EcoliWiki - User contributions [en]

PMID:319345

2007-08-10T21:18:08Z

Durf: New PMID: Page!

<protect>
{{RightTOC}}

 '''Fiil, NP, Willumsen, BM, Friesen, JD and von Meyenburg, K''' (1977) Interaction of alleles of the relA, relC and spoT genes in Escherichia coli: analysis of the interconversion of GTP, ppGpp and pppGpp.''Mol. Gen. Genet.'' '''150''':87-101

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || Mutants in the spo T gene have been isolated as stringent second site revertants of the relC mutation. These show varying degrees of the characteristics associated with the spoT1 gene, viz relative amount and absolute levels of both pppGpp and ppGpp and the decay rate of the latter. The entry of 3H-guanosine into GTP and ppGpr pools in spoT+ and spoT1 cells either growing exponentially or during amino acid starvation was determined, and the rate of ppGpp synthesis and its decay constant calculated. During exponential growth the ppGpp pool is 2-fold higher, its decay constant 10-fold lower, and its synthesis rate 5-fold lower in spoT- than in spoT+ cells; during amino acid starvation the ppGpp pool is 2-fold higher, its decay constant 20-fold lower, and its synthesis rate 10-fold lower in spoT than in spoT+ cells. In one of the "intermediate" spoT mutants the rate of entry of 3H-guanosine into GTP, ppGpp and pppGpp was measured during amino acid starvation. The data form the basis of a model for the interconversion of the guanosine nucleotides in which the flow is: GDP leads to GTP leads to pppGpp leads to ppGpp leads to Y. Calculations of the rates of synthesis and conversion of pppGpp and ppGpp under various conditions in various spoT+ and spoT- strains indicate that the ppGpp concentration indirectly controls the rate of pppGpp synthesis.
</noinclude>
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=319345 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='220175'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.T46bcd60ff1097&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==References==
{{RefHelp}}
<references/>

spoT:Gene

2007-08-10T21:17:45Z

Durf: edited by Durf via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|spoT}}{{Tab On|Gene|spoT}}{{Tab|Gene Product(s)|spoT}}{{Tab|Expression|spoT}}{{Tab|Evolution|spoT}}{{Tab|On One Page|spoT}}{{TabsBottom}}
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude><protect>
==Nomenclature==
{{BacktoTop}}


{|{{Prettytable}}
|-
!{{table_heading_style}} |Standard name
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''spoT''
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!{{table_heading_style}} |Mnemonic
|

|-
!{{table_heading_style}} |Synonyms
|
''ECK3640, b3650, JW3625''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.U46a9fb5d00e88&page=17855&pagename={{FULLPAGENAMEE}} edit table]
|}

{{Gene_nomenclature_help}}
</protect>
===Notes===

==Location(s) and DNA Sequence==
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<protect>


{|class = 'sortable' {{Prettytable}} id='146769'
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
82.34 minutes 
|
MG1655: 3820423..3822531 {{GBrowseFigureByCoord|3819423|3823531|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10966 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3819423..3823531 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3820423..3822531&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=EG10966 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 3818015..3815907 {{GBrowseFigureByCoord|3814907|3819015|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3814907..3819015 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3815907..3818015&plugin_action=Go FASTA Dump]
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.X46a9fb5d821f7&page=17855&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|}

{{Gene_location_help}}
</protect>
===Notes===

==Sequence Features==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='146770'
|- {{table_heading_style}}
!Feature type!!Location!!Description
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.O46a9fb5e45982&page=17855&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_sequence_features_help}}
<protect></protect>
====Notes====

==Alleles and Phenotypes==
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{|class = 'sortable' {{Prettytable}} id='146771'
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
ΔspoT (Keio:)
|
deletion
|
deletion
|

|

|
[[PMID:16738554]]<ref name=PMID:16738554/>
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|

|-
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spoT1
|

|

|

|

|
[[PMID:319345]]<ref name=PMID:319345/>
|

|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.U46a9fb5e8f362&page=17855&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|}

{{Gene_alleles_help}}
<protect></protect>
===Notes===

==Genetic Resources==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='146772'
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
|-
|
JW3625
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
[[PMID:16769691]]<ref name=PMID:16769691/>

Status:Clone OK

Primer 1:GCCTATCTGTTTGAAAGCCTGAA

Primer 2:CCATTTCGGTTTCGGGTGACTTT
|-
|
zhg-50::Tn10
|
Linked marker
|
CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:zhf-50::Tn10, zhf-5::Tn10
|-
|
zic-4901::Tn10
|
Linked marker
|
CAG18492 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38944 CGSC7457]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 78% <ref name='LIB:Nichols_linked_Tn'/>
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.U46a9fb5f52bc4&page=17855&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}

{{Gene_resources_help}}
<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='146773'
|- {{table_heading_style}}
!Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10966 EcoCyc:EG10966]
|

|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0959 EchoBASE:EB0959]
|

|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3650 EcoliGenExpDB:b3650]
|

|-
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C4475 ECOL199310CYC:C4475]
|

|-
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG10966 EcoGene:EG10966]
|

|-
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOO157/new-image?object=SPOT ECOO157CYC:SPOT]
|

|-
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/156 CGSC:156]
|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.O46a9fb5ff20ed&page=17855&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_accessions_help}}
<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='99754'
|- {{table_heading_style}}
!Name!!URL!!Comments
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.N46a715bdb70e6&page=17855&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Links_help}}

<noinclude><protect>
==References==
{{BacktoTop}}
{{RefHelp}}
<references/>
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]

spoT:Gene

2007-08-10T21:15:12Z

Durf: edited by Durf via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|spoT}}{{Tab On|Gene|spoT}}{{Tab|Gene Product(s)|spoT}}{{Tab|Expression|spoT}}{{Tab|Evolution|spoT}}{{Tab|On One Page|spoT}}{{TabsBottom}}
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude><protect>
==Nomenclature==
{{BacktoTop}}


{|{{Prettytable}}
|-
!{{table_heading_style}} |Standard name
|
''spoT''
|-
!{{table_heading_style}} |Mnemonic
|

|-
!{{table_heading_style}} |Synonyms
|
''ECK3640, b3650, JW3625''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.U46a9fb5d00e88&page=17855&pagename={{FULLPAGENAMEE}} edit table]
|}

{{Gene_nomenclature_help}}
</protect>
===Notes===

==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>


{|class = 'sortable' {{Prettytable}} id='146769'
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
82.34 minutes 
|
MG1655: 3820423..3822531 {{GBrowseFigureByCoord|3819423|3823531|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10966 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3819423..3823531 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3820423..3822531&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=EG10966 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 3818015..3815907 {{GBrowseFigureByCoord|3814907|3819015|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3814907..3819015 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3815907..3818015&plugin_action=Go FASTA Dump]
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.X46a9fb5d821f7&page=17855&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|}

{{Gene_location_help}}
</protect>
===Notes===

==Sequence Features==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='146770'
|- {{table_heading_style}}
!Feature type!!Location!!Description
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.O46a9fb5e45982&page=17855&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_sequence_features_help}}
<protect></protect>
====Notes====

==Alleles and Phenotypes==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='146771'
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
ΔspoT (Keio:)
|
deletion
|
deletion
|

|

|
[[PMID:16738554]]<ref name=PMID:16738554/>
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|

|-
|
spoT1
|

|

|

|

|

|

|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.U46a9fb5e8f362&page=17855&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|}

{{Gene_alleles_help}}
<protect></protect>
===Notes===

==Genetic Resources==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='146772'
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
|-
|
JW3625
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
[[PMID:16769691]]<ref name=PMID:16769691/>

Status:Clone OK

Primer 1:GCCTATCTGTTTGAAAGCCTGAA

Primer 2:CCATTTCGGTTTCGGGTGACTTT
|-
|
zhg-50::Tn10
|
Linked marker
|
CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:zhf-50::Tn10, zhf-5::Tn10
|-
|
zic-4901::Tn10
|
Linked marker
|
CAG18492 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38944 CGSC7457]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 78% <ref name='LIB:Nichols_linked_Tn'/>
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.U46a9fb5f52bc4&page=17855&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}

{{Gene_resources_help}}
<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='146773'
|- {{table_heading_style}}
!Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10966 EcoCyc:EG10966]
|

|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0959 EchoBASE:EB0959]
|

|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3650 EcoliGenExpDB:b3650]
|

|-
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C4475 ECOL199310CYC:C4475]
|

|-
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG10966 EcoGene:EG10966]
|

|-
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOO157/new-image?object=SPOT ECOO157CYC:SPOT]
|

|-
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/156 CGSC:156]
|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.O46a9fb5ff20ed&page=17855&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_accessions_help}}
<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='99754'
|- {{table_heading_style}}
!Name!!URL!!Comments
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17855.N46a715bdb70e6&page=17855&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Links_help}}

<noinclude><protect>
==References==
{{BacktoTop}}
{{RefHelp}}
<references/>
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]