cydB:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|cydB}}{{Tab On|Gene|cydB}}{{Tab|Gene Product(s)|cydB}}{{Tab|Expression|cydB}}{{Tab|Evolution|cydB}}{{Tab|On One Page|cydB}}{{TabsBottom}}
{{Tab|Quickview|cydB}}{{Tab On|Gene|cydB}}{{Tab|Gene Product(s)|cydB}}{{Tab|Expression|cydB}}{{Tab|Evolution|cydB}}{{Tab|On One Page|cydB}}{{TabsBottom}}
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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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</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|  id="O46a9b781107d5"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''cydB''  
''cydB''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Cytochrome d
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0722, b0734, JW0723, cyd-2''<ref name='LIB:Riley_2006'/>
''ECK0722, b0734, JW0723, cyd-2''<ref name='LIB:Riley_2006'/>
|-
 
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<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="X46a9b7818883d"  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
|-
|-  
|
|
MG1655
MG1655
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16.64 minutes&nbsp;
16.64 minutes&nbsp;
|
|
MG1655: 772265..773404<br />{{GBrowseFigureByCoord|771265|774404|ecoli|MG1655}}
MG1655: 772265..773404<br /><gbrowseImage>
name=NC_000913:772265..773404
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10174 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10174 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:771265..774404 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|771265|774404|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:772265..773404&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|772265|773404|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10174 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10174 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 753924..755063<br /><gbrowseImage>
name=NC_012967:753924..755063
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|753924|755063|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|753924|755063|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 675025..676164<br /><gbrowseImage>
name=NC_012759:675025..676164
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|675025|676164|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|675025|676164|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 773464..774603<br />{{GBrowseFigureByCoord|772464|775603|ecoli_W3110|W3110}}  
W3110: 773464..774603<br /><gbrowseImage>
name=NC_007779:773464..774603
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|772464|775603|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|773464|774603|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 824857..825996<br /><gbrowseImage>
name=NC_010473:824857..825996
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:772464..775603 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|822579|828274|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:773464..774603&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|822579|828274|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9b78230eb4"  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====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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''cydB(del)'' (Keio:JW0723)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=107071 CGSC8790]<ref name='LIB:cgsc'/>
|
|-
|
''cydB(del)''::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Hydroxybutyrate]]
|
PMID:16095938
|
 
|
|-
|
''cydB(del)''::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketobutyrate]]
|
PMID:16095938
|
 
|
|-
|
''cydB3''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:9473|CGSC:9473]]
|
|-
|
''cydB782(del)::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100464|CGSC:100464]]
|
|-
|
''CydAB (del), cyoABCD (del), cbdAB (del), ygiN (del)''
|
deletion
|
deletion
|
 
|
deletion of all genes decreased oxygen uptake by 98% via activation of ''arcA'', table 1.
|
PMID:20709841
|
 
|
|-
|
''CydAB(del), cyoABCD(del), cbdAB(del), ygiN(del)''
|
deletion
|
deletion
|
Growth Phenotype
|
Mutaiton causes decreased growth rate via inhibition of arcA, table 1.
|
PMID:20709841
|
 
|
|-
|
''CydAB(del), cyoABCD(del), cbdAB(del), ygiN(del)''
|
deletion
|
deletion
|
 
|
* Increase in glucose uptake rate
* increase in lactate secretion rate
* Decrease in acetate secretion rate
|
PMID:20709841
|
 
|
 
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===Notes===
===Notes===


==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A4e04b95059830"  class=" tableEdit Genetic_interaction_table dataTable" 
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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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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW0723
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCATCGATTATGAAGTATTGCG
 
Primer 2:CCGTACAGAGAGTGGGTGTTACG
|-
|
[[:Category:Kohara_Phage:18F11|18F11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=177 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:10G5|10G5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=178 Genobase]
|
PMID:3038334
|-
|
[[asnB:Gene|asnB3057::Tn10]]
|
Linked marker
|
CAG18433 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39394 CGSC7349]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 1% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.
|-
|
[[nadA:Gene|nadA57::Tn10]]
|
Linked marker
|
CAG12147 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38017 CGSC7351]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 78% <ref name='LIB:Nichols_linked_Tn'/>
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10174 EcoCyc:EG10174] 
EcoCyc:EG10174
|
|
''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=EB0171 EchoBASE:EB0171] 
EcoGene:EG10174
|
|
''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=b0734 EcoliGenExpDB:b0734] 
RegulonDB:ECK120000169
|
|
''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=C0812 ECOL199310CYC:C0812]
[http://www.ncbi.nlm.nih.gov/gene?term=945347 GeneID:945347]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10174 EcoGene:EG10174] 
EchoBASE:EB0171
|
|
''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=CYDB ECOO157CYC:CYDB] 
ASAP:ABE-0002501
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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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:cyd genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:34, 19 September 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

cydB

Mnemonic

Cytochrome d

Synonyms

ECK0722, b0734, JW0723, cyd-2[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

16.64 minutes 

MG1655: 772265..773404
<gbrowseImage> name=NC_000913:772265..773404 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 753924..755063
<gbrowseImage> name=NC_012967:753924..755063 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 675025..676164
<gbrowseImage> name=NC_012759:675025..676164 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 773464..774603
<gbrowseImage> name=NC_007779:773464..774603 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 824857..825996
<gbrowseImage> name=NC_010473:824857..825996 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

cydB(del) (Keio:JW0723)

deletion

deletion

PMID:16738554[2]

Shigen

CGSC8790[3]

cydB(del)::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938[4]

cydB(del)::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[4]

cydB3

CGSC:9473

cydB782(del)::kan

PMID:16738554[2]

CGSC:100464

CydAB (del), cyoABCD (del), cbdAB (del), ygiN (del)

deletion

deletion

deletion of all genes decreased oxygen uptake by 98% via activation of arcA, table 1.

PMID:20709841[5]

CydAB(del), cyoABCD(del), cbdAB(del), ygiN(del)

deletion

deletion

Growth Phenotype

Mutaiton causes decreased growth rate via inhibition of arcA, table 1.

PMID:20709841[5]

CydAB(del), cyoABCD(del), cbdAB(del), ygiN(del)

deletion

deletion

  • Increase in glucose uptake rate
  • increase in lactate secretion rate
  • Decrease in acetate secretion rate

PMID:20709841[5]


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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

JW0723

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCATCGATTATGAAGTATTGCG

Primer 2:CCGTACAGAGAGTGGGTGTTACG

18F11

Kohara Phage

Genobase

PMID:3038334[7]

10G5

Kohara Phage

Genobase

PMID:3038334[7]

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[3]

est. P1 cotransduction: 1% [8]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[3]

est. P1 cotransduction: 78% [8]

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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:EG10174

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10174

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000169

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945347

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0171

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002501

Escherichia coli str. K-12 substr. MG1655

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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. ↑ 4.0 4.1 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  5. ↑ 5.0 5.1 5.2 Portnoy, VA et al. (2010) Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. Appl. Environ. Microbiol. 76 6529-40 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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