envR:Gene: Difference between revisions

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Fixing Blattner deletion strains in alleles table.
Adding section & Genetic interactions table to Gene pages.
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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{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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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==

Revision as of 16:25, 24 June 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

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

Standard name

envR

Mnemonic

Envelope

Synonyms

ECK3251, b3264, JW3232, acrS, yhdK[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

73.51 minutes 

MG1655: 3411487..3410825
<gbrowseImage> name=NC_000913:3410825..3411487 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3341356..3340694
<gbrowseImage> name=NC_012967:3340694..3341356 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3297973..3298635
<gbrowseImage> name=NC_012759:3297973..3298635 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3413320..3412658
<gbrowseImage> name=AC_000091:3412658..3413320 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3509232..3508570
<gbrowseImage> name=NC_010473:3508570..3509232 source=ecoli_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

ΔenvR (Keio:JW3232)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10445[3]

envR::Tn5KAN-I-SceI (FB21089)

Insertion at nt 577 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB21089

contains pKD46

envR::Tn5KAN-I-SceI (FB21090)

Insertion at nt 577 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB21090

does not contain pKD46

ΔenvR::kan

deletion

Biolog:respiration

unable to respire N-Acetyl-D-glucosamine

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire b-Methyl-D-glucoside

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[5]

ΔenvR782::kan

PMID:16738554[2]

CGSC:100722


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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

JW3232

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGCAAAAAGAACCAAAGCCGA

Primer 2:CCCATGACACTTAATTCATTCGT

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[3]

est. P1 cotransduction: 12% [7]
Synonyms:zha-6::Tn10

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[3]

est. P1 cotransduction: 88% [7]
Synonyms:zhd-3083::Tn10, zhe-3083::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:EG11741

EchoBASE (EcoliWiki Page)

EchoBASE:EB1692

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3264

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4030

EcoGene (EcoliWiki Page)

EcoGene:EG11741

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:ENVR

ASAP (EcoliWikiPage)

ASAP:ABE-0010712


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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 5.2 5.3 5.4 5.5 5.6 5.7 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. ↑ 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
  7. ↑ 7.0 7.1 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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