malF:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Data loaded by TableEdit_Loader.
Update TableEdit tables.
Line 31: Line 31:
*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{| id="Y46aa0543b0c08" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left |Standard name
||
||
''malF''  
''malF''  
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left |Mnemonic
||
||


|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left |Synonyms
||
||
''ECK4025, b4033, JW3993''<ref name='LIB:Riley_2006'/>
''ECK4025, b4033, JW3993''<ref name='LIB:Riley_2006'/>


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.Y46aa0543b0c08&page=18625&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.Y46aa0543b0c08&page=18625&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.Y46aa0543b0c08-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.Y46aa0543b0c08-->
Line 65: Line 65:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="R46aa05443f453" class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
|-
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-  
|-  
Line 82: Line 82:
{{GBrowseFastaLink|ecoli|NC_000913|4241554|4243098|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|4241554|4243098|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10555 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10555 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 4222463..4224007<br />{{GBrowseFigureByCoord|4222463|4224007|REL606|NC_012967}}
|
{{GBrowseLink|REL606|NC_012967|4222463|4224007|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4222463|4224007|FASTA Dump}}
|-  
|-  
|
|
Line 104: Line 115:
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4338162|4345882|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4338162|4345882|FASTA Dump}}  
|-
|
[[REL606]]
|
|
NC_012967: 4222463..4224007<br />{{GBrowseFigureByCoord|4222463|4224007|REL606|NC_012967}}
|
{{GBrowseLink|REL606|NC_012967|4222463|4224007|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4222463|4224007|FASTA Dump}}


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.R46aa05443f453&page=18625&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.R46aa05443f453&page=18625&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.R46aa05443f453-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.R46aa05443f453-->
Line 134: Line 134:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="H46aa054506203" class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|-
!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.H46aa054506203&page=18625&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.H46aa054506203&page=18625&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.H46aa054506203-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.H46aa054506203-->
Line 156: Line 156:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{|   id="D46aa0545516e9" class=" tableEdit Gene_allele_table"
|- {{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
|-  
|-  
Line 296: Line 296:
   
   


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.D46aa0545516e9&page=18625&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.D46aa0545516e9&page=18625&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.D46aa0545516e9-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.D46aa0545516e9-->
Line 314: Line 314:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="J46aa0546185ab" class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|-
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-  
|-  
Line 352: Line 352:
est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/>  


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.J46aa0546185ab&page=18625&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table] || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.J46aa0546185ab&page=18625&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.J46aa0546185ab-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.J46aa0546185ab-->
Line 370: Line 370:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="Z46aa0546ba1d6" class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|-
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
Line 430: Line 430:
   
   


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.Z46aa0546ba1d6&page=18625&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.Z46aa0546ba1d6&page=18625&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.Z46aa0546ba1d6-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.Z46aa0546ba1d6-->
Line 448: Line 448:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="Q46a71e8f6cf9f" class=" tableEdit Links_table"   
|- {{table_heading_style}}
|-
!|Name!!URL!!Comments
!|Name!!URL!!Comments


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.Q46a71e8f6cf9f&page=18625&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.Q46a71e8f6cf9f&page=18625&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.Q46a71e8f6cf9f-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18625.Q46a71e8f6cf9f-->

Revision as of 02:02, 9 January 2010

{{#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 Alleles and Phenotypes 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

malF

Mnemonic
Synonyms

ECK4025, b4033, JW3993[1]

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

91.42 minutes, 91.42 minutes 

MG1655: 4243098..4241554
gbrowse_img.php?coord=4241554..4243098&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 4222463..4224007
gbrowse_img.php?coord=4222463..4224007&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 4248665..4247121
gbrowse_img.php?coord=4247121..4248665&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 4342794..4341250
gbrowse_img.php?coord=4341250..4342794&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

edit table


Notes

Sequence Features

[back to top]


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

Feature type Location Description
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

ΔmalF (Keio:JW3993)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10874[3]

malF3089::Tn10

Insertion at 4,242,342 bp in MG1655 (NC_000913)

adapted from Nichols et al.[4]

CAG12164 = CGSC7476[3]

Synonyms:

malF64(Oc)

CGSC:7076

ochre (UAA) mutation

malF55::Tn10

CGSC:9952

malF59::Tn5

CGSC:9960

malF3089::Tn10

PMID:2540407[5]

CGSC:40369

malF3180::Tn10kan

PMID:2540407[5]

CGSC:40372

ΔmalF729::kan

PMID:16738554[2]

CGSC:101732


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

JW3993

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGATGTCATTAAAAAGAAACA

Primer 2:CCATCAAACTTCATTCGCGTGGC

thiC39::Tn10

Linked marker

CAG18500 = CGSC7472[3]

est. P1 cotransduction: 12% [4]
Synonyms:thi-39::Tn10

zje-2241::Tn10

Linked marker

CAG18427 = CGSC7481[3]

est. P1 cotransduction: 3% [4]

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 (EcoliWiki Page)

EcoCyc:EG10555

EchoBASE (EcoliWiki Page)

EchoBASE:EB0550

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4033

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C5003

EcoGene (EcoliWiki Page)

EcoGene:EG10555

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:MALF

CGSC (EcoliWiki Page)

CGSC:531

ASAP (EcoliWikiPage)

ASAP:ABE-0013195


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 3.3 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 4.2 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).
  5. ↑ 5.0 5.1 Singer, M et al. (1989) A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53 1-24 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

Categories

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=malF:Gene&oldid=981753"