trxB:Gene: Difference between revisions

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W3110: 932472..931507<br /><gbrowseImage>
W3110: 932472..931507<br /><gbrowseImage>
name=AC_000091:931507..932472
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{{GBrowseLink|W3110|AC_000091|930507|933472|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|930507|933472|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|931507|932472|FASTA Dump}}  
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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="B46a9baf6552d1"  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="B46a9baf6552d1"  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;trxB (Keio:JW0871)
''trxB(del)'' (Keio:JW0871)
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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=107181 CGSC8900]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=107181 CGSC8900]<ref name='LIB:cgsc'/>  
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''&#916;trxB786::kan''
''trxB786(del)::kan''
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fig 2  
fig 2  
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''trxB786''(del)::FRTKanFRT
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Mutagenesis rate
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Decreased stress-induced mutagenesis (SIM) phenotype.
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PMID:23224554
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Parental Strain: SMR4562
Experimental Strain: SMR11969
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Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
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CAG45114 ''trxB786(del)''::FRTKanFRT
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Deletion
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Sigma<sup>E</sup> activity
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Decrease in Sigma<sup>E</sup> activity
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PMID:23224554
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Parental Strain: CAG45114
Experimental Strain: SMR15283
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See table S11 for full experimental data. 


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B4e04c500dee77"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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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=EG11032 ECOCYC:EG11032]
EcoCyc:EG11032
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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:EG11032
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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=EG11032 EcoGene:EG11032]
RegulonDB:ECK120001021
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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:EB1025
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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-0003018
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 20:32, 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

trxB

Mnemonic

Thioredoxin

Synonyms

ECK0879, b0888, JW0871, trxR[1][2]

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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

20.05 minutes 

MG1655: 931273..930308
<gbrowseImage> name=NC_000913:930308..931273 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 949108..948143
<gbrowseImage> name=NC_012967:948143..949108 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 833276..834241
<gbrowseImage> name=NC_012759:833276..834241 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 932472..931507
<gbrowseImage> name=NC_007779:931507..932472 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 985201..984236
<gbrowseImage> name=NC_010473:984236..985201 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

930311

Edman degradation

PMID:1575737[3]
PMID:3288628[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

trxB(del) (Keio:JW0871)

deletion

deletion

PMID:16738554[5]

Shigen

CGSC8900[6]

trxB::Tn5KAN-2 (FB20247)

Insertion at nt 609 in Plus orientation

PMID:15262929[7]

E. coli Genome Project:FB20247

does not contain pKD46

trxB20

CGSC:10949

trxB15::kan

CGSC:10952

trxB786(del)::kan

PMID:16738554[5]

CGSC:103242

trxB

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[8]

fig 2

trxB786(del)::FRTKanFRT

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554[9]

Parental Strain: SMR4562

Experimental Strain: SMR11969

Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.

CAG45114 trxB786(del)::FRTKanFRT

Deletion

SigmaE activity

Decrease in SigmaE activity

PMID:23224554[9]

Parental Strain: CAG45114 Experimental Strain: SMR15283

See table S11 for full experimental data.

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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

JW0871

Plasmid clone

Shigen

PMID:16769691[10]

Status:Clone OK

Primer 1:GCCGGCACGACCAAACACAGTAA

Primer 2:CCTTTTGCGTCAGCTAAACCATC

1H1

Kohara Phage

Genobase

PMID:3038334[11]

1F10

Kohara Phage

Genobase

PMID:3038334[11]

E6H3

Kohara Phage

Genobase

PMID:3038334[11]

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[6]

est. P1 cotransduction: % [12]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[6]

est. P1 cotransduction: 56% [12]
Synonyms:zbj-1230::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:EG11032

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11032

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001021

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949054

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1025

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003018

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Ueshima, R et al. (1992) Identification of Escherichia coli proteins cross-reacting with antibodies against region 2.2 peptide of RNA polymerase sigma subunit. Biochem. Biophys. Res. Commun. 184 634-9 PubMed
  4. ↑ Russel, M & Model, P (1988) Sequence of thioredoxin reductase from Escherichia coli. Relationship to other flavoprotein disulfide oxidoreductases. J. Biol. Chem. 263 9015-9 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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  8. ↑ 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
  9. ↑ 9.0 9.1 Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  10. ↑ 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
  11. ↑ 11.0 11.1 11.2 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
  12. ↑ 12.0 12.1 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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