proA: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 16:55, 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

proA

Mnemonic

Proline

Synonyms

ECK0244, b0243, JW0233, pro1, pro(1)[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

5.62 minutes 

MG1655: 260727..261980
<gbrowseImage> name=NC_000913:260727..261980 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 265995..267248
<gbrowseImage> name=NC_012967:265995..267248 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 260726..261979
<gbrowseImage> name=NC_012759:260726..261979 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 260727..261980
<gbrowseImage> name=AC_000091:260727..261980 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 234831..236084
<gbrowseImage> name=NC_010473:234831..236084 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

260727

Edman degradation

PMID:6089111[2]


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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

ΔproA (Keio:JW0233)

deletion

deletion

Auxotrophies

Requires proline for growth

PMID:16738554[3]

Shigen

CGSC8468[4]

proA::Tn5KAN-2 (FB20067)

Insertion at nt 192 in Plus orientation

Auxotrophies

Requires proline for growth

PMID:15262929[5]

E. coli Genome Project:FB20067

does not contain pKD46

proA81::Tn10

Insertion at 261,286 bp in MG1655 (NC_000913)

Auxotrophies

Requires proline for growth

adapted from Nichols et al.[6]

CAG18447 = CGSC7330[4]

Synonyms:

proA761(del)::kan

insertion

insertion

Auxotrophies

Requires proline for growth

proA23

Auxotrophies

Requires proline for growth

CGSC:5573

proA44

Auxotrophies

Requires proline for growth

CGSC:6453

proA81::Tn10

Auxotrophies

Requires proline for growth

PMID:9829956[7]

CGSC:7088

proA35

Auxotrophies

Requires proline for growth

CGSC:8556

proA30

Auxotrophies

Requires proline for growth

CGSC:11535

proA181

Auxotrophies

Requires proline for growth

CGSC:12290

proA180

Auxotrophies

Requires proline for growth

CGSC:12291

proA

Auxotrophies

Requires proline for growth

CGSC:14522

proA3096::Tn10kan

Auxotrophies

Requires proline for growth

PMID:2540407[8] PMID:9829956[7]

CGSC:38994

ΔproA761::kan

deletion

deletion

Auxotrophies

Requires proline for growth

PMID:16738554[3]

CGSC:102466


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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

JW0233

Plasmid clone

Shigen

PMID:16769691[9]

Status:Clone OK

Primer 1:GCCCTGGAACAAATGGGCATTGC

Primer 2:CCCGCACGAATGGTGTAATCACC

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[4]

est. P1 cotransduction: 33% [6]
Synonyms:zae-502::Tn10

lacI3042::Tn10

Linked marker

CAG18439 = CGSC7334[4]

est. P1 cotransduction: % [6]
Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).

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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:EG10767

EchoBASE (EcoliWiki Page)

EchoBASE:EB0760

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0243

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0390

EcoGene (EcoliWiki Page)

EcoGene:EG10767

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:PROA

CGSC (EcoliWiki Page)

CGSC:364

ASAP (EcoliWikiPage)

ASAP:ABE-0000832


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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. ↑ Deutch, AH et al. (1984) Analysis of the Escherichia coli proBA locus by DNA and protein sequencing. Nucleic Acids Res. 12 6337-55 PubMed
  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 4.3 CGSC: The Coli Genetics Stock Center
  5. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ 6.0 6.1 6.2 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).
  7. ↑ 7.0 7.1 Nichols, BP et al. (1998) Sequence analysis of Tn10 insertion sites in a collection of Escherichia coli strains used for genetic mapping and strain construction. J. Bacteriol. 180 6408-11 PubMed
  8. ↑ Singer, M et al. (1989) A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53 1-24 PubMed
  9. ↑ 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

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