hupB:Gene: Difference between revisions

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Fixing Blattner deletion strains in alleles table.
Adding section & Genetic interactions table to Gene pages.
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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==

Revision as of 16:37, 24 June 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

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
<gbrowseImage> name=NC_000913:460675..460947 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 433506..433778
<gbrowseImage> name=NC_012967:433506..433778 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 363434..363706
<gbrowseImage> name=NC_012759:363434..363706 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 460675..460947
<gbrowseImage> name=AC_000091:460675..460947 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 400006..400278
<gbrowseImage> name=NC_010473:400006..400278 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

460675

Edman degradation

PMID:215461[3]
PMID:350619[4]
PMID:6987059[5]
PMID:9298646[6]


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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[7]

Shigen
CGSC8593[8]

hupB::Tn5KAN-2 (FB20176)

Insertion at nt 210 in Minus orientation

PMID:15262929[9]

E. coli Genome Project:FB20176

does not contain pKD46

ΔhupB::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[10]

ΔhupB726::kan

PMID:16738554[7]

CGSC:101442


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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

JW0430

Plasmid clone

Shigen

PMID:16769691[11]

Status:Clone OK

Primer 1:GCCAATAAATCTCAATTGATCGA

Primer 2:CCGTTTACCGCGTCTTTCAGTGC

zaj-3054::Tn10

Linked marker

CAG12017 = CGSC7339[8]

est. P1 cotransduction: 96% [12]
Synonyms:zba-3054::Tn10

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[8]

est. P1 cotransduction: 18% [12]
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. ↑ Mende, L et al. (1978) Primary structures of two homologous ribosome-associated DNA-binding proteins of Escherichia coli. FEBS Lett. 96 395-8 PubMed
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 7.0 7.1 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
  8. ↑ 8.0 8.1 8.2 CGSC: The Coli Genetics Stock Center
  9. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  10. ↑ Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  11. ↑ 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
  12. ↑ 12.0 12.1 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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