hypF:Gene: Difference between revisions

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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 16:38, 24 June 2011

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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 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

hypF

Mnemonic

Hydrogenase pleiotropic

Synonyms

ECK2707, b2712, JW5433, hydA[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

61.06 minutes 

MG1655: 2835447..2833195
<gbrowseImage> name=NC_000913:2833195..2835447 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2732285..2730033
<gbrowseImage> name=NC_012967:2730033..2732285 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2719007..2721259
<gbrowseImage> name=NC_012759:2719007..2721259 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2836081..2833829
<gbrowseImage> name=AC_000091:2833829..2836081 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2927989..2925737
<gbrowseImage> name=NC_010473:2925737..2927989 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

ΔhypF (Keio:JW5433)

deletion

deletion

PMID:16738554[2]

Shigen

hypFH476A

H476A

Carbamoyl phosphate-dependent ATP hydrolysis activity diminished in vitro but sufficient for wild-type-like phenotype

seeded from UniProt:P30131

hypFR23E,H,K

R23E,H,K

Loss of activity

seeded from UniProt:P30131

hypFR23Q

R23Q

Diminishes activity

seeded from UniProt:P30131

hypFC112A

C112A

Loss of activity

seeded from UniProt:P30131

hypFC162A

C162A

Loss of activity

seeded from UniProt:P30131

hypFH475A

H475A

Loss of activity

seeded from UniProt:P30131

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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

JW5433

Plasmid clone

Shigen

PMID:16769691[3]

Status:cloned as old JW

Primer 1:GCCGCAAAAAACACATCTTGCGG

Primer 2:CCTCCGTTCTGGACTTCACCCGC

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[4]

est. P1 cotransduction: 77% [5]
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10

cysI95::Tn10

Linked marker

CAG12173 = CGSC7425[4]

est. P1 cotransduction: 8% [5]
Synonyms:cysC95::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:EG11551

EchoBASE (EcoliWiki Page)

EchoBASE:EB1512

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2712

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3268

EcoGene (EcoliWiki Page)

EcoGene:EG11551

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:HYPF

CGSC (EcoliWiki Page)

CGSC:18232

ASAP (EcoliWikiPage)

ASAP:ABE-0008915


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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. ↑ 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
  3. ↑ 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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).

Categories

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