ompR:Gene: Difference between revisions

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W3110: 4103832..4104551<br /><gbrowseImage>
W3110: 4103832..4104551<br /><gbrowseImage>
name=AC_000091:4103832..4104551
name=NC_007779:4103832..4104551
source=W3110
source=W3110
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{{GBrowseLink|W3110|AC_000091|4102832|4105551|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|4102832|4105551|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|4103832|4104551|FASTA Dump}}  
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9f51b962bb"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="F46a9f51bdf20d"  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="F46a9f51bdf20d"  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;ompR (Keio:JW3368)
''ompR(del)'' (Keio:JW3368)
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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=108791 CGSC10510]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=108791 CGSC10510]<ref name='LIB:cgsc'/>  
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&Delta;ompR::kan
''ompR(del)''::kan
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deletion
deletion
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&Delta;ompR::kan
''ompR(del)''::kan
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deletion
deletion
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''&#916;ompR739::kan''
''ompR739(del)''::kan
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''ompR(del)''
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deletion
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Change in the expression of a gene
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Decrease in the expression of ''rybB'' gene.
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PMID:17416652
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See Figure 1 A. 
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''ompR'' in strain 834
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Resistant to
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chlormaphenicol resistant
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PMID:346560
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Strain: 834
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''ompR'' in strain 834
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Resistant to
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copper resistance
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PMID:346560
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Strain: 834
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''ompR'' in strain CS197
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Resistant to
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Resistant to colicin A
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PMID:346560
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CS197
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Table 2
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''ompR'' in strain CS197
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Resistant to
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Resistant to colicin E2
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PMID:346560
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CS197
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Table 2
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''ompR'' in strain CS197
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Resistant to
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Resistant to colicin E3
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PMID:346560
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CS197
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Table 2
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''ompR'' in strain CS197
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Resistant to
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Resistant to colicin K
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PMID:346560
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CS197
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Table 2
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''ompR'' in strain CS197
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Resistant to
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Resistant to colicin L
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PMID:346560
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CS197
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Table 2
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''ompR'' in strain CS197
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Resistant to
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Resistant to colicin S4
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PMID:346560
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CS197
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Table 2
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''ompR'' in strain CS197
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Resistant to
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partially Resistant to colicin X
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PMID:346560
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CS197
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Table 2
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''ompR'' in strain CS197
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Resistant to
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Resistant to Me1
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PMID:346560
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CS197
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Table 2
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''ompR'' in strain CS197
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Resistant to
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Resistant to hy2
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PMID:346560
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CS197
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Table 2
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''ompR'' in strain CS197
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Resistant to
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Resistant to Tulb
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PMID:346560
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CS197
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Table 2
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''ompB1422''
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Resistant to
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Resistance to beta lactam Cefoxitin
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PMID:6760806
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Strains: B1436, B1437 (''omp1350''), pop1389 (''ompB101'')
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Table 3.
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''ompB1422''
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Resistant to
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Resistance to Beta Lactam Ampicillin.
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PMID:6760806
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Strains: B1436, B1437 (''omp1350''), pop1389 (''ompB101'')
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Table 3.
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''ompR<sup>-</sup>''
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Resistant to
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Small increase in Microcin B17 resistance
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PMID:3543211
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See table 4 for results of level of resistance test. 
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''ompR<sup>-</sup>''''recA <sup>-</sup>''
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Resistant to
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Double mutation caused partial increase in Microcin B17 resistance
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PMID:3543211
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See table 4 for results of resistance experiment. 


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A4e04c081f3a5d"  class=" tableEdit Genetic_interaction_table dataTable"   
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9f51d48ccf"  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=EG10672 ECOCYC:EG10672]
EcoCyc:EG10672
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG10672
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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]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10672 EcoGene:EG10672]
RegulonDB:ECK120000665
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[EchoBASE]]
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EchoBASE:EB0666
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0011110
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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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

ompR

Mnemonic

Outer membrane protein

Synonyms

ECK3392, b3405, JW3368, cry, ompB, kmt[1], kmt

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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

76.17 minutes 

MG1655: 3534606..3533887
<gbrowseImage> name=NC_000913:3533887..3534606 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3465268..3464549
<gbrowseImage> name=NC_012967:3464549..3465268 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3421044..3421763
<gbrowseImage> name=NC_012759:3421044..3421763 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4103832..4104551
<gbrowseImage> name=NC_007779:4103832..4104551 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3632351..3631632
<gbrowseImage> name=NC_010473:3631632..3632351 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

ompR(del) (Keio:JW3368)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10510[3]

ompR::Tn5KAN-I-SceI (FB21168)

Insertion at nt 434 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB21168

does not contain pKD46

ompR::Tn5KAN-I-SceI (FB21169)

Insertion at nt 434 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB21169

contains pKD46

ompR(del)::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[5]

ompR(del)::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[5]

ompR321(Am, polar)

polar

PMID:3157679[6]

CGSC:10590

amber (UAG) mutation

ompR739(del)::kan

PMID:16738554[2]

CGSC:102184

ompR101

164-182

inframe deletion

Growth Phenotype

produces no protein even though ompR mRNA is present

PMID:1695892[7]

ompR1

deletion

deletion of amino acids 164-182 near the C-terminus

lost proteins

lack both OmpF and OmpC proteins

PMID:3010044[8]

PMID:6799653[9]

ompR3

point mutation at N-terminal

at amino acid 15 (C43 to T)

increased protein expression

OmpC expression is significant even in low-osmolarity medium

PMID:3010044[8]

ompR4

point mutation

C211 is changed to T at amino acid 71

protein expression

Expression of OmpC was significant even in low-osmolarity medium

PMID:3010044[8]

ompR20

point mutation at the C-terminal

C448 is changed to T at amino acid 150

protein expression

OmpF expression was significant in high-osmolarity medium

PMID:3010044[8]

ompR2

point mutation at the C-terminal

G607 was changed to A at amino acid 203

protein expression

OmpF expression was significant in high-osmolarity medium

PMID:3010044[8]

PMID:6799653[9]

ompR77

point mutation

Leu-to-Gln at amino acid 16 from the N-terminus of OmpR

protein expression

Suppresses envZ11 pleiotropic defects

PMID:3536870[10]

ompRres

protein expresison

ompF expression increases with increasing osmolarity and ompC expression has no apparent change

PMID:6378888[11]

ompR(del)

deletion

Change in the expression of a gene

Decrease in the expression of rybB gene.

PMID:17416652[12]

See Figure 1 A.

ompR in strain 834

Resistant to

chlormaphenicol resistant

PMID:346560[13]

Strain: 834

ompR in strain 834

Resistant to

copper resistance

PMID:346560[13]

Strain: 834

ompR in strain CS197

Resistant to

Resistant to colicin A

PMID:346560[13]

CS197

Table 2

ompR in strain CS197

Resistant to

Resistant to colicin E2

PMID:346560[13]

CS197

Table 2

ompR in strain CS197

Resistant to

Resistant to colicin E3

PMID:346560[13]

CS197

Table 2

ompR in strain CS197

Resistant to

Resistant to colicin K

PMID:346560[13]

CS197

Table 2

ompR in strain CS197

Resistant to

Resistant to colicin L

PMID:346560[13]

CS197

Table 2

ompR in strain CS197

Resistant to

Resistant to colicin S4

PMID:346560[13]

CS197

Table 2

ompR in strain CS197

Resistant to

partially Resistant to colicin X

PMID:346560[13]

CS197

Table 2

ompR in strain CS197

Resistant to

Resistant to Me1

PMID:346560[13]

CS197

Table 2

ompR in strain CS197

Resistant to

Resistant to hy2

PMID:346560[13]

CS197

Table 2

ompR in strain CS197

Resistant to

Resistant to Tulb

PMID:346560[13]

CS197

Table 2

ompB1422

Resistant to

Resistance to beta lactam Cefoxitin

PMID:6760806[14]

Strains: B1436, B1437 (omp1350), pop1389 (ompB101)

Table 3.

ompB1422

Resistant to

Resistance to Beta Lactam Ampicillin.

PMID:6760806[14]

Strains: B1436, B1437 (omp1350), pop1389 (ompB101)

Table 3.

ompR-

Resistant to

Small increase in Microcin B17 resistance

PMID:3543211[15]

See table 4 for results of level of resistance test.

ompR-'recA -

Resistant to

Double mutation caused partial increase in Microcin B17 resistance

PMID:3543211[15]

See table 4 for results of resistance experiment.

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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

JW3368

Plasmid clone

Shigen

PMID:16769691[16]

Status:Clone OK

Primer 1:GCCCAAGAGAACTACAAGATTCT

Primer 2:CCTGCTTTAGAGCCGTCCGGTAC

2F6

Kohara Phage

Genobase

PMID:3038334[17]

1C9

Kohara Phage

Genobase

PMID:3038334[17]

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[3]

est. P1 cotransduction: 30% [18]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[3]

est. P1 cotransduction: 32% [18]
Synonyms:zhg-3086::Tn10, zhh-21::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:EG10672

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10672

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000665

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947913

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0666

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011110

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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 5.0 5.1 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
  6. ↑ Garrett, S et al. (1985) Isolation and characterization of delta ompB strains of Escherichia coli by a general method based on gene fusions. J. Bacteriol. 162 840-4 PubMed
  7. ↑ Coyer, J et al. (1990) micF RNA in ompB mutants of Escherichia coli: different pathways regulate micF RNA levels in response to osmolarity and temperature change. J. Bacteriol. 172 4143-50 PubMed
  8. ↑ 8.0 8.1 8.2 8.3 8.4 Nara, F et al. (1986) Molecular analysis of mutant ompR genes exhibiting different phenotypes as to osmoregulation of the ompF and ompC genes of Escherichia coli. Mol Gen Genet 202 194-9 PubMed
  9. ↑ 9.0 9.1 Hall, MN & Silhavy, TJ (1981) Genetic analysis of the ompB locus in Escherichia coli K-12. J. Mol. Biol. 151 1-15 PubMed
  10. ↑ Matsuyama, S et al. (1986) Interaction between two regulatory proteins in osmoregulatory expression of ompF and ompC genes in Escherichia coli: a novel ompR mutation suppresses pleiotropic defects caused by an envZ mutation. J. Bacteriol. 168 1309-14 PubMed
  11. ↑ Nara, F et al. (1984) Mutation causing reverse osmoregulation of synthesis of OmpF, a major outer membrane protein of Escherichia coli. J. Bacteriol. 159 688-92 PubMed
  12. ↑ Thompson, KM et al. (2007) SigmaE regulates and is regulated by a small RNA in Escherichia coli. J. Bacteriol. 189 4243-56 PubMed
  13. ↑ 13.00 13.01 13.02 13.03 13.04 13.05 13.06 13.07 13.08 13.09 13.10 13.11 Pugsley, AP & Schnaitman, CA (1978) Outer membrane proteins of Escherichia coli. VII. Evidence that bacteriophage-directed protein 2 functions as a pore. J. Bacteriol. 133 1181-9 PubMed
  14. ↑ 14.0 14.1 Jaffe, A et al. (1982) Role of porin proteins OmpF and OmpC in the permeation of beta-lactams. Antimicrob. Agents Chemother. 22 942-8 PubMed
  15. ↑ 15.0 15.1 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
  16. ↑ 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
  17. ↑ 17.0 17.1 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
  18. ↑ 18.0 18.1 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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