hupA:Gene: Difference between revisions

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{{GBrowseLink|ecoli_W3110|AC_000091|3435128|3437400|GBrowse(W3110)}}  
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{{GBrowseLink|ecoli_DH10B|NC_010473|4297456|4298816|GBrowse(DH10B)}}
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Revision as of 20:04, 17 August 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

hupA

Mnemonic

HU protein

Synonyms

ECK3992, b4000, JW3964, G119, hydL[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

90.49 minutes 

MG1655: 4198304..4198576
<gbrowseImage> name=NC_000913:4198304..4198576 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4179893..4180165
<gbrowseImage> name=NC_012967:4179893..4180165 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4087984..4088256
<gbrowseImage> name=NC_012759:4087984..4088256 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3436400..3436128
<gbrowseImage> name=AC_000091:3436128..3436400 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4298000..4298272
<gbrowseImage> name=NC_010473:4298000..4298272 source=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

4198304

Edman degradation

PMID:350619[3]
PMID:6987059[4]
PMID:9298646[5]


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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

ΔhupA (Keio:JW3964)

deletion

deletion

PMID:16738554[6]

Shigen
CGSC10851[7]

ΔhupA771::kan

PMID:16738554[6]

CGSC:101440


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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

JW3964

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCAACAAGACTCAACTGATTGA

Primer 2:CCtTTAACTGCGTCTTTCAGTGC

thiC39::Tn10

Linked marker

CAG18500 = CGSC7472[7]

est. P1 cotransduction: 88% [9]
Synonyms:thi-39::Tn10

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[7]

est. P1 cotransduction: 16% [9]

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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:EG10466

EchoBASE (EcoliWiki Page)

EchoBASE:EB0461

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4000

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4957

EcoGene (EcoliWiki Page)

EcoGene:EG10466

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:HUPA

CGSC (EcoliWiki Page)

CGSC:34243

ASAP (EcoliWikiPage)

ASAP:ABE-0013077


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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. ↑ Laine, B et al. (1978) The amino- and carboxy-terminal amino acid sequences of protein HU from Escherichia coli. FEBS Lett. 89 116-20 PubMed
  4. ↑ Laine, B et al. (1980) Complete amino-acid sequences of DNA-binding proteins HU-1 and HU-2 from Escherichia coli. Eur. J. Biochem. 103 447-61 PubMed
  5. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 7.2 CGSC: The Coli Genetics Stock Center
  8. ↑ 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
  9. ↑ 9.0 9.1 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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