ompC:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK2207, b2215, JW2203, meoA, par''<ref name='LIB:Riley_2006'/>
''ECK2207, b2215, JW2203, meoA, par''<ref name='LIB:Riley_2006'/>, par''


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9d8ba8a830"  class=" tableEdit Gene_location_table"   
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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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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10670 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10670 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2308668|2311771|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2308668|2311771|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|2309668|2310771|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2309668|2310771|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10670 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10670 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|2195473|NC_2196576|GBrowse (BW2952)}}
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W3110: 2316083..2314980<br /><gbrowseImage>
W3110: 2316083..2314980<br /><gbrowseImage>
name=AC_000091:2314980..2316083
name=NC_007779:2314980..2316083
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|2313980|2317083|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2313980|2317083|GBrowse(W3110)}}  
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DH10B: 2401759..2400656<br /><gbrowseImage>
DH10B: 2401759..2400656<br /><gbrowseImage>
name=NC_010473:2400656..2401759
name=NC_010473:2400656..2401759
source=MG1655_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|ecoli_DH10B|NC_010473|2398450|2403965|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|2398450|2403965|GBrowse(DH10B)}}
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{|   id="Q46a9d8bb41357"  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="Q46a9d8bb41357"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="H46a9d8bb86487"  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="H46a9d8bb86487"  class=" tableEdit Gene_allele_table dataTable"   
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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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&Delta;ompC (Keio:JW2203)
''ompC(del)'' (Keio:JW2203)
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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=108062 CGSC9781]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=108062 CGSC9781]<ref name='LIB:cgsc'/>  
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''&#916;ompC768::kan''
''ompC768(del)''::kan
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[[cgscmutation:102176|CGSC:102176]]
[[cgscmutation:102176|CGSC:102176]]
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ompCp1
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protein expression
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OmpC protein synthesis is constitutive, less repression in ompCp1 than in wild-type
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PMID:7007334
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''ompC<sup>-</sup>''
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insertion
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Sensitivity to
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Decreased Sensitivity to Micromycin B17
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PMID:3543211
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See table 4 for full results. 
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''ompC'' in strain CE104
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Resistant to
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Resistant to Me1 phage.
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PMID:375003
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Experimental Strain: CE104
Parental Strain: PC0479
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{|   id="X4e04c07bd0d7e"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X4e04c07bd0d7e"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!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="C46a9d8bc3c666"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCGAACTGGTAAACCAGACCCAG  
Primer 2:CCGAACTGGTAAACCAGACCCAG  
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[[:Category:Kohara_Phage:22A6|22A6]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=373 Genobase]
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PMID:3038334
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{|   id="N46a9d8bcd062c"  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="N46a9d8bcd062c"  class=" tableEdit Gene_accessions_table"   
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!|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=EG10670 EcoCyc:EG10670]
EcoCyc:EG10670
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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=EB0664 EchoBASE:EB0664]
EcoGene:EG10670
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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]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b2215 EcoliGenExpDB:b2215]
RegulonDB:ECK120000663
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C2758 ECOL199310CYC:C2758]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG10670 EcoGene:EG10670]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=OMPC ECOO157CYC:OMPC]
[http://www.ncbi.nlm.nih.gov/gene?term=946716 GeneID:946716]
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Escherichia coli str. K-12 substr. MG1655
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/436 CGSC:436]
EchoBASE:EB0664
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0007321&formSubmitReturn=1 ASAP:ABE-0007321]
ASAP:ABE-0007321
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:41, 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

ompC

Mnemonic

Outer membrane protein

Synonyms

ECK2207, b2215, JW2203, meoA, par[1], par

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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

49.78 minutes, 49.78 minutes 

MG1655: 2310771..2309668
<gbrowseImage> name=NC_000913:2309668..2310771 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2262685..2261750
<gbrowseImage> name=NC_012967:2261750..2262685 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2195473..2196576
<gbrowseImage> name=NC_012759:2195473..2196576 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2316083..2314980
<gbrowseImage> name=NC_007779:2314980..2316083 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2401759..2400656
<gbrowseImage> name=NC_010473:2400656..2401759 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

2309671

Edman degradation

PMID:6297988[2]
PMID:9298646[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

ompC(del) (Keio:JW2203)

deletion

deletion

PMID:16738554[5]

Shigen
CGSC9781[6]

ompC::Tn5KAN-2 (FB20710)

Insertion at nt 469 in Plus orientation

PMID:15262929[7]

E. coli Genome Project:FB20710

contains pKD46

ompC::Tn5KAN-2 (FB20711)

Insertion at nt 469 in Plus orientation

PMID:15262929[7]

E. coli Genome Project:FB20711

does not contain pKD46

ompC171

CGSC:6820

ompC161

CGSC:8752

ompC263

CGSC:9903

ompC264

CGSC:9913

ompC262

CGSC:9918

ompC172

CGSC:14635

ompC768(del)::kan

PMID:16738554[5]

CGSC:102176

ompCp1

protein expression

OmpC protein synthesis is constitutive, less repression in ompCp1 than in wild-type

PMID:7007334[8]

ompC-

insertion

Sensitivity to

Decreased Sensitivity to Micromycin B17

PMID:3543211[9]

See table 4 for full results.

ompC in strain CE104

Resistant to

Resistant to Me1 phage.

PMID:375003[10]

Experimental Strain: CE104

Parental Strain: PC0479


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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

JW2203

Plasmid clone

Shigen

PMID:16769691[11]

Status:Clone OK

Primer 1:GCCAAAGTTAAAGTACTGTCCCT

Primer 2:CCGAACTGGTAAACCAGACCCAG

22A6

Kohara Phage

Genobase

PMID:3038334[12]

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[6]

est. P1 cotransduction: 75% [13]
Synonyms:zeg-722, zei-722::Tn10

atoS298::Tn10

Linked marker

CAG12177 gyrA+ = CGSC7525[6]

est. P1 cotransduction: 71% [13]
Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (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:EG10670

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10670

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000663

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946716

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0664

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007321

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. ↑ Mizuno, T et al. (1983) DNA sequence of the promoter region of the ompC gene and the amino acid sequence of the signal peptide of pro-OmpC protein of Escherichia coli. FEBS Lett. 151 159-64 PubMed
  3. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 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. ↑ 7.0 7.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  8. ↑ Sato, T & Yura, T (1981) Regulatory mutations conferring constitutive synthesis of major outer membrane proteins (OmpC and OmpF) in Escherichia coli. J. Bacteriol. 145 88-96 PubMed
  9. ↑ Laviña, M et al. (1986) Identification, mapping, cloning and characterization of a gene (sbmA) required for microcin B17 action on Escherichia coli K12. J. Gen. Microbiol. 132 1685-93 PubMed
  10. ↑ Verhoef, C et al. (1979) Genetics and biochemistry of the peptidoglycan-associated proteins b and c of Escherichia coli K12. Mol. Gen. Genet. 169 137-46 PubMed
  11. ↑ 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
  12. ↑ 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
  13. ↑ 13.0 13.1 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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