hupB:Gene: Difference between revisions

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!align=left |Standard name
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''hupB''  
''hupB''
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!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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HU protein
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!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0434, b0440, JW0430, dpeA, hopD, dbhB, gsp*''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK0434, b0440, JW0430, dpeA, hopD, dbhB, gsp*''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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!|Feature type!!Location!!Description
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No effect
No effect
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seeded from [http://www.uniprot.org/uniprot/P0ACF4 UniProt:P0ACF4]
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hupBRTGR58GTGG
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RTGR58GTGG
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Reduced DNA-binding
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hupBRTGR58GTGG
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RTGR58GTGG
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Reduced DNA-binding
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seeded from [http://www.uniprot.org/uniprot/P0ACF4 UniProt:P0ACF4]


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Revision as of 21:18, 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

hupB

Mnemonic

HU protein

Synonyms

ECK0434, b0440, JW0430, dpeA, hopD, dbhB, gsp*[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

9.93 minutes 

MG1655: 460675..460947
gbrowse_img.php?coord=460675..460947&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 433506..433778
gbrowse_img.php?coord=433506..433778&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 460675..460947
gbrowse_img.php?coord=460675..460947&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 400006..400278
gbrowse_img.php?coord=400006..400278&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

hupBA30D

A30D

No effect

seeded from UniProt:P0ACF4

hupBRTGR58GTGG

RTGR58GTGG

Reduced DNA-binding

seeded from UniProt:P0ACF4

hupBF47T

F47T

Reduced DNA-binding

seeded from UniProt:P0ACF4

hupBK37Q

K37Q

No effect

seeded from UniProt:P0ACF4

ΔhupB (Keio:JW0430)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8593[4]

hupB

PMID:12519969[5]

ASAP

At position 210 in Minus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20176

ΔhupB726::kan

PMID:16738554[3]

CGSC:101442


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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

JW0430

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAATAAATCTCAATTGATCGA

Primer 2:CCGTTTACCGCGTCTTTCAGTGC

zaj-3054::Tn10

Linked marker

CAG12017 = CGSC7339[4]

est. P1 cotransduction: 96% [7]
Synonyms:zba-3054::Tn10

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[4]

est. P1 cotransduction: 18% [7]
Synonyms:zbb-30-55::TnlO, zba-3055::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:EG10467

EchoBASE (EcoliWiki Page)

EchoBASE:EB0462

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0440

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0556

EcoGene (EcoliWiki Page)

EcoGene:EG10467

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:HUPB

CGSC (EcoliWiki Page)

CGSC:18235

ASAP (EcoliWikiPage)

ASAP:ABE-0001527


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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. ↑ 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. ↑ 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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