bfd:Gene: Difference between revisions

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Revision as of 20:23, 26 July 2010

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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

bfd

Mnemonic

Bfr regulating

Synonyms

ECK3324, b3337, JW3299, yheA, gen-64[1][2]

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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

74.68 minutes 

MG1655: 3465013..3464819
<gbrowseImage> name=NC_000913:3464819..3465013 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3394896..3394702
<gbrowseImage> name=NC_012967:3394702..3394896 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3351976..3352170
<gbrowseImage> name=NC_012759:3351976..3352170 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4173425..4173619
<gbrowseImage> name=AC_000091:4173425..4173619 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3562758..3562564
<gbrowseImage> name=NC_010473:3562564..3562758 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

bfdSPH22HPQ

SPH22HPQ

(in strain: ECOR 30)

Strain variation; seeded from UniProt:P0AE56

bfdK30R

K30R

(in strain: ECOR 30)

Strain variation; seeded from UniProt:P0AE56

bfdV43I

V43I

(in strain: ECOR 30)

Strain variation; seeded from UniProt:P0AE56

bfdE51Q

E51Q

(in strain: ECOR 30)

Strain variation; seeded from UniProt:P0AE56

bfdL57M

L57M

(in strain: ECOR 30)

Strain variation; seeded from UniProt:P0AE56

bfdI9V

I9V

(in strain: ECOR 30)

Strain variation; seeded from UniProt:P0AE56

bfdS63I

S63I

(in strain: ECOR 30)

Strain variation; seeded from UniProt:P0AE56

Δbfd (Keio:JW3299)

deletion

deletion

PMID:16738554[3]

Shigen


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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

JW3299

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCTACGTTTGTCTTTGTAATGG

Primer 2:CCTGCGGACTCCTTAAACTCCGG

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[5]

est. P1 cotransduction: 23% [6]
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[5]

est. P1 cotransduction: 20% [6]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (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:EG11181

EchoBASE (EcoliWiki Page)

EchoBASE:EB1168

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3337

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4108

EcoGene (EcoliWiki Page)

EcoGene:EG11181

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YHEA

ASAP (EcoliWikiPage)

ASAP:ABE-0010906


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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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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. ↑ 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  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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