amiC:Gene: Difference between revisions

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Update TableEdit tables.
Fixing REL gene coord display.
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!align=left |Standard name
!align=left {{table_heading_style}} |Standard name
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''amiC''  
''amiC''  
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!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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amidase
amidase
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!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK2813, b2817, JW5449, ygdN''<ref name='LIB:Riley_2006'/>
''ECK2813, b2817, JW5449, ygdN''<ref name='LIB:Riley_2006'/>
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{|  id="Q46a9e6f926039"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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NC_012967: 2842376..2843629<br />{{GBrowseFigureByCoord|2842376|2843629|REL606|NC_012967}}
NC_012967: 2843629..2842376<br />{{GBrowseFigureByCoord|2842376|2843629|REL606|NC_012967}}
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{{GBrowseLink|REL606|NC_012967|2842376|2843629|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|2842376|2843629|GBrowse (REL606)}}
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!|Feature type!!Location!!Description
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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!|Resource!!Resource Type!!Source!!Notes/Reference
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!|Database!!Accession!!Notes
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!|Name!!URL!!Comments
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Revision as of 20:08, 21 January 2010

{{#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 Alleles and Phenotypes 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

amiC

Mnemonic

amidase

Synonyms

ECK2813, b2817, JW5449, ygdN[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

63.49 minutes 

MG1655: 2947032..2945779
gbrowse_img.php?coord=2945779..2947032&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 2843629..2842376
gbrowse_img.php?coord=2842376..2843629&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 2947666..2946413
gbrowse_img.php?coord=2946413..2947666&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3040902..3039649
gbrowse_img.php?coord=3039649..3040902&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

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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 Location Description
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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

ΔamiC (Keio:JW5449)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11395[3]

ΔamiC742::kan

PMID:16738554[2]

CGSC:99994

∆amiC::Kan

Colony Morphology

20-30% of the population exists as chains of 3 to 6 unseparated cells.

PMID:11454209[4]

ΔamiC ΔamiA ΔamiB

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345[5]


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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

JW5449

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCTCAGGATCCAACACTGCAAT

Primer 2:CCTCCCCTTCTCGCCAGCGTCGC

fucP3072::Tn10

Linked marker

CAG12079 = CGSC7427[3]

est. P1 cotransduction: 62% [7]
Synonyms:fuc-3072::Tn10

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[3]

est. P1 cotransduction: 85% [7]

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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:G7458

EchoBASE (EcoliWiki Page)

EchoBASE:EB2895

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2817

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3411

EcoGene (EcoliWiki Page)

EcoGene:EG13086

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z4134

ASAP (EcoliWikiPage)

ASAP:ABE-0009238


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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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ Heidrich, C et al. (2001) Involvement of N-acetylmuramyl-L-alanine amidases in cell separation and antibiotic-induced autolysis of Escherichia coli. Mol. Microbiol. 41 167-78 PubMed
  5. ↑ Uehara, T et al. (2009) LytM-domain factors are required for daughter cell separation and rapid ampicillin-induced lysis in Escherichia coli. J. Bacteriol. 191 5094-107 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 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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