dnaX:Gene: Difference between revisions
Table edited by Azweifel via TableEdit |
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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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{| | {| id="G46a9b1755630e" class=" tableEdit Gene_nomenclature_table" | ||
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!align=left | !align=left {{table_heading_style}} |Standard name | ||
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!align=left | !align=left {{table_heading_style}} |Mnemonic | ||
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!align=left | !align=left {{table_heading_style}} |Synonyms | ||
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{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="I46a9b1760848b" class=" tableEdit Gene_location_table" | ||
|- | |- {{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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10.59 minutes | 10.59 minutes | ||
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MG1655: 491316..493247<br /> | MG1655: 491316..493247<br /><gbrowseImage> | ||
name=NC_000913:491316..493247 | |||
source=MG1655 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10245 EcoCyc] | *[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10245 EcoCyc] | ||
{{GBrowseLink| | {{GBrowseLink|MG1655|NC_000913|490316|494247|GBrowse(MG1655)}} | ||
| | | | ||
{{GBrowseFastaLink| | {{GBrowseFastaLink|MG1655|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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NC_012967: 464159..466090<br /> | NC_012967: 464159..466090<br /><gbrowseImage> | ||
name=NC_012967:464159..466090 | |||
source=REL606 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
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{{GBrowseLink|REL606|NC_012967|464159|466090|GBrowse (REL606)}} | {{GBrowseLink|REL606|NC_012967|464159|466090|GBrowse (REL606)}} | ||
| | | | ||
{{GBrowseFastaLink|REL606|NC_012967|464159|466090|FASTA Dump}} | {{GBrowseFastaLink|REL606|NC_012967|464159|466090|FASTA Dump}} | ||
|- | |||
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[[BW2952]] | |||
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NC_012759: 394075..396006<br /><gbrowseImage> | |||
name=NC_012759:394075..396006 | |||
source=BW2952 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
| | |||
{{GBrowseLink|BW2952|NC_012759|394075|396006|GBrowse (BW2952)}} | |||
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{{GBrowseFastaLink|BW2952|NC_012759|394075|396006|FASTA Dump}} | |||
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W3110: 491316..493247<br /> | W3110: 491316..493247<br /><gbrowseImage> | ||
name=NC_007779:491316..493247 | |||
source=W3110 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
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{{GBrowseLink| | {{GBrowseLink|W3110|NC_007779|490316|494247|GBrowse(W3110)}} | ||
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{{GBrowseFastaLink| | {{GBrowseFastaLink|W3110|NC_007779|491316|493247|FASTA Dump}} | ||
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DH10B: 430647..432578<br /> | DH10B: 430647..432578<br /><gbrowseImage> | ||
name=NC_010473:430647..432578 | |||
source=DH10B | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
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{{GBrowseLink| | {{GBrowseLink|DH10B|NC_010473|426785|436440|GBrowse(DH10B)}} | ||
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{{GBrowseFastaLink| | {{GBrowseFastaLink|DH10B|NC_010473|426785|436440|FASTA Dump}} | ||
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!|Feature | !|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes | ||
|- | |||
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Coding Start (SO:0000323) | |||
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[[MG1655]] | |||
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491319 | |||
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Edman degradation | |||
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PMID:3283125<br /> | |||
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{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Y46a9b1775c6d3" 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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Weak mutator in mismatch repair deficient strain | Weak mutator in mismatch repair deficient strain | ||
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phenotype suppressed by | phenotype suppressed by mutations in DnaA | ||
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<protect><!--Alleles_notes--></protect> | <protect><!--Alleles_notes--></protect> | ||
===Notes=== | ===Notes=== | ||
The dnaX locus was identified by the J, Walker lab<ref name='PMID:391641'/> as the site of one of several ts mutations in strain SG133, which was originally thought to contain a single mutation in [[dnaZ]].<ref name='PMID:333440'/> | |||
==Genetic Interactions== | |||
{{BacktoTop}} | |||
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O4e04ba055e416" class=" tableEdit Genetic_interaction_table dataTable" | |||
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===Notes=== | |||
==Genetic Resources== | ==Genetic Resources== | ||
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!|Resource!!Resource Type!!Source!!Notes/Reference | !|Resource!!Resource Type!!Source!!Notes/Reference | ||
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Primer 2:CCAATGGGGCGGATACTTTCTTC | Primer 2:CCAATGGGGCGGATACTTTCTTC | ||
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[[:Category:Kohara_Phage:8C4|8C4]] | |||
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Kohara Phage | |||
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=151 Genobase] | |||
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PMID:3038334 | |||
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[[:Category:Kohara_Phage:12H5|12H5]] | |||
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Kohara Phage | |||
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=152 Genobase] | |||
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PMID:3038334 | |||
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{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="X46a9b17929b14" class=" tableEdit Gene_accessions_table" | ||
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!|Database!!Accession!!Notes | !|Database!!Accession!!Notes | ||
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[ | [[EcoCyc]] | ||
[ | |||
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EcoCyc:EG10245 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[[EcoGene]] | |||
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EcoGene:EG10245 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[[RegulonDB]] | |||
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RegulonDB:ECK120000239 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[http:// | [http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]]) | ||
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[http:// | [http://www.ncbi.nlm.nih.gov/gene?term=945105 GeneID:945105] | ||
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Escherichia coli str. K-12 substr. MG1655 | |||
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[[EchoBASE]] | |||
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EchoBASE:EB0241 | |||
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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-0001633 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[[Category:Genes in the ASKA clone collection]] | [[Category:Genes in the ASKA clone collection]] | ||
[[Category:dna genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]] | [[Category:dna genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]] | ||
[[Category:Gene_List:BW2952]] | |||
Latest revision as of 20:18, 22 April 2014
{{#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
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name | |
|---|---|
| Mnemonic | |
| Synonyms |
|
| edit table |
Notes
Location(s) and DNA Sequence
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 |
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NC_012967: 464159..466090 |
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NC_012759: 394075..396006 |
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W3110 |
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W3110: 491316..493247 |
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|
DH10B: 430647..432578 |
||||
| edit table |
Notes
Sequence Features
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) |
491319 |
Edman degradation |
| ||
| edit table |
Notes
Alleles and Phenotypes
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° |
Affects Tau but not Gamma | |||
|
dnaX36 |
Weak mutator in mismatch repair deficient strain |
||||||
|
dnaX0 |
|||||||
|
dnaX2016 |
G118D |
Growth Phenotype |
Ts for replication and growth |
||||
|
dnaX36(ts) |
temperature sensitive |
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|
dnaXE145A |
E145A |
failure to suppress parE10 when overexpressed |
|||||
|
dnaX(Ts) |
G118D |
Growth Phenotype |
temperature sensitive for replication and growth |
phenotype suppressed by mutations in DnaA | |||
| edit table |
Notes
The dnaX locus was identified by the J, Walker lab[6] as the site of one of several ts mutations in strain SG133, which was originally thought to contain a single mutation in dnaZ.[7]
Genetic Interactions
| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
| edit table |
Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
|
JW0459 |
Plasmid clone |
Status:Clone OK Primer 1:GCCAGTTATCAGGTCTTAGCCCG Primer 2:CCAATGGGGCGGATACTTTCTTC | |
|
Kohara Phage |
|||
|
Kohara Phage |
|||
|
Linked marker |
est. P1 cotransduction: 28% [11] | ||
|
Linked marker |
est. P1 cotransduction: 72% [11] | ||
| edit table |
Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
<protect>
References
See Help:References for how to manage references in EcoliWiki.
- ↑ Maki, S & Kornberg, A (1988) DNA polymerase III holoenzyme of Escherichia coli. I. Purification and distinctive functions of subunits tau and gamma, the dnaZX gene products. J. Biol. Chem. 263 6547-54 PubMed
- ↑ 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
- ↑ 3.0 3.1 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
- ↑ Espeli, O et al. (2003) Temporal regulation of topoisomerase IV activity in E. coli. Mol. Cell 11 189-201 PubMed
- ↑ Blinkova, A et al. (2003) Suppression of temperature-sensitive chromosome replication of an Escherichia coli dnaX(Ts) mutant by reduction of initiation efficiency. J. Bacteriol. 185 3583-95 PubMed
- ↑ Henson, JM et al. (1979) Isolation and characterization of dnaX and dnaY temperature-sensitive mutants of Escherichia coli. Genetics 92 1041-59 PubMed
- ↑ 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
- ↑ 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
- ↑ 9.0 9.1 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
- ↑ 10.0 10.1 CGSC: The Coli Genetics Stock Center
- ↑ 11.0 11.1 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).