dnaX:Gene: Difference between revisions

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!{{table_heading_style}} |Standard name
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''dnaX''  
''dnaX''  
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0464, b0470, JW0459, dnaZ''<ref name='LIB:Riley_2006'/>
''ECK0464, b0470, JW0459, dnaZ''<ref name='LIB:Riley_2006'/>
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
MG1655
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{{GBrowseFastaLink|ecoli|NC_000913|491316|493247|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|491316|493247|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10245 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10245 EcoCyc Sequence Dump]  
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W3110
W3110
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|491316|493247|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|491316|493247|FASTA Dump}}  
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ts growth.  Fast stop DNA replication arrest at 44°
ts growth.  Fast stop DNA replication arrest at 44°
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[[PMID:16430690]]
[[[PMID:16430690]]<ref name=PMID:16430690/>]]
[[PMID:8376347]]
[[[PMID:8376347]]<ref name=PMID:8376347/>]]
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Weak mutator in mismatch repair deficient strain
Weak mutator in mismatch repair deficient strain
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[[PMID:16430690]]
[[[PMID:16430690]]<ref name=PMID:16430690/>]]
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failure to suppress parE10 when overexpressed
failure to suppress parE10 when overexpressed
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|[[PMID:12535532]]<ref name=PMID:12535532/>
[[PMID:12535532]]<ref name=PMID:12535532/>
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JW0459
JW0459
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
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|[[PMID:16769691]]<ref name=PMID:16769691/>
[[PMID:16769691]]<ref name=PMID:16769691/>


Status:Clone OK
Status:Clone OK
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Primer 2:CCAATGGGGCGGATACTTTCTTC  
Primer 2:CCAATGGGGCGGATACTTTCTTC  
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[[ppiD:Gene|zaj-3054::Tn10]]
[[ppiD:Gene|zaj-3054::Tn10]]
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CAG12017 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39373 CGSC7339]<ref name='LIB:cgsc'/>
CAG12017 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39373 CGSC7339]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zba-3054::Tn10  
 
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[[gsk:Gene|gsk-3055::Tn10]]
[[gsk:Gene|gsk-3055::Tn10]]
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CAG12154 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39379 CGSC7341]<ref name='LIB:cgsc'/>
CAG12154 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39379 CGSC7341]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 72% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 72% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zbb-30-55::TnlO, zba-3055::Tn10


Synonyms:zbb-30-55::TnlO, zba-3055::Tn10
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[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=0001633&formSubmitReturn=1 ASAP:ABE-0001633]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0001633&formSubmitReturn=1 ASAP:ABE-0001633]
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Revision as of 18:43, 21 January 2009

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Alleles and Phenotypes 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

dnaX

Mnemonic
Synonyms

ECK0464, b0470, JW0459, dnaZ[1]

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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

10.59 minutes 

MG1655: 491316..493247
gbrowse_img.php?coord=490316..494247&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 491316..493247
gbrowse_img.php?coord=490316..494247&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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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 Location Description
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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

dnaX36

E601K

Growth Phenotype

ts growth. Fast stop DNA replication arrest at 44°

[[[PMID:16430690]][2]]] [[[PMID:8376347]][3]]]

Affects Tau but not Gamma

dnaX36

Other

Weak mutator in mismatch repair deficient strain

[[[PMID:16430690]][2]]]

dnaX0

CGSC:10600

dnaX2016

CGSC:10601

dnaX36(ts)

temperature sensitive

CGSC:10704

dnaXE145A

E145A

failure to suppress parE10 when overexpressed

PMID:12535532[4]


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Notes

The dnaX locus was identified by the J, Walker lab[5] as the site of one of several ts mutations in strain SG133, which was originally thought to contain a single mutation in dnaZ[6].

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

JW0459

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAGTTATCAGGTCTTAGCCCG

Primer 2:CCAATGGGGCGGATACTTTCTTC

zaj-3054::Tn10

Linked marker

CAG12017 = CGSC7339[8]

est. P1 cotransduction: 28% [9]nnSynonyms:zba-3054::Tn10

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[8]

est. P1 cotransduction: 72% [9]nnSynonyms:zbb-30-55::TnlO, zba-3055::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 (EcoliWiki Page)

EcoCyc:EG10245

EchoBASE (EcoliWiki Page)

EchoBASE:EB0241

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0470

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0589

EcoGene (EcoliWiki Page)

EcoGene:EG10245

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:DNAX

CGSC (EcoliWiki Page)

CGSC:838

ASAP (EcoliWikiPage)

ASAP:ABE-0001633


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Notes

Links

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Name URL Comments
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References

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  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 Pham, PT et al. (2006) Mutator mutants of Escherichia coli carrying a defect in the DNA polymerase III tau subunit. Mol. Microbiol. 59 1149-61 PubMed
  3. ↑ Blinkova, A et al. (1993) The Escherichia coli DNA polymerase III holoenzyme contains both products of the dnaX gene, tau and gamma, but only tau is essential. J. Bacteriol. 175 6018-27 PubMed
  4. ↑ Espeli, O et al. (2003) Temporal regulation of topoisomerase IV activity in E. coli. Mol. Cell 11 189-201 PubMed
  5. ↑ Henson, JM et al. (1979) Isolation and characterization of dnaX and dnaY temperature-sensitive mutants of Escherichia coli. Genetics 92 1041-59 PubMed
  6. ↑ Sevastopoulos, CG et al. (1977) Large-scale automated isolation of Escherichia coli mutants with thermosensitive DNA replication. Proc. Natl. Acad. Sci. U.S.A. 74 3485-9 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 CGSC: The Coli Genetics Stock Center
  9. ↑ 9.0 9.1 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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