proX: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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
!align=left {{table_heading_style}} |Standard name
||
''proX''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''proX''
Proline
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2673, b2679, JW2654, osrA, proU''<ref name='LIB:Riley_2006'/>, proU''


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!{{table_heading_style}} |Synonyms
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''ECK2673, b2679, JW2654, osrA, proU''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a9e3970f8b0"  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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MG1655
MG1655
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60.46 minutes&nbsp;
60.46 minutes&nbsp;
|
|
MG1655: 2805154..2806146<br />{{GBrowseFigureByCoord|2804154|2807146|ecoli|MG1655}}
MG1655: 2805154..2806146<br /><gbrowseImage>
name=NC_000913:2805154..2806146
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10773 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10773 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2804154..2807146 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2804154|2807146|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2805154..2806146&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2805154|2806146|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10773 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10773 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2701884..2702876<br /><gbrowseImage>
name=NC_012967:2701884..2702876
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2701884|2702876|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|2701884|2702876|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2690966..2691958<br /><gbrowseImage>
name=NC_012759:2690966..2691958
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2690966|2691958|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|2690966|2691958|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2805788..2806780<br />{{GBrowseFigureByCoord|2804788|2807780|ecoli_W3110|W3110}}
W3110: 2805788..2806780<br /><gbrowseImage>
name=NC_007779:2805788..2806780
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2804788..2807780 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2804788|2807780|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2805788..2806780&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2805788|2806780|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 2897696..2898688<br /><gbrowseImage>
name=NC_010473:2897696..2898688
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2895712|2900672|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2895712|2900672|FASTA Dump}}
 
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46a9e397be552"  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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Coding Start (SO:0000323)
|
[[MG1655]]
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2805217
|
Edman degradation
|
PMID:3305496<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9e39810caf"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
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&Delta;proX (Keio:JW2654)
&Delta;proX (Keio:JW2654)
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[[PMID:16738554]]<ref name=PMID:16738554/>|[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108374 CGSC10093]<ref name='LIB:cgsc'/>
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''&#916;proX770::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102480|CGSC:102480]]
|
 
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
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JW2654
JW2654
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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:Clone OK
Status:Clone OK
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Primer 2:CCtTTCTGCGCTGCCAGCGCCTC  
Primer 2:CCtTTCTGCGCTGCCAGCGCCTC  
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[[:Category:Kohara_Phage:8G10|8G10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=445 Genobase]
|
PMID:3038334
|-
|
[[pheA:Gene|pheA18::Tn10]]
|
Linked marker
|
CAG12158 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40091 CGSC7421]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 2% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[srlD:Gene|srlD3131::Tn10]]
|
Linked marker
|
CAG18642 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40097 CGSC7423]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 47% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10
 
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10773 EcoCyc:EG10773] 
EcoCyc:EG10773
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0766 EchoBASE:EB0766] 
|
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2679 EcoliGenExpDB:b2679] 
EcoGene:EG10773
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3232 ECOL199310CYC:C3232] 
RegulonDB:ECK120000764
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[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=EG10773 EcoGene:EG10773]
[http://www.ncbi.nlm.nih.gov/gene?term=947165 GeneID:947165]
|
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Escherichia coli str. K-12 substr. MG1655
|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=PROX ECOO157CYC:PROX] 
EchoBASE:EB0766
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/35653 CGSC:35653] 
ASAP:ABE-0008818
|
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''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:pro genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:43, 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

proX

Mnemonic

Proline

Synonyms

ECK2673, b2679, JW2654, osrA, proU[1], proU

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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

60.46 minutes 

MG1655: 2805154..2806146
<gbrowseImage> name=NC_000913:2805154..2806146 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2701884..2702876
<gbrowseImage> name=NC_012967:2701884..2702876 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2690966..2691958
<gbrowseImage> name=NC_012759:2690966..2691958 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2805788..2806780
<gbrowseImage> name=NC_007779:2805788..2806780 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2897696..2898688
<gbrowseImage> name=NC_010473:2897696..2898688 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

Coding Start (SO:0000323)

MG1655

2805217

Edman degradation

PMID:3305496[2]


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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

ΔproX (Keio:JW2654)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10093[4]

ΔproX770::kan

PMID:16738554[3]

CGSC:102480


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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

JW2654

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCCGACATAGCGTACTTTTTGC

Primer 2:CCtTTCTGCGCTGCCAGCGCCTC

8G10

Kohara Phage

Genobase

PMID:3038334[6]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[4]

est. P1 cotransduction: 2% [7]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[4]

est. P1 cotransduction: 47% [7]
Synonyms:zfh-3131::Tn10, zfi-3131::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:EG10773

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10773

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000764

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947165

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0766

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008818

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. ↑ Barron, A et al. (1987) Purification and characterization of a glycine betaine binding protein from Escherichia coli. J. Biol. Chem. 262 11841-6 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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
  6. ↑ 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
  7. ↑ 7.0 7.1 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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