poxB:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Edited by wikibot
Fixing Gbrowse links (bug #119)
Line 84: Line 84:
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10754 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10754 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|907554|911272|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|907554|911272|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|908554|910272|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|908554|910272|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10754 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10754 EcoCyc Sequence Dump]  
|-  
|-  
Line 118: Line 118:


|
|
{{GBrowseLink|BW2952|012759|811522|NC_813240|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|811522|813240|GBrowse (BW2952)}}
|
|
{{GBrowseFastaLink|BW2952|012759|811522|NC_813240|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|811522|813240|FASTA Dump}}  
|-  
|-  
|
|
Line 134: Line 134:


|
|
{{GBrowseLink|ecoli_W3110|AC_000091|908753|912471|GBrowse(W3110)}}  
{{GBrowseLink|W3110|AC_000091|908753|912471|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|909753|911471|FASTA Dump}}  
{{GBrowseFastaLink|W3110|AC_000091|909753|911471|FASTA Dump}}  
|-  
|-  
|
|
Line 150: Line 150:


|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|959046|967636|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|959046|967636|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|959046|967636|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|959046|967636|FASTA Dump}}  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  

Revision as of 20:17, 17 August 2011

{{#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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

poxB

Mnemonic

Pyruvate oxidase

Synonyms

ECK0862, b0871, JW0855[1]

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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

19.58 minutes 

MG1655: 910272..908554
<gbrowseImage> name=NC_000913:908554..910272 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 927756..926038
<gbrowseImage> name=NC_012967:926038..927756 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 811522..813240
<gbrowseImage> name=NC_012759:811522..813240 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 911471..909753
<gbrowseImage> name=AC_000091:909753..911471 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 964200..962482
<gbrowseImage> name=NC_010473:962482..964200 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


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

908554

Edman degradation

PMID:3902830[2]


edit table


Notes

Alleles and Phenotypes

[back to top]


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

ΔpoxB (Keio:JW0855)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8889[4]

poxBA553V

A553V

In poxB14

seeded from UniProt:P07003

poxBD560P

D560P

In poxB15; normal activity

seeded from UniProt:P07003

poxB

Deletion

poxBE564P

E564P

In poxB16; loss of activity

seeded from UniProt:P07003

poxB

Deletion

poxBR572G

R572G

In poxB10; reduced activity; may interact less with membranes

seeded from UniProt:P07003

poxBA533T

A533T

In poxB11

seeded from UniProt:P07003

poxB

Deletion

ΔpoxB::kan

deletion

Biolog:respiration

unable to respire b-Methyl-D-glucoside

PMID:16095938[5]

ΔpoxB::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[5]

ΔpoxB::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938[5]

ΔpoxB::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[5]

ΔpoxB::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[5]

ΔpoxB::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[5]

poxB11

CGSC:10582

poxB14::kan

PMID:3045082[6]

CGSC:64804

poxB15::lacZ::CmR

PMID:8022274[7]

CGSC:64823

ΔpoxB772::kan

PMID:16738554[3]

CGSC:102414


edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0855

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCAAACAAACGGTTGCAGCTTA

Primer 2:CCCCTTAGCCAGTTTGTTTTCGC

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[4]

est. P1 cotransduction: % [9]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[4]

est. P1 cotransduction: 21% [9]
Synonyms:zbj-1230::Tn10

edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10754

EchoBASE (EcoliWiki Page)

EchoBASE:EB0747

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0871

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C1004

EcoGene (EcoliWiki Page)

EcoGene:EG10754

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:POXB

CGSC (EcoliWiki Page)

CGSC:369

ASAP (EcoliWikiPage)

ASAP:ABE-0002958


edit table


Notes

Links

[back to top]



<protect>

References

[back to top]


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. ↑ Recny, MA et al. (1985) Characterization of the alpha-peptide released upon protease activation of pyruvate oxidase. J. Biol. Chem. 260 14287-91 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 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. ↑ Chang, YY & Cronan, JE Jr (1988) Common ancestry of Escherichia coli pyruvate oxidase and the acetohydroxy acid synthases of the branched-chain amino acid biosynthetic pathway. J Bacteriol 170 3937-45 PubMed
  7. ↑ Chang, YY et al. (1994) Expression of Escherichia coli pyruvate oxidase (PoxB) depends on the sigma factor encoded by the rpoS(katF) gene. Mol. Microbiol. 11 1019-28 PubMed
  8. ↑ 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. ↑ 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).

Categories

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=poxB:Gene&oldid=1311992"