hypF: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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*  
*  
****************************************************************************************** -->{{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="C46a9e466b99cc" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''hypF''  
''hypF''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Hydrogenase pleiotropic
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK2707, b2712, JW5433, hydA''<ref name='LIB:Riley_2006'/>
''ECK2707, b2712, JW5433, hydA''<ref name='LIB:Riley_2006'/>, hydA''


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*  
*  
****************************************************************************************** -->{{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;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a9e46743ff9"  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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61.06 minutes&nbsp;
61.06 minutes&nbsp;
|
|
MG1655: 2835447..2833195<br />{{GBrowseFigureByCoord|2832195|2836447|ecoli|MG1655}}
MG1655: 2835447..2833195<br /><gbrowseImage>
name=NC_000913:2833195..2835447
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11551 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11551 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2832195|2836447|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2832195|2836447|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|2833195|2835447|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2833195|2835447|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11551 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11551 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 2732285..2730033<br /><gbrowseImage>
name=NC_012967:2730033..2732285
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|2730033|2732285|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2730033|2732285|FASTA Dump}}
|-
|
[[BW2952]]
|
|
NC_012759: 2719007..2721259<br /><gbrowseImage>
name=NC_012759:2719007..2721259
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|2719007|2721259|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2719007|2721259|FASTA Dump}}
|-  
|-  
|
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&nbsp;
&nbsp;
|
|
W3110: 2836081..2833829<br />{{GBrowseFigureByCoord|2832829|2837081|ecoli_W3110|W3110}}
W3110: 2836081..2833829<br /><gbrowseImage>
name=NC_007779:2833829..2836081
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|2832829|2837081|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2832829|2837081|GBrowse(W3110)}}  
|
{{GBrowseFastaLink|W3110|NC_007779|2833829|2836081|FASTA Dump}}
|-
|
[[DH10B]]
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|2833829|2836081|FASTA Dump}}


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DH10B: 2927989..2925737<br /><gbrowseImage>
name=NC_010473:2925737..2927989
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2921233|2932493|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2921233|2932493|FASTA Dump}}
 
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*  
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****************************************************************************************** -->{{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;"   
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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*  
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****************************************************************************************** -->{{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}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="B46a9e46844ce1"  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
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|
|


|[[PMID:16738554]]<ref name=PMID:16738554/>
|
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|
   
   
|-
|
hypFH476A
|
|
H476A
|
|
Carbamoyl phosphate-dependent ATP hydrolysis activity diminished in vitro but sufficient for wild-type-like phenotype
|
|
|
seeded from [http://www.uniprot.org/uniprot/P30131 UniProt:P30131]
|-
|
hypFR23E,H,K
|


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R23E,H,K
|
 
|
Loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P30131 UniProt:P30131]
|-
|
hypFR23Q
|
 
|
R23Q
|
 
|
Diminishes activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P30131 UniProt:P30131]
|-
|
hypFC112A
|
 
|
C112A
|
 
|
Loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P30131 UniProt:P30131]
|-
|
hypFC162A
|
 
|
C162A
|
 
|
Loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P30131 UniProt:P30131]
|-
|
hypFH475A
|
 
|
H475A
|
 
|
Loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P30131 UniProt:P30131]
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15989.L4e04bd8708f32-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L4e04bd8708f32"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.15989.L4e04bd8708f32&page=15989&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15989.L4e04bd8708f32--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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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:cloned as old JW
Status:cloned as old JW
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Primer 2:CCTCCGTTCTGGACTTCACCCGC  
Primer 2:CCTCCGTTCTGGACTTCACCCGC  
|-
|
[[:Category:Kohara_Phage:9G10|9G10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=447 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1B2|1B2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=448 Genobase]
|
PMID:3038334
|-  
|-  
|
|
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Synonyms:cysC95::Tn10  
Synonyms:cysC95::Tn10  


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*  
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46a9e4699688e"  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=EG11551 EcoCyc:EG11551]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1512 EchoBASE:EB1512]
|
|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2712 EcoliGenExpDB:b2712]
EcoCyc:EG11551
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3268 ECOL199310CYC:C3268]
EcoGene:EG11551
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11551 EcoGene:EG11551]
RegulonDB:ECK120001504
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOO157/new-image?object=HYPF ECOO157CYC:HYPF]
[http://www.ncbi.nlm.nih.gov/gene?term=944963 GeneID:944963]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/18232 CGSC:18232]
EchoBASE:EB1512
|
|
''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=0008915&formSubmitReturn=1 ASAP:ABE-0008915]
ASAP:ABE-0008915
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:hyp genes]]
[[Category:hyp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:43, 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

hypF

Mnemonic

Hydrogenase pleiotropic

Synonyms

ECK2707, b2712, JW5433, hydA[1], hydA

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

61.06 minutes 

MG1655: 2835447..2833195
<gbrowseImage> name=NC_000913:2833195..2835447 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2732285..2730033
<gbrowseImage> name=NC_012967:2730033..2732285 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2719007..2721259
<gbrowseImage> name=NC_012759:2719007..2721259 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2836081..2833829
<gbrowseImage> name=NC_007779:2833829..2836081 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2927989..2925737
<gbrowseImage> name=NC_010473:2925737..2927989 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

ΔhypF (Keio:JW5433)

deletion

deletion

PMID:16738554[2]

Shigen

hypFH476A

H476A

Carbamoyl phosphate-dependent ATP hydrolysis activity diminished in vitro but sufficient for wild-type-like phenotype

seeded from UniProt:P30131

hypFR23E,H,K

R23E,H,K

Loss of activity

seeded from UniProt:P30131

hypFR23Q

R23Q

Diminishes activity

seeded from UniProt:P30131

hypFC112A

C112A

Loss of activity

seeded from UniProt:P30131

hypFC162A

C162A

Loss of activity

seeded from UniProt:P30131

hypFH475A

H475A

Loss of activity

seeded from UniProt:P30131

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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

JW5433

Plasmid clone

Shigen

PMID:16769691[3]

Status:cloned as old JW

Primer 1:GCCGCAAAAAACACATCTTGCGG

Primer 2:CCTCCGTTCTGGACTTCACCCGC

9G10

Kohara Phage

Genobase

PMID:3038334[4]

1B2

Kohara Phage

Genobase

PMID:3038334[4]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: 77% [6]
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10

cysI95::Tn10

Linked marker

CAG12173 = CGSC7425[5]

est. P1 cotransduction: 8% [6]
Synonyms:cysC95::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:EG11551

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11551

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001504

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944963

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1512

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008915

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. ↑ 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. ↑ 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
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  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).

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