ccmD:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''ccmD''  
''ccmD''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Cytochrome c maturation
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2190, b2198, JW2186, yojM''<ref name='LIB:Riley_2006'/>, yojM''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14955.G46a9d84be0a79&page=14955&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2190, b2198, JW2186, yojM''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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<protect>
<protect>
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{| 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" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
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MG1655
MG1655
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49.43 minutes&nbsp;
49.43 minutes&nbsp;
|
|
MG1655: 2293608..2293399<br />{{GBrowseFigureByCoord|2292399|2294608|ecoli|MG1655}}
MG1655: 2293608..2293399<br /><gbrowseImage>
name=NC_000913:2293399..2293608
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[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]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2292399..2294608 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2292399|2294608|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2293399..2293608&plugin_action=Go 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]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2245575..2245366<br /><gbrowseImage>
name=NC_012967:2245366..2245575
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2245366|2245575|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|2245366|2245575|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2179204..2179413<br /><gbrowseImage>
name=NC_012759:2179204..2179413
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2179204|2179413|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2179204|2179413|FASTA Dump}}
|-  
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|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2298920..2298711<br />{{GBrowseFigureByCoord|2297711|2299920|ecoli_W3110|W3110}}  
W3110: 2298920..2298711<br /><gbrowseImage>
name=NC_007779:2298711..2298920
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2297711|2299920|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|2298711|2298920|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2297711..2299920 GBrowse(W3110)]
DH10B: 2384596..2384387<br /><gbrowseImage>
name=NC_010473:2384387..2384596
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2298711..2298920&plugin_action=Go FASTA Dump]
{{GBrowseLink|DH10B|NC_010473|2383969|2385014|GBrowse(DH10B)}}
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===Notes===
===Notes===
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{| 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" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
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{| 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" 
|- {{table_heading_style}}
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-
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''ccmD(del)'' (Keio:JW2186)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[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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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007273 ccmD::Tn5KAN-2] (FB20686)
|
Insertion at nt 94 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20686]
|
does not contain [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007273 ccmD::Tn5KAN-2] (FB20687)
|
Insertion at nt 94 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20687]
|
contains [[pKD46]]
|-
|
''ccmD751(del)''::kan
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100258|CGSC:100258]]
|
|-  
|
|
&Delta;ccmD (Keio:JW2186)
''ccmABCDEFG(del)''
|
|
deletion
deletion
|
|
Protien Accumulation
|
Loss of heme-containing membrane proteins.
|
PMID:7635817
|
|
See figure 3 for experimental results. 
|-
|
''ccmABCDEFG(del)''
|
|
deletion
deletion
|
|


|
cytochrome accumulation
|
Loss of cytochrome <sub>c550</sub>.
|
PMID:7635817
|
|
See figure 4 for experimental results. 
|-
|
''ccmABCDEFG(del)''
|
deletion
|
|


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
cytochrome biogenesis
|
Deficient cytochrome biogenesis
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
PMID:7635817
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|
See figure 5 for experimental results.
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW2186
JW2186
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
Line 160: Line 375:


Primer 2:CCTGCAGCCTCCTGCTGTTGCGC  
Primer 2:CCTGCAGCCTCCTGCTGTTGCGC  
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[[:Category:Kohara_Phage:20F6|20F6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=371 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:19D1|19D1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=372 Genobase]
|
PMID:3038334
|-
|
[[gatY:Gene|zbd-3104::Tn10]]
|
Linked marker
|
CAG12021 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39386 CGSC7344]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10
|-
|
[[napA:Gene|napA722::Tn10]]
|
Linked marker
|
CAG12098 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40003 CGSC7400]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 77% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zeg-722, zei-722::Tn10
 
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[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]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2088 EchoBASE:EB2088] 
EcoGene:EG12169
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2198 EcoliGenExpDB:b2198] 
RegulonDB:ECK120002065
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2735 ECOL199310CYC:C2735]
[http://www.ncbi.nlm.nih.gov/gene?term=946709 GeneID:946709]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12169 EcoGene:EG12169] 
EchoBASE:EB2088
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=CCMD ECOO157CYC:CCMD] 
ASAP:ABE-0007273
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
|
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:ccm genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

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.

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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

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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