hns: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 16:36, 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

hns

Mnemonic

Histone-like protein H-NS

Synonyms

ECK1232, b1237, JW1225, bglY, cur, drc, drdX, drs, irk, mssyA, msyA, osmZ, pilG, topX, virR, hnsA, topS, B1, H1[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

27.84 minutes 

MG1655: 1292145..1291732
<gbrowseImage> name=NC_000913:1291732..1292145 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1292716..1292303
<gbrowseImage> name=NC_012967:1292303..1292716 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1181230..1181643
<gbrowseImage> name=NC_012759:1181230..1181643 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1294499..1294086
<gbrowseImage> name=AC_000091:1294086..1294499 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1332386..1331973
<gbrowseImage> name=NC_010473:1331973..1332386 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

1291735

Edman degradation

PMID:2020545[2]
PMID:2126011[3]
PMID:6370250[4]
PMID:8740179[5]
PMID:9298646[6]
PMID:9600841[7]
PMID:9740056[8]


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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

Δhns (Keio:JW1225)

deletion

deletion

PMID:16738554[9]

Shigen
CGSC9111[10]

hns::Tn5KAN-2 (FB20271)

Insertion at nt 323 in Plus orientation

PMID:15262929[11]

E. coli Genome Project:FB20271

does not contain pKD46

Δhns::kan

deletion

Biolog:respiration

unable to respire D-Galactoniate

PMID:16095938[12]

Δhns::kan

deletion

Biolog:respiration

unable to respire D-Galacturonate

PMID:16095938[12]

Δhns::kan

deletion

Biolog:respiration

unable to respire D-Glucuronate

PMID:16095938[12]

Δhns::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[12]

Δhns::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938[12]

Δhns::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[12]

Δhns::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[12]

Δhns::kan

deletion

Biolog:respiration

unable to respire Succinate

PMID:16095938[12]

Δhns::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[12]

Δhns::kan

deletion

Biolog:respiration

unable to respire L-Alanine

PMID:16095938[12]

Δhns::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938[12]

Δhns::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[12]

hns-206

CGSC:19435

hns-1

CGSC:26967

Δhns-746::kan

PMID:16738554[9]

CGSC:101388


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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

JW1225

Plasmid clone

Shigen

PMID:16769691[13]

Status:Clone OK

Primer 1:GCCAGCGAAGCACTTAAAATTCT

Primer 2:CCTTGCTTGATCAGGAAATCGTC

fadR13::Tn10

Linked marker

CAG18497 = CGSC7365[10]

est. P1 cotransduction: 5% [14]

oppC506::Tn10

Linked marker

CAG12169 = CGSC7369[10]

est. P1 cotransduction: 66% [14]
Synonyms:zch-506::Tn10, zci-506::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:EG10457

EchoBASE (EcoliWiki Page)

EchoBASE:EB0452

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1237

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C1701

EcoGene (EcoliWiki Page)

EcoGene:EG10457

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:HNS

CGSC (EcoliWiki Page)

CGSC:960

ASAP (EcoliWikiPage)

ASAP:ABE-0004152


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Notes

Links

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<protect>

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. ↑ Kajitani, M & Ishihama, A (1991) Identification and sequence determination of the host factor gene for bacteriophage Q beta. Nucleic Acids Res. 19 1063-6 PubMed
  3. ↑ Yamada, H et al. (1990) An Escherichia coli protein that preferentially binds to sharply curved DNA. J. Biochem. 108 420-5 PubMed
  4. ↑ Laine, B et al. (1984) A DNA-binding protein from E. coli isolation, characterization and its relationship with proteins H1 and B1. Biochem. Biophys. Res. Commun. 119 1147-53 PubMed
  5. ↑ Pasquali, C et al. (1996) Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database. Electrophoresis 17 547-55 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. ↑ Wilkins, MR et al. (1998) Protein identification with N and C-terminal sequence tags in proteome projects. J. Mol. Biol. 278 599-608 PubMed
  8. ↑ Tonella, L et al. (1998) '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 19 1960-71 PubMed
  9. ↑ 9.0 9.1 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
  10. ↑ 10.0 10.1 10.2 CGSC: The Coli Genetics Stock Center
  11. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  12. ↑ 12.00 12.01 12.02 12.03 12.04 12.05 12.06 12.07 12.08 12.09 12.10 12.11 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
  13. ↑ 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
  14. ↑ 14.0 14.1 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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