ccmD:Gene: Difference between revisions

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Refreshing information from GenBank record NC_000913
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Table edited by Wameza via TableEdit
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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ΔccmD (Keio:JW2186)
''ccmD(del)'' (Keio:JW2186)
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deletion
deletion
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PMID:16738554
PMID:16738554
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108049 CGSC9768]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=108049 CGSC9768]<ref name='LIB:cgsc'/>  
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''&#916;ccmD751::kan''
''ccmD751(del)''::kan
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''ccmABCDEFG(del)''
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deletion
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Protien Accumulation
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Loss of heme-containing membrane proteins.
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PMID:7635817
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See figure 3 for experimental results. 


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Revision as of 23:55, 9 April 2013

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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

ccmD

Mnemonic

Cytochrome c maturation

Synonyms

ECK2190, b2198, JW2186, yojM[1], yojM

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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

49.43 minutes 

MG1655: 2293608..2293399
<gbrowseImage> name=NC_000913:2293399..2293608 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2245575..2245366
<gbrowseImage> name=NC_012967:2245366..2245575 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2179204..2179413
<gbrowseImage> name=NC_012759:2179204..2179413 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2298920..2298711
<gbrowseImage> name=AC_000091:2298711..2298920 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2384596..2384387
<gbrowseImage> name=NC_010473:2384387..2384596 source=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

ccmD(del) (Keio:JW2186)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9768[3]

ccmD::Tn5KAN-2 (FB20686)

Insertion at nt 94 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20686

does not contain pKD46

ccmD::Tn5KAN-2 (FB20687)

Insertion at nt 94 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20687

contains pKD46

ccmD751(del)::kan

PMID:16738554[2]

CGSC:100258

ccmABCDEFG(del)

deletion

Protien Accumulation

Loss of heme-containing membrane proteins.

PMID:7635817[5]

See figure 3 for experimental results.

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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

JW2186

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCACCCCTGCATTTGCTTCCTG

Primer 2:CCTGCAGCCTCCTGCTGTTGCGC

20F6

Kohara Phage

Genobase

PMID:3038334[7]

19D1

Kohara Phage

Genobase

PMID:3038334[7]

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[3]

est. P1 cotransduction: % [8]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[3]

est. P1 cotransduction: 77% [8]
Synonyms:zeg-722, zei-722::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:EG12169

Escherichia coli str. K-12 substr. MG1655

EcoGene (EcoliWiki Page)

EcoGene:EG12169

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946709

Escherichia coli str. K-12 substr. MG1655

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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. ↑ 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. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ Thöny-Meyer, L et al. (1995) Escherichia coli genes required for cytochrome c maturation. J. Bacteriol. 177 4321-6 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 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  8. ↑ 8.0 8.1 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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