modE:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Data loaded by TableEdit_Loader.
touch
 
(4 intermediate revisions by 2 users not shown)
Line 46: Line 46:
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK0750, b0761, JW0744, modR, chlD''<ref name='LIB:Riley_2006'/>
''ECK0750, b0761, JW0744, modR, chlD''<ref name='LIB:Riley_2006'/>, chlD''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 67: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="S46a9b81bb4253"  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="S46a9b81bb4253"  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: 795066..794278<br /><gbrowseImage>
W3110: 795066..794278<br /><gbrowseImage>
name=AC_000091:794278..795066
name=NC_007779:794278..795066
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
Line 134: Line 134:


|
|
{{GBrowseLink|W3110|AC_000091|793278|796066|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|793278|796066|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|W3110|AC_000091|794278|795066|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|794278|795066|FASTA Dump}}  
|-  
|-  
|
|
Line 172: Line 172:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="I46a9b81c5ca2f"  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="I46a9b81c5ca2f"  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="K46a9b81c9c6ff"  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="K46a9b81c9c6ff"  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
Line 319: Line 319:
*  
*  
****************************************************************************************** -->{{Genetic_interaction_help}}
****************************************************************************************** -->{{Genetic_interaction_help}}
{|   id="Q4e04bf7f0bedf"  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="Q4e04bf7f0bedf"  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 340: Line 340:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="G46a9b81d44e42"  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="G46a9b81d44e42"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 358: Line 358:


Primer 2:CCGCACAGCGTGGCGATAATCAC  
Primer 2:CCGCACAGCGTGGCGATAATCAC  
|-
|
[[:Category:Kohara_Phage:4H1|4H1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=179 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:10F3|10F3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=180 Genobase]
|
PMID:3038334
|-  
|-  
|
|
Line 377: Line 395:
est. P1 cotransduction: 34% <ref name='LIB:Nichols_linked_Tn'/> <br />  
est. P1 cotransduction: 34% <ref name='LIB:Nichols_linked_Tn'/> <br />  
Synonyms:zbi-29::Tn10  
Synonyms:zbi-29::Tn10  
|-
|
[[:Category:Kohara_Phage:4H1|4H1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=179 Genobase]
|
PMID:3038334


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 405: Line 414:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="K46a9b81dcd571"  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="K46a9b81dcd571"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6395 EcoCyc:G6395]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3017 EchoBASE:EB3017]
EcoCyc:G6395
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0761 EcoliGenExpDB:b0761]
EcoGene:EG13227
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0837 ECOL199310CYC:C0837]
RegulonDB:ECK120002995
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13227 EcoGene:EG13227]
[http://www.ncbi.nlm.nih.gov/gene?term=945366 GeneID:945366]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=MODE ECOO157CYC:MODE]
EchoBASE:EB3017
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0002585&formSubmitReturn=1 ASAP:ABE-0002585]
ASAP:ABE-0002585
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 476: Line 478:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="E46a6d559da3de"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a6d559da3de"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:33, 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

modE

Mnemonic

Molybdenum

Synonyms

ECK0750, b0761, JW0744, modR, chlD[1], chlD

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

17.09 minutes 

MG1655: 793867..793079
<gbrowseImage> name=NC_000913:793079..793867 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 775273..774485
<gbrowseImage> name=NC_012967:774485..775273 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 696047..696835
<gbrowseImage> name=NC_012759:696047..696835 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 795066..794278
<gbrowseImage> name=NC_007779:794278..795066 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 847795..847007
<gbrowseImage> name=NC_010473:847007..847795 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

ΔmodE (Keio:JW0744)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8806[3]

modEG133D

G133D

Transcription repression by modE even in the absence of molybdate

seeded from UniProt:P0A9G8

modE

Deletion

modEA76V

A76V

Partial loss of repression by modE

seeded from UniProt:P0A9G8

modET125I

T125I

Transcription repression by modE even in the absence of molybdate

seeded from UniProt:P0A9G8

ΔmodE733::kan

PMID:16738554[2]

CGSC:101916


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

JW0744

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCAGGCCGAAATCCTTCTCAC

Primer 2:CCGCACAGCGTGGCGATAATCAC

4H1

Kohara Phage

Genobase

PMID:3038334[5]

10F3

Kohara Phage

Genobase

PMID:3038334[5]

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[3]

est. P1 cotransduction: 62% [6]

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[3]

est. P1 cotransduction: 34% [6]
Synonyms:zbi-29::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:G6395

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13227

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002995

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945366

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3017

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002585

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. ↑ 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
  5. ↑ 5.0 5.1 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
  6. ↑ 6.0 6.1 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=modE:Gene&oldid=1477120"