menD:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Standard name
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''menD''  
''menD''
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!align=left {{table_heading_style}} |Mnemonic
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Menaquinone (vitamin K2)
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!align=left {{table_heading_style}} |Synonyms
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''ΔmenD746::kan''
menDE55Q
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E55Q
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Loss of activity
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PMID:16738554
seeded from [http://www.uniprot.org/uniprot/P17109 UniProt:P17109]  
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[[cgscmutation:101816|CGSC:101816]]
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menDE55Q
''ΔmenD746::kan''
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E55Q
 
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Loss of activity
 
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PMID:16738554
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[[cgscmutation:101816|CGSC:101816]]
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seeded from [http://www.uniprot.org/uniprot/P17109 UniProt:P17109]


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Revision as of 21:26, 25 February 2010

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence 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

menD

Mnemonic

Menaquinone (vitamin K2)

Synonyms

ECK2258, b2264, JW5374[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

51.2 minutes 

MG1655: 2377281..2375611
gbrowse_img.php?coord=2375611..2377281&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 2325772..2324102
gbrowse_img.php?coord=2324102..2325772&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 2383929..2382259
gbrowse_img.php?coord=2382259..2383929&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 2468269..2466599
gbrowse_img.php?coord=2466599..2468269&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

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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 Location Description
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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

ΔmenD (Keio:JW5374)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11349[3]

menD

PMID:12519969[4]

ASAP

At position 234 in Minus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20733

menD

PMID:12519969[4]

ASAP

At position 234 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB20734

menDE55Q

E55Q

Loss of activity

seeded from UniProt:P17109

ΔmenD746::kan

PMID:16738554[2]

CGSC:101816


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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

JW5374

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTCAGTAAGCGCATTTAACCG

Primer 2:CCTAAATGGCTTACCTGCGCCAG

zfa-723::Tn10

Linked marker

CAG12178 gyrA+ = CGSC7526[3]

est. P1 cotransduction: 27% [6]
Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[3]

est. P1 cotransduction: 62% [6]
Synonyms:zej-223::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:EG10579

EchoBASE (EcoliWiki Page)

EchoBASE:EB0574

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2264

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2808

EcoGene (EcoliWiki Page)

EcoGene:EG10579

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:MEND

CGSC (EcoliWiki Page)

CGSC:517

ASAP (EcoliWikiPage)

ASAP:ABE-0007482


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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. ↑ 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 Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 PubMed
  5. ↑ 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
  6. ↑ 6.0 6.1 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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