alkB:Gene: Difference between revisions

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Revision as of 20:15, 26 July 2010

{{#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 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

alkB

Mnemonic

Alkylation

Synonyms

ECK2204, b2212, JW2200, aidD[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

49.72 minutes, 49.72 minutes 

MG1655: 2307363..2306713
<gbrowseImage> name=NC_000913:2306713..2307363 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2259445..2258795
<gbrowseImage> name=NC_012967:2258795..2259445 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2192518..2193168
<gbrowseImage> name=NC_012759:2192518..2193168 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2312675..2312025
<gbrowseImage> name=AC_000091:2312025..2312675 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2398351..2397701
<gbrowseImage> name=NC_010473:2397701..2398351 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

2306713

Edman degradation

PMID:3536913[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

ΔalkB (Keio:JW2200)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9779[4]

alkB

PMID:12519969[5]

ASAP

At position 334 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB20706

alkB

PMID:12519969[5]

ASAP

At position 334 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20707

ΔalkB765::kan

PMID:16738554[3]

CGSC:99968


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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

JW2200

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCTTGGATCTGTTTGCCGATGC

Primer 2:CCTTCTTTTTTACCTGCCTGACG

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[4]

est. P1 cotransduction: 83% [7]
Synonyms:zeg-722, zei-722::Tn10

atoS298::Tn10

Linked marker

CAG12177 gyrA+ = CGSC7525[4]

est. P1 cotransduction: 63% [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:EG10037

EchoBASE (EcoliWiki Page)

EchoBASE:EB0036

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2212

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2753

EcoGene (EcoliWiki Page)

EcoGene:EG10037

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:ALKB

CGSC (EcoliWiki Page)

CGSC:18544

ASAP (EcoliWikiPage)

ASAP:ABE-0007308


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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. ↑ Kondo, H et al. (1986) Structure and expression of the alkB gene of Escherichia coli related to the repair of alkylated DNA. J. Biol. Chem. 261 15772-7 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 Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 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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