ccmD:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK2190, b2198, JW2186, yojM''<ref name='LIB:Riley_2006'/>
''ECK2190, b2198, JW2186, yojM''<ref name='LIB:Riley_2006'/>, yojM''


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{|   id="C46a9d84c698d2"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9d84c698d2"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12169 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12169 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2292399|2294608|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2292399|2294608|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|2293399|2293608|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2293399|2293608|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12169 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12169 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|2179204|NC_2179413|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|2179204|2179413|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|2179204|NC_2179413|FASTA Dump}}  
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W3110: 2298920..2298711<br /><gbrowseImage>
W3110: 2298920..2298711<br /><gbrowseImage>
name=AC_000091:2298711..2298920
name=NC_007779:2298711..2298920
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|2297711|2299920|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2297711|2299920|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|2298711|2298920|FASTA Dump}}  
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DH10B: 2384596..2384387<br /><gbrowseImage>
DH10B: 2384596..2384387<br /><gbrowseImage>
name=NC_010473:2384387..2384596
name=NC_010473:2384387..2384596
source=MG1655_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|2383969|2385014|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|2383969|2385014|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|2383969|2385014|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|2383969|2385014|FASTA Dump}}  


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{|   id="N46a9d84d2557d"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9d84d2557d"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="U46a9d84d6a403"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="U46a9d84d6a403"  class=" tableEdit Gene_allele_table dataTable"   
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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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&Delta;ccmD (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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''ccmABCDEFG(del)''
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deletion
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cytochrome accumulation
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Loss of cytochrome <sub>c550</sub>.
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PMID:7635817
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See figure 4 for experimental results. 
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''ccmABCDEFG(del)''
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deletion
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cytochrome biogenesis
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Deficient cytochrome biogenesis
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PMID:7635817
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See figure 5 for experimental results. 


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{|   id="W4e04b88f52331"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W4e04b88f52331"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="C46a9d84e202f4"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9d84e202f4"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCTGCAGCCTCCTGCTGTTGCGC  
Primer 2:CCTGCAGCCTCCTGCTGTTGCGC  
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[[:Category:Kohara_Phage:20F6|20F6]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=371 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:19D1|19D1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=372 Genobase]
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PMID:3038334
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{|   id="W46a9d84eb4298"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a9d84eb4298"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12169 EcoCyc:EG12169]
EcoCyc:EG12169
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2088 EchoBASE:EB2088]
EcoGene:EG12169
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b2198 EcoliGenExpDB:b2198]
RegulonDB:ECK120002065
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C2735 ECOL199310CYC:C2735]
[http://www.ncbi.nlm.nih.gov/gene?term=946709 GeneID:946709]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG12169 EcoGene:EG12169]
EchoBASE:EB2088
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=CCMD ECOO157CYC:CCMD]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
ASAP:ABE-0007273
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/36584 CGSC:36584]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0007273&formSubmitReturn=1 ASAP:ABE-0007273]
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:41, 19 September 2013

{{#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

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=NC_007779:2298711..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.

ccmABCDEFG(del)

deletion

cytochrome accumulation

Loss of cytochrome c550.

PMID:7635817[5]

See figure 4 for experimental results.

ccmABCDEFG(del)

deletion

cytochrome biogenesis

Deficient cytochrome biogenesis

PMID:7635817[5]

See figure 5 for experimental results.

edit table


Notes

Genetic Interactions

[back to top]



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

EcoCyc:EG12169

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12169

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002065

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946709

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2088

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007273

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. ↑ 5.0 5.1 5.2 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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