ccmA:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
imported>Wikientrybot
Bulk deleting accessions.
touch
 
(7 intermediate revisions by 3 users not shown)
Line 46: Line 46:
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK2193, b2201, JW5366, yejW''<ref name='LIB:Riley_2006'/>
''ECK2193, b2201, JW5366, yejW''<ref name='LIB:Riley_2006'/>, yejW''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 67: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="U46a9d86035ac9"  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="U46a9d86035ac9"  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
Line 128: Line 128:
|
|
W3110: 2300978..2300355<br /><gbrowseImage>
W3110: 2300978..2300355<br /><gbrowseImage>
name=AC_000091:2300355..2300978
name=NC_007779:2300355..2300978
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
Line 134: Line 134:


|
|
{{GBrowseLink|W3110|AC_000091|2299355|2301978|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2299355|2301978|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|W3110|AC_000091|2300355|2300978|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|2300355|2300978|FASTA Dump}}  
|-  
|-  
|
|
Line 172: Line 172:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="B46a9d860dfa61"  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="B46a9d860dfa61"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
Line 194: Line 194:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="B46a9d86130552"  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="B46a9d86130552"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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
|-  
|-  
|
|
&Delta;ccmA (Keio:JW5366)
''ccmA(del)'' (Keio:JW5366)
|
|
deletion
deletion
Line 211: Line 211:
PMID:16738554
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109625 CGSC11344]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=109625 CGSC11344]<ref name='LIB:cgsc'/>  
|
|
   
   
Line 250: Line 250:
|-  
|-  
|
|
''&#916;ccmA754::kan''
''ccmA754(del)''::kan
|
|


Line 265: Line 265:
|
|
   
   
|-
|
''ccmABCDEFG(del)''
|
deletion
|
|
Protien production
|
Loss of heme-containing membrane proteins
|
PMID:7635817
|
|
See Figure 3 for experimental results. 
|-
|
''ccmABCDEFG(del)''
|
deletion
|
|
cytochrome accumulation
|
Loss of mature cytochrome<sub>c550</sub>
|
PMID:7635817
|
|
See Figure 4 for experimental results. 
|-
|
''ccmABCDEFG(del)''
|
deletion
|
|
cytochrome biogenesis
|
Deficient cytochrome biogenesis
|
PMID:7635817
|
|
See Figure 5 for experimental results. 


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 285: Line 336:
*  
*  
****************************************************************************************** -->{{Genetic_interaction_help}}
****************************************************************************************** -->{{Genetic_interaction_help}}
{|   id="T4e04b88b2e4d6"  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="T4e04b88b2e4d6"  class=" tableEdit Genetic_interaction_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
Line 306: Line 357:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="C46a9d861da966"  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="C46a9d861da966"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 381: Line 432:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="B46a9d8627a2c0"  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="B46a9d8627a2c0"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|
[[EcoCyc]]
|
EcoCyc:EG12059
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG12059
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120001971
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=946714 GeneID:946714]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EchoBASE]]
|
EchoBASE:EB1989
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[ASAP]]
|
ASAP:ABE-0007279
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 403: Line 496:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="Z46a6f59172614"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a6f59172614"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

ccmA

Mnemonic

Cytochrome c maturation

Synonyms

ECK2193, b2201, JW5366, yejW[1], yejW

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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

49.47 minutes 

MG1655: 2295666..2295043
<gbrowseImage> name=NC_000913:2295043..2295666 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2247633..2247010
<gbrowseImage> name=NC_012967:2247010..2247633 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2180848..2181471
<gbrowseImage> name=NC_012759:2180848..2181471 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2300978..2300355
<gbrowseImage> name=NC_007779:2300355..2300978 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2386654..2386031
<gbrowseImage> name=NC_010473:2386031..2386654 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
edit table


Notes

Alleles and Phenotypes

[back to top]


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

ccmA(del) (Keio:JW5366)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11344[3]

ccmA::Tn5KAN-2 (FB20692)

Insertion at nt 163 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20692

does not contain pKD46

ccmA::Tn5KAN-2 (FB20693)

Insertion at nt 163 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20693

contains pKD46

ccmA754(del)::kan

PMID:16738554[2]

CGSC:100252

ccmABCDEFG(del)

deletion

Protien production

Loss of heme-containing membrane proteins

PMID:7635817[5]

See Figure 3 for experimental results.

ccmABCDEFG(del)

deletion

cytochrome accumulation

Loss of mature cytochromec550

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
edit table


Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW5366

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGGTATGCTTGAAGCCAGAGA

Primer 2:CCTGCGGCCCTCGTTTGCGTCAG

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: 81% [8]
Synonyms:zeg-722, zei-722::Tn10

edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG12059

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12059

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001971

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946714

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1989

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007279

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]



<protect>

References

[back to top]


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

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=ccmA:Gene&oldid=1478653"