EcoliWiki - User contributions [en]

rpoE:Gene Product(s)

2007-08-10T20:19:46Z

Bnichols: edited by Bnichols via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|rpoE}}{{Tab|Gene|rpoE}}{{Tab On|Gene Product(s)|rpoE}}{{Tab|Expression|rpoE}}{{Tab|Evolution|rpoE}}{{Tab|On One Page|rpoE}}{{TabsBottom}}
{|
|-
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Function |Function]]
|{{Sub}}[[#Interactions |Interactions]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References| References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude>
==Nomenclature==


{|{{Prettytable}}
|-
!{{table heading style}} |Standard name
|
RpoE product
|-
!{{table heading style}} |Synonyms
|
RNA polymerase, sigma 24 (sigma E) factor product<ref name='LIB:Riley_2006'/>, B2573 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, SigE product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, RpoE product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, sigma E factor product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, sigma24 factor product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, sigma 24 factor product<ref name='LIB:EcoCyc11.1'/><ref name='LIB:Riley_2006'/>
|-
!{{table heading style}} |Product description
|
sigmaE<ref name='LIB:EcoCyc10.6'/>; RNA polymerase, sigma 24 (sigma E) factor<ref name='LIB:EcoCyc11.1'/>;

Component of ; [[:Category:Complex:RNA polymerase sigma 24|RNA polymerase sigma 24]]<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>

|-
!{{table heading style}} |EC number (for enzymes)
|
*
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25440.V46aab0c3821f7&page=25440&pagename={{FULLPAGENAMEE}} edit table]
|}

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

==Function==
{{BacktoTop}}
<protect>
<big>'''Gene Ontology'''</big>


{|class = 'sortable' {{Prettytable}} id='170383'
|- {{table_heading_style}}
!Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|

|
GO:0006979
|
response to oxidative stress
|

|

|

|
P
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
|
required fields missing
|-
|

|
GO:0005737
|
cytoplasm
|

|

|

|
C
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
|
required fields missing
|-
|

|
GO:0016987
|
sigma factor activity
|

|

|

|
F
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
|
required fields missing
|-
|

|
GO:0006352
|
transcription initiation
|

|

|

|
P
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
|
required fields missing
|-
|

|
GO:0009266
|
response to temperature stimulus
|

|

|

|
P
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
|
required fields missing
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25440.X46aab0c5086fd&page=25440&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}

{{Product_GO_help}}

<big>'''Interactions'''</big>


{|class = 'sortable' {{Prettytable}} id='170384'
|- {{table heading style}}
!Partner Type!!Partner!!Notes
|-
|
Protein
|
Subunits of [[:Category:Complex:RNA polymerase sigma 24|RNA polymerase sigma 24]]
|
could be indirect
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25440.R46aab0e074942&page=25440&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

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

==Localization==


{|class = 'sortable' {{Prettytable}} id='170385'
|- {{table heading style}}
!Compartment!!Description!!Evidence!!Notes
|-
|
cytoplasm
|

|

|
From EcoCyc<ref name='LIB:EcoCyc11.1'/>
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25440.X46aab0e1a9d4e&page=25440&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}

{{Product_localization_help}}
<protect></protect>

===Notes===

==Structure and Physical Properties==
{{BacktoTop}}
<protect>
<big>'''Physical Properties'''</big>


{|{{Prettytable}}
|-
!{{table heading style}} |Sequence
|
[http://biocyc.org/ECOLI/sequence-aa?object=RPOE-MONOMER at EcoCyc]
<pre>MSEQLTDQVL VERVQKGDQK AFNLLVVRYQ HKVASLVSRY VPSGDVPDVV QEAFIKAYRA
LDSFRGDSAF YTWLYRIAVN TAKNYLVAQG RRPPSSDVDA IEAENFESGG ALKEISNPEN
LMLSEELRQI VFRTIESLPE DLRMAITLRE LDGLSYEEIA AIMDCPVGTV RSRIFRAREA
IDNKVQPLIR R</pre>
|-
!{{table heading style}} |Mol. Wt
|
21.7 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
|-
!{{table heading style}} |pI
|

|-
!{{table heading style}} |Extinction coefficient
|
15930 - 16055 (calc based on 7 Y, 1 W, and 1 C residues)
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25440.F46aab0e348616&page=25440&pagename={{FULLPAGENAMEE}} edit table]
|}

{{Product_physical_properties_help}}

<big>'''Domains/Motifs/Modification Sites'''</big>


{|class = 'sortable' {{Prettytable}} id='170387'
|- {{table heading style}}
!Type!!Residues!!Description!!Notes
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25440.N46aab0e3b76fc&page=25440&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}

{{Product_domains_motifs_help}}

<big>'''Structure'''</big>


{|class = 'sortable' {{Prettytable}} id='170388'
|- {{table heading style}}
!Structure Type!!Organism!!Accession!!Residues covered!!Notes
|-
|
X-RAY DIFFRACTION

|
Escherichia coli

|
[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1OR7 1OR7] Crystal Structure of Escherichia coli sigmaE with the Cytoplasmic Domain of its Anti-sigma RseA
|

|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25440.L46aab0e420fc5&page=25440&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|}

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

==Gene Product Resources==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='170389'
|- {{table_heading_style}}
!Resource type!!Source!!Notes/Reference
|-
|
Assay
|
Doodle database
[http://dimer.tamu.edu/doodle http://dimer.tamu.edu/doodle]
[[Doodle]]
|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25440.M46aab0e507882&page=25440&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

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

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


{|class = 'sortable' {{Prettytable}} id='170390'
|- {{table_heading_style}}
!Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=RPOE-MONOMER EcoCyc:RPOE-MONOMER]
|

|-
|
[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
|
[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P0AGB6 SwissModel:P0AGB6]
|

|-
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.expasy.ch/cgi-bin/sprot-search-ac?P0AGB6 UniProt:P0AGB6]
|

|-
|
[http://www.sanger.ac.uk/Software/Pfam/ PFAM] ([[PFAM|EcoliWiki Page]])
|
[http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF04542 PFAM:PF04542]
|

|-
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417068 RefSeq:NP_417068]
|

|-
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
|
[http://salilab.org/modbase/searchbyid?databaseID=P0AGB6 ModBase:P0AGB6]
|

|-
|
[http://www.rcsb.org/pdb PDB] ([[PDB|EcoliWiki Page]])
|
[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1OR7 PDB:1OR7]
|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25440.P46aab0e565b9e&page=25440&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

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

==Links==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='115562'
|- {{table_heading_style}}
!Name!!URL!!Comments
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.25440.F46a8490a1b34a&page=25440&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Links_help}}

<noinclude>
==References==
{{BacktoTop}}
{{RefHelp}}
<references/>
__NOTOC__
</noinclude>
===Categories===
{{BacktoTop}}
[[Category:GO:0006979_!_response to oxidative stress]][[Category:GO:0005737_!_cytoplasm]][[Category:GO:0016987_!_sigma factor activity]][[Category:GO:0006352_!_transcription initiation]][[Category:GO:0009266_!_response to temperature stimulus]][[Category:Complex:RNA polymerase sigma 24]][[Category:Location:cytoplasm]][[Category:Products with structures in PDB]]

rpoE:Gene

2007-08-10T20:14:00Z

Bnichols: edited by Bnichols via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|rpoE}}{{Tab On|Gene|rpoE}}{{Tab|Gene Product(s)|rpoE}}{{Tab|Expression|rpoE}}{{Tab|Evolution|rpoE}}{{Tab|On One Page|rpoE}}{{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
|
''rpoE''
|-
!{{table_heading_style}} |Mnemonic
|

|-
!{{table_heading_style}} |Synonyms
|
''ECK2571, b2573, JW2557, sigE''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15717.M46a9e141ec1ca&page=15717&pagename={{FULLPAGENAMEE}} edit table]
|}

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

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


{|class = 'sortable' {{Prettytable}} id='140347'
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
58.35 minutes 
|
MG1655: 2708034..2707459 {{GBrowseFigureByCoord|2706459|2709034|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11897 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2706459..2709034 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2707459..2708034&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=EG11897 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 2708668..2708093 {{GBrowseFigureByCoord|2707093|2709668|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2707093..2709668 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2708093..2708668&plugin_action=Go FASTA Dump]
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15717.C46a9e142765d4&page=15717&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|}

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

==Sequence Features==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='140348'
|- {{table_heading_style}}
!Feature type!!Location!!Description
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15717.F46a9e143303a3&page=15717&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

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

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


{|class = 'sortable' {{Prettytable}} id='140349'
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
ΔrpoE (Keio:)
|
deletion
|
deletion
|

|

|
[[PMID:16738554]]<ref name=PMID:16738554/>
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
rpoE is essential <ref name=PMID:/>. Does this strain carry a suppressor?
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15717.E46a9e143766ff&page=15717&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|}

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

==Genetic Resources==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='140350'
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
|-
|
JW2557
|
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:GCCAGCGAGCAGTTAACGGACCA

Primer 2:CCACGCCTGATAAGCGGTTGAAC
|-
|
[[hcaT:Gene|zfh-208::Tn10]]
|
Linked marker
|
CAG18481 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40086 CGSC7417]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 14% <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:zff-208::Tn10
|-
|
[[nadB:Gene|nadB51::Tn10]]
|
Linked marker
|
CAG18480 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40090 CGSC7419]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 93% <ref name='LIB:Nichols_linked_Tn'/>
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15717.O46a9e14430b8b&page=15717&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}

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

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


{|class = 'sortable' {{Prettytable}} id='140351'
|- {{table_heading_style}}
!Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11897 EcoCyc:EG11897]
|

|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1843 EchoBASE:EB1843]
|

|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2573 EcoliGenExpDB:b2573]
|

|-
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C3097 ECOL199310CYC:C3097]
|

|-
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG11897 EcoGene:EG11897]
|

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

|-
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/36181 CGSC:36181]
|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15717.X46a9e144c7863&page=15717&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

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

==Links==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='98693'
|- {{table_heading_style}}
!Name!!URL!!Comments
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15717.D46a6fdfb1c8b1&page=15717&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]]