ada: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]]
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|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{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 16:10, 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

ada

Mnemonic

Adaptive (response)

Synonyms

ECK2205, b2213, JW2201[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

49.73 minutes 

MG1655: 2308427..2307363
<gbrowseImage> name=NC_000913:2307363..2308427 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2260509..2259445
<gbrowseImage> name=NC_012967:2259445..2260509 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2193168..2194232
<gbrowseImage> name=NC_012759:2193168..2194232 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2313739..2312675
<gbrowseImage> name=AC_000091:2312675..2313739 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2399415..2398351
<gbrowseImage> name=NC_010473:2398351..2399415 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

Coding Start (SO:0000323)

MG1655

2307363

Edman degradation

PMID:2987251[2]


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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

adaE75D

E75D

(in strain: B)

Strain variation; seeded from UniProt:P06134

adaAQ79PR

AQ79PR

(in strain: B)

Strain variation; seeded from UniProt:P06134

adaI318V

I318V

(in strain: B)

Strain variation; seeded from UniProt:P06134

adaT330S

T330S

(in strain: B)

Strain variation; seeded from UniProt:P06134

Δada (Keio:JW2201)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9780[4]

ada::Tn5KAN-2 (FB20708)

Insertion at nt 687 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20708

does not contain pKD46

ada::Tn5KAN-2 (FB20709)

Insertion at nt 687 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20709

contains pKD46

ada-1

CGSC:12943

ada-2

CGSC:12946

ada-3

CGSC:12948

ada-4

CGSC:12950

ada-5

CGSC:12952

ada-6

CGSC:12954

Δada-766::kan

PMID:16738554[3]

CGSC:99908


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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

JW2201

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAAAAAAGCCACATGCTTAAC

Primer 2:CCtCTCTCCTCATTTTCAGCTTC

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[4]

est. P1 cotransduction: 82% [7]
Synonyms:zeg-722, zei-722::Tn10

atoS298::Tn10

Linked marker

CAG12177 gyrA+ = CGSC7525[4]

est. P1 cotransduction: 65% [7]
Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

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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:EG10029

EchoBASE (EcoliWiki Page)

EchoBASE:EB0028

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2213

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2754

EcoGene (EcoliWiki Page)

EcoGene:EG10029

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:ADA

CGSC (EcoliWiki Page)

CGSC:1043

ASAP (EcoliWikiPage)

ASAP:ABE-0007311


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Notes

Links

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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. ↑ Nakabeppu, Y et al. (1985) Purification and structure of the intact Ada regulatory protein of Escherichia coli K12, O6-methylguanine-DNA methyltransferase. J. Biol. Chem. 260 7281-8 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 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 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).

Categories

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