|560984|GBrowse (REL606)}}
{{GBrowseLink|DH10B|NC_010473|634589|639354|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|REL606|NC_012967|560031|560984|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|634589|639354|FASTA Dump}}  


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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="R46a9b396df8ad"  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]]
|
583906
|
Edman degradation
|
PMID:3056908<br />PMID:3278297<br />PMID:9629924<br />
|


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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="D46a9b3972b50c"  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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|
|
   
   
|-
|
ompTD103A
|
|
D103A
|
|
Loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09169 UniProt:P09169]
|-
|
ompTD105A
|
|
D105A
|
|
Loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09169 UniProt:P09169]
|-
|
ompTD230A
|
|
D230A
|
|
Loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09169 UniProt:P09169]
|-
|
ompTGK236KG
|
|
GK236KG
|
|
70% of wild-type enzymatic activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09169 UniProt:P09169]
|-
|
ompTK237T
|
|
K237T
|
|
40% of wild-type enzymatic activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09169 UniProt:P09169]
|-
|
ompTR238L
|
|
R238L
|
|
Loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P09169 UniProt:P09169]
|-  
|-  
|
|
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deletion
deletion
|
|
 
|
|
lack ompT protease activity.  lack the ability to cleave between specific paired basic amino acids
lack ompT protease activity.  lack the ability to cleave between specific paired basic amino acids
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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****************************************************************************************** -->{{Gene_resources_help}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCAAATGTGTACTTAAGACCAGC  
Primer 2:CCAAATGTGTACTTAAGACCAGC  
|-
|
[[:Category:Kohara_Phage:23E10|23E10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=160 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12A1|12A1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=161 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:2F5|2F5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=162 Genobase]
|
PMID:3038334
|-  
|-  
|
|
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Synonyms:zbd-601::Tn10, zbe-601::Tn10  
Synonyms:zbd-601::Tn10, zbe-601::Tn10  


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*  
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****************************************************************************************** -->{{Gene_accessions_help}}
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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="H46a9b3985bbba"  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=EG10673 EcoCyc:EG10673]
EcoCyc:EG10673
|
|
''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=EB0667 EchoBASE:EB0667]
EcoGene:EG10673
|
|
''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=b0565 EcoliGenExpDB:b0565]
RegulonDB:ECK120000666
|
|
''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=C0652 ECOL199310CYC:C0652]
[http://www.ncbi.nlm.nih.gov/gene?term=945185 GeneID:945185]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10673 EcoGene:EG10673]
EchoBASE:EB0667
|
|
''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=Z1931 ECOO157CYC:Z1931]
ASAP:ABE-0001931
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/4984 CGSC:4984]
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0001931&formSubmitReturn=1 ASAP:ABE-0001931]
|


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[[Category:Gene List:DLP12 prophage]]
[[Category:Gene List:DLP12 prophage]]
[[Category:omp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:omp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 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

ompT

Mnemonic

Outer membrane protein

Synonyms

ECK0557, b0565, JW0554[1], JW0554

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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

12.58 minutes 

MG1655: 584856..583903
<gbrowseImage> name=NC_000913:583903..584856 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 560984..560031
<gbrowseImage> name=NC_012967:560031..560984 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 486663..487616
<gbrowseImage> name=NC_012759:486663..487616 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 584856..583903
<gbrowseImage> name=NC_007779:583903..584856 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 524188..523235
<gbrowseImage> name=NC_010473:523235..524188 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 637448..636495
<gbrowseImage> name=NC_010473:636495..637448 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

583906

Edman degradation

PMID:3056908[2]
PMID:3278297[3]
PMID:9629924[4]


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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

ΔompT (Keio:JW0554)

deletion

deletion

PMID:16738554[5]

Shigen
CGSC8680[6]

ompTD103A

D103A

Loss of activity

seeded from UniProt:P09169

ompTD105A

D105A

Loss of activity

seeded from UniProt:P09169

ompTD230A

D230A

Loss of activity

seeded from UniProt:P09169

ompTGK236KG

GK236KG

70% of wild-type enzymatic activity

seeded from UniProt:P09169

ompTK237T

K237T

40% of wild-type enzymatic activity

seeded from UniProt:P09169

ompTR238L

R238L

Loss of activity

seeded from UniProt:P09169

ΔompT

deletion

deletion

lack ompT protease activity. lack the ability to cleave between specific paired basic amino acids

PMID:17880914[7]

ΔompT504

CGSC:28510

ompT1000::kan

CGSC:30156

ΔompT774::kan

PMID:16738554[5]

CGSC:102186


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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

JW0554

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCCGGGCGAAACTTCTGGGAAT

Primer 2:CCAAATGTGTACTTAAGACCAGC

23E10

Kohara Phage

Genobase

PMID:3038334[9]

12A1

Kohara Phage

Genobase

PMID:3038334[9]

2F5

Kohara Phage

Genobase

PMID:3038334[9]

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[6]

est. P1 cotransduction: 28% [10]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[6]

est. P1 cotransduction: 9% [10]
Synonyms:zbd-601::Tn10, zbe-601::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:EG10673

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10673

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000666

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945185

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0667

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001931

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. ↑ Sugimura, K & Nishihara, T (1988) Purification, characterization, and primary structure of Escherichia coli protease VII with specificity for paired basic residues: identity of protease VII and OmpT. J. Bacteriol. 170 5625-32 PubMed
  3. ↑ Grodberg, J et al. (1988) Complete nucleotide sequence and deduced amino acid sequence of the ompT gene of Escherichia coli K-12. Nucleic Acids Res. 16 1209 PubMed
  4. ↑ Molloy, MP et al. (1998) Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis 19 837-44 PubMed
  5. ↑ 5.0 5.1 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
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ Bishop, RE (2008) Structural biology of membrane-intrinsic beta-barrel enzymes: sentinels of the bacterial outer membrane. Biochim. Biophys. Acta 1778 1881-96 PubMed
  8. ↑ 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
  9. ↑ 9.0 9.1 9.2 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
  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).

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