pheS: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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{|{{Prettytable}}
{|   id="D46a9cd392a667"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''pheS''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''pheS''
Phenylalanine
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1712, b1714, JW5277, phe-act''<ref name='LIB:Riley_2006'/>, phe-act''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13999.D46a9cd392a667&page=13999&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK1712, b1714, JW5277, phe-act''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='135198'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9cd39a5648"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
MG1655
Line 72: Line 76:
38.71 minutes&nbsp;
38.71 minutes&nbsp;
|
|
MG1655: 1796966..1795983<br />{{GBrowseFigureByCoord|1794983|1797966|ecoli|MG1655}}
MG1655: 1796966..1795983<br /><gbrowseImage>
name=NC_000913:1795983..1796966
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10709 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10709 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1794983|1797966|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1794983|1797966|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1795983..1796966&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1795983|1796966|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10709 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10709 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 1776209..1775226<br /><gbrowseImage>
name=NC_012967:1775226..1776209
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1775226|1776209|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|1775226|1776209|FASTA Dump}}
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[[BW2952]]
|
 
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NC_012759: 1688042..1689025<br /><gbrowseImage>
name=NC_012759:1688042..1689025
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1688042|1689025|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|1688042|1689025|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1800656..1799673<br />{{GBrowseFigureByCoord|1798673|1801656|ecoli_W3110|W3110}}  
W3110: 1800656..1799673<br /><gbrowseImage>
name=NC_007779:1799673..1800656
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1798673|1801656|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|1799673|1800656|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 1887537..1886554<br /><gbrowseImage>
name=NC_010473:1886554..1887537
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1798673..1801656 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|1884588|1889503|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1799673..1800656&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|1884588|1889503|FASTA Dump}}
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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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;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="W46a9cd3a9a733"  class=" tableEdit Gene_allele_table dataTable" 
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!|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
|-
|
pheSG98D
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|
G98D
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(in thermosensitive mutant pheS5; might cause subunit disaggregation due to electrostatic repulsion)
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|
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P08312 UniProt:P08312]
|-
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pheSG191D
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|
G191D
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|
(decreased affinity for Phe)
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|
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Strain variation; seeded from [http://www.uniprot.org/uniprot/P08312 UniProt:P08312]
|-
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''pheS11''
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|
|
|
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[[cgscmutation:8052|CGSC:8052]]
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temperature sensitive
temperature sensitive
|
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[[PMID:1537809]]<ref name=PMID:1537809/>
PMID:1537809
|
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[[cgscmutation:4877|CGSC:4877]]
[[cgscmutation:4877|CGSC:4877]]
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''pheS11''
''pheS'' in strain PFP-10
|
 
|
 
|
Resistant to
|
Resistant to Gluoro(4)phenylalanine
|
PMID:14213362
|
Strain: PFP-10
|
|-
|
''pheS294''
|
|


|
Serine to Alanine at position 294
|
Resistant to
|
Resistant to Fluoro(4)phenylalanine
|
PMID:1942071
|
Strain: AB1360-12
|
table 3
|-
|
''pheS'' in strain KB1360
|
|


|
|


|
Resistant to
|
Resistance to Fluoro(4)phenyalanine
|
PMID:3032903
|
Strain: KB1360
|
table 1
|-
|
''pheS''  in strain 6C5
|
|


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|
|
[[cgscmutation:8052|CGSC:8052]]
Resistant to
|
Thymineless death resistance in ''thyA''. Under the condition of 42C.
|
PMID:4868365
|
Strain: 6C5
|
|
Figure 4


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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13999.K4e04c1003fd73-->
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW5277
JW5277
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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:CCTTTAAACTGTTTGAGGAAACG  
Primer 2:CCTTTAAACTGTTTGAGGAAACG  
|-
|-
|
[[:Category:Kohara_Phage:20F5|20F5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=322 Genobase]
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PMID:3038334
|-
|
[[:Category:Kohara_Phage:20H8|20H8]]
|
Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=323 Genobase]
|
PMID:3038334
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zdi-925::Tn10
zdi-925::Tn10
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CAG12151 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39862 CGSC7385]<ref name='LIB:cgsc'/>
CAG12151 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39862 CGSC7385]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 50% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 50% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zdh-925::Tn10  
Synonyms:zdh-925::Tn10  
|-
|-  
|
|
[[ynjB:Gene|zdj-276::Tn10]]
[[ynjB:Gene|zdj-276::Tn10]]
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CAG18464 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39972 CGSC7387]<ref name='LIB:cgsc'/>
CAG18464 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39972 CGSC7387]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 22% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 22% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zdi-276::Tn10


Synonyms:zdi-276::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=EG10709 EcoCyc:EG10709]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0703 EchoBASE:EB0703]
|
|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1714 EcoliGenExpDB:b1714]
EcoCyc:EG10709
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EcoGene]]
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|
[http://BioCyc.org/ECOL199310/new-image?object=C2112 ECOL199310CYC:C2112]
EcoGene:EG10709
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''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=EG10709 EcoGene:EG10709]
RegulonDB:ECK120000701
|
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''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=PHES ECOO157CYC:PHES]
[http://www.ncbi.nlm.nih.gov/gene?term=946223 GeneID:946223]
|
|
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/400 CGSC:400]
EchoBASE:EB0703
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0005722&formSubmitReturn=1 ASAP:ABE-0005722] 
ASAP:ABE-0005722
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Categories===
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[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:phe genes]]
[[Category:phe genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:38, 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

pheS

Mnemonic

Phenylalanine

Synonyms

ECK1712, b1714, JW5277, phe-act[1], phe-act

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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

38.71 minutes 

MG1655: 1796966..1795983
<gbrowseImage> name=NC_000913:1795983..1796966 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1776209..1775226
<gbrowseImage> name=NC_012967:1775226..1776209 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1688042..1689025
<gbrowseImage> name=NC_012759:1688042..1689025 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1800656..1799673
<gbrowseImage> name=NC_007779:1799673..1800656 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1887537..1886554
<gbrowseImage> name=NC_010473:1886554..1887537 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

pheSG98D

G98D

(in thermosensitive mutant pheS5; might cause subunit disaggregation due to electrostatic repulsion)

Strain variation; seeded from UniProt:P08312

pheSG191D

G191D

(decreased affinity for Phe)

Strain variation; seeded from UniProt:P08312

pheS11

CGSC:8052

pheS5(ts)

temperature sensitive

PMID:1537809[2]

CGSC:4877

pheS in strain PFP-10

Resistant to

Resistant to Gluoro(4)phenylalanine

PMID:14213362[3]

Strain: PFP-10

pheS294

Serine to Alanine at position 294

Resistant to

Resistant to Fluoro(4)phenylalanine

PMID:1942071[4]

Strain: AB1360-12

table 3

pheS in strain KB1360

Resistant to

Resistance to Fluoro(4)phenyalanine

PMID:3032903[5]

Strain: KB1360

table 1

pheS in strain 6C5

Resistant to

Thymineless death resistance in thyA. Under the condition of 42C.

PMID:4868365[6]

Strain: 6C5

Figure 4

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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

JW5277

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCTCACATCTCGCAGAACTGGT

Primer 2:CCTTTAAACTGTTTGAGGAAACG

20F5

Kohara Phage

Genobase

PMID:3038334[8]

20H8

Kohara Phage

Genobase

PMID:3038334[8]

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[9]

est. P1 cotransduction: 50% [10]
Synonyms:zdh-925::Tn10

zdj-276::Tn10

Linked marker

CAG18464 = CGSC7387[9]

est. P1 cotransduction: 22% [10]
Synonyms:zdi-276::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:EG10709

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10709

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000701

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946223

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0703

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005722

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. ↑ Kast, P et al. (1992) Identification of the pheS5 mutation, which causes thermosensitivity of Escherichia coli mutant NP37. J. Bacteriol. 174 1686-9 PubMed
  3. ↑ FANGMAN, WL & NEIDHARDT, FC (1964) DEMONSTRATION OF AN ALTERED AMINOACYL RIBONUCLEIC ACID SYNTHETASE IN A MUTANT OF ESCHERICHIA COLI. J. Biol. Chem. 239 1839-43 PubMed
  4. ↑ Kast, P & Hennecke, H (1991) Amino acid substrate specificity of Escherichia coli phenylalanyl-tRNA synthetase altered by distinct mutations. J. Mol. Biol. 222 99-124 PubMed
  5. ↑ Borg-Olivier, SA et al. (1987) Defective regulation of the phenylalanine biosynthetic operon in mutants of the phenylalanyl-tRNA synthetase operon. J. Bacteriol. 169 1949-53 PubMed
  6. ↑ Kaplan, S & Anderson, D (1968) Selection of temperature-sensitive activating enzyme mutants in Escherichia coli. J. Bacteriol. 95 991-7 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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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