SubtiWiki - User contributions [en]

Main Page

2012-03-12T09:31:30Z

MLehnik:

<big>Welcome to '''''Subti''Wiki'''! </big> - ''Bacillus subtilis'' annotation the "wiki" way! 
[[File:Start_page_small.png|right|link=http://www.subtiwiki.uni-goettingen.de/]]
[[File:Playground_small.png|right|link=http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Playground]]
[[File:Wish_List_small.png|right|link=http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Wish_List]]
 
<big>'''Contact:'''</big> [http://wwwuser.gwdg.de/~genmibio/stuelke.html General Microbiology, University of Göttingen], [mailto:jstuelk@gwdg.de send mail]

 
<big>'''Upcoming events:'''</big>
* '''April 16 - 19, 2012:''' The 5th European Spore Conference will take place in London, UK. [mailto:s.cutting@rhul.ac.uk contact], [http://www.sporesconference.com conference website]
* '''April 24 - 25, 2012:''' The BACELL meeting 2012 will be organized by [[Kevin Devine]] in Dublin, Ireland. [mailto:KDEVINE@tcd.ie contact], '''The deadline for registration is approaching!'''
'''[[Past conferences]]'''

 
<big>'''New: Subtiwiki is now on [http://www.facebook.com/pages/SubtiWiki/201847669864806 Facebook] - please give it a +1!'''</big>

 
<big>'''Now online: A description of ''Subti''Wiki, ''Subti''Pathways, and ''Subt''Interact in the [http://nar.oxfordjournals.org/content/40/D1/D1278.full.pdf+html 2012 Database issue of Nucleic Acids Research]'''</big>
<pubmed> 22096228 </pubmed>

 
<big>'''Paper of the month: March 2012'''</big>
* [http://www.ncbi.nlm.nih.gov/pubmed/22383848 Buescher ''et al''.] and [http://www.ncbi.nlm.nih.gov/pubmed/22383849 Nicolas ''et al''.] from the BaSysBio consortium directed by [[Philippe Noirot]] studied the dynamic metabolic and transcriptional responses of ''B. subtilis'' to changes of the growth conditions. One of the major issues is the adaptation of the cells upon a nutrient switch from glucose to malate and ''vice versa''. Importantly, the study by [http://www.ncbi.nlm.nih.gov/pubmed/22383849 Nicholas ''et al''.] provides an analysis of gene expression at 104 different conditions as revealed by tiling arrays.
* '''Relevant ''Subti''Wiki pages:''' [[Philippe Noirot]], [[Michael Hecker]], [[Uwe Völker]], [[Philippe Bessières]], [[Uwe Sauer]], [[Stephane Aymerich]], [[Tony Wilkinson]], [[metabolism]], [[transcription]], [[CcpA]], [[Sigma factors]], [[ncRNA|sRNAs]], [[Rho]]
<pubmed>22383848 22383849</pubmed>
* '''A comment on these papers:'''
<pubmed> 22383834 </pubmed>

* [[Previous papers of the month]]

 
<big>'''New procedure for account creation:'''</big>
* Due to massive spam attacks, we had to change our policy for the creation of accounts. If you want to create an account, just [mailto:jstuelk@gwdg.de send me a mail]. We will create the account for you as quickly as possible, then you can change your password. This does not affect existing accounts, which remain active. 
* '''Please remember that all members of the ''Bacillus'' community are invited to create accounts and to contribute to ''Subti''Wiki!'''
 
<big>'''News in ''Subti''Wiki:'''</big>
* '''June 2011:''' updated Excel files that map all genes to [[categories]] and [[regulons]] as well as the general updated identity mapping of all genes were uploaded.
* '''April 2011:''' [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact], a presentation of [[protein-protein interactions]] in ''B. subtilis'', is online!
* '''December 2010:''' [http://cellpublisher.gobics.de/scp.html SubtiCellPublisher] allows the conversion of CellDesigner diagrams to navigatable presentations in the style of [[SubtiPathways]]
* '''December 2010:''' all genes are linked to [[regulons]], and the pages of the [[regulons]] provide an overview on all genes that are members of this specific regulon.
* '''December 2010:''' all genes/proteins are linked to [[categories]], and the pages of the [[categories]] provide an overview on all genes/proteins that are members of this specific category.
* '''August 2010:''' several new pathway maps including [http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Utilization of other nitrogen sources], [http://subtiwiki.uni-goettingen.de/pathways/biotin/index.html Biotin synthesis], [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling], and [http://subtiwiki.uni-goettingen.de/pathways/secretion/index.html Protein secretion] were uploaded to [[SubtiPathways]]
* '''March 2010:''' novel [[plasmids]] for the creation of strains expressing proteins with a C-terminal triple FLAG-tag (for simple immunological analysis of the proteins, [[pGP1087]] and [[pGP1331]])

 
{| border="0" cellpadding="1"
|width="300"|<big>'''Genes''' (examples)</big>
|width="300"|<big>'''Additional pages'''</big>
|- style="height:20px"
| ''[[spo0A]]'' || '''[http://subtipathways.uni-goettingen.de ''Subti''Pathways]'''
|-
| ''[[glnA]]'' || '''[[Lists of genes, proteins and RNAs]]'''
|-
| ''[[rny]]'' || '''[[Categories]]'''
|-
| ''[[psdA]]'' || '''[[Regulons]]'''
|-
| ''[[pckA]]'' || '''[[methods]]'''
|-
| ''[[dnaA]]'' || '''[[metabolism]]'''
|-
| ''[[rnpA]]'' || '''[[protein-protein interactions]]'''
|-
| ''[[sigB]]'' || '''[[genome-wide analyses]]'''
|-
| ''[[ptkA]]'' || '''[[list of plasmids]]'''
|-
| ''[[mreC]]'' || '''[[labs working on Bacillus|labs working on ''Bacillus'']]'''
|-
| ''[[ccpA]]'' || '''[[the people behind SubtiWiki|the people behind ''Subti''Wiki]]'''
|-
| ''[[sr1]]'' || '''[[template]]'''
|-
| ||
|}
 
<big>'''Publications describing ''Subti''Wiki and ''Subti''Pathways:'''</big>
<div style="width:73%"><pubmed>20157485 19959575</pubmed></div>

SigB

2012-01-03T13:39:22Z

MLehnik:

* '''Description:''' [[RNA polymerase]] [[sigma factor]] SigB 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rpoF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNA polymerase]] [[sigma factor]] SigB
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || general stress response
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SigB SigB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.418
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbW]]'', ''[[rsbX]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12280]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sigB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription]]}},
{{SubtiWiki category|[[sigma factors and their control]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[SigB regulon]]}}

=The [[SigB regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04730

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10735]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' SigB subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[SigB]]-[[RsbW]] {{PubMed|12270815}}
** [[SigB]]-[[RpoB]]-[[RpoC]]

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P06574 P06574]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04730]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[rsbR]]-[[rsbS]]-[[rsbT]]-[[rsbU]]-[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
** ''[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2170324 PubMed]

* '''[[Sigma factor]]:'''
** ''[[rsbR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
** ''[[rsbV]]:'' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]

* '''Regulation:'''
** ''[[rsbV]]:'' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' QB5344 (cat), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

* [[Bill Haldenwang]], San Antonio, USA
* [[Chet Price]], Davis, USA [http://foodscience.ucdavis.edu/price_lab/pricelab.html homepage]

=Your additional remarks=

=References=

==Reviews==
<pubmed> 19575568, 18035607, 11407115, 9767581 20658979 </pubmed>

==Control of SigB activity by protein-protein interactions==
<pubmed> 11377871, 12270815, 15312768, 8460143, 8682769, 8002610, 11591687, 7601843, 17498739, 15342582, </pubmed>

==Identification of the SigB regulon==
<pubmed> 11544224, 11532142, 11717291, 10482513, 10220166,22174379 </pubmed>

==Other publications==
<big>''Locke JC, Young JW, Fontes M, Hernández Jiménez MJ, Elowitz MB'' </big>
<big>'''Stochastic pulse regulation in bacterial stress response.''' </big>
<big>Science. 2011 334:366-369. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21979936 PubMed:21979936]
<pubmed> 8655572,, 3123466, 10369900,3112122, 8468294,8458834, 13129942, 6784117, 12867438, 3100810, 8253681, 12486038, 8764398,3027048, 15342585,17575448, 17586624,,3016731,11902719,14651641,10503549,15205443,6405278, 10383961, 15805528 6790515 116131, 39767581 19948797 </pubmed>

[[Category:Protein-coding genes]]

SigB

2012-01-03T13:37:55Z

MLehnik: /* Other publications */

* '''Description:''' [[RNA polymerase]] [[sigma factor]] SigB 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rpoF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNA polymerase]] [[sigma factor]] SigB
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || general stress response
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SigB SigB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.418
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbW]]'', ''[[rsbX]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12280]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sigB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription]]}},
{{SubtiWiki category|[[sigma factors and their control]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[SigB regulon]]}}

=The [[SigB regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04730

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10735]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' SigB subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[SigB]]-[[RsbW]] {{PubMed|12270815}}
** [[SigB]]-[[RpoB]]-[[RpoC]]

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P06574 P06574]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04730]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[rsbR]]-[[rsbS]]-[[rsbT]]-[[rsbU]]-[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
** ''[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2170324 PubMed]

* '''[[Sigma factor]]:'''
** ''[[rsbR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
** ''[[rsbV]]:'' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]

* '''Regulation:'''
** ''[[rsbV]]:'' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' QB5344 (cat), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

* [[Bill Haldenwang]], San Antonio, USA
* [[Chet Price]], Davis, USA [http://foodscience.ucdavis.edu/price_lab/pricelab.html homepage]

=Your additional remarks=

=References=

==Reviews==
<pubmed> 19575568, 18035607, 11407115, 9767581 20658979 </pubmed>

==Control of SigB activity by protein-protein interactions==
<pubmed> 11377871, 12270815, 15312768, 8460143, 8682769, 8002610, 11591687, 7601843, 17498739, 15342582, </pubmed>

==Identification of the SigB regulon==
<pubmed> 11544224, 11532142, 11717291, 10482513, 10220166,22174379 </pubmed>

==Other publications==
<big>''Locke JC, Young JW, Fontes M, Hernández Jiménez MJ, Elowitz MB'' </big>
<big>'''Stochastic pulse regulation in bacterial stress response.''' </big>
<big>Science. 2011 334:366-369. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21979936 PubMed:21979936]
<pubmed> 8655572,, 22210769, 3123466, 10369900,3112122, 8468294,8458834, 13129942, 6784117, 12867438, 3100810, 8253681, 12486038, 8764398,3027048, 15342585,17575448, 17586624,,3016731,11902719,14651641,10503549,15205443,6405278, 10383961, 15805528 6790515 116131, 39767581 19948797 </pubmed>

[[Category:Protein-coding genes]]

SigB

2012-01-03T13:36:13Z

MLehnik:

SigB

2012-01-03T13:34:23Z

MLehnik: Undo revision 148110 by MLehnik (talk)

* '''Description:''' [[RNA polymerase]] [[sigma factor]] SigB 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rpoF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNA polymerase]] [[sigma factor]] SigB
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || general stress response
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SigB SigB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.418
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbW]]'', ''[[rsbX]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12280]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sigB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription]]}},
{{SubtiWiki category|[[sigma factors and their control]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[SigB regulon]]}}

=The [[SigB regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04730

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10735]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' SigB subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[SigB]]-[[RsbW]] {{PubMed|12270815}}
** [[SigB]]-[[RpoB]]-[[RpoC]]

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P06574 P06574]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04730]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[rsbR]]-[[rsbS]]-[[rsbT]]-[[rsbU]]-[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
** ''[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2170324 PubMed]

* '''[[Sigma factor]]:'''
** ''[[rsbR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
** ''[[rsbV]]:'' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]

* '''Regulation:'''
** ''[[rsbV]]:'' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' QB5344 (cat), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

* [[Bill Haldenwang]], San Antonio, USA
* [[Chet Price]], Davis, USA [http://foodscience.ucdavis.edu/price_lab/pricelab.html homepage]

=Your additional remarks=

=References=

==Reviews==
<pubmed> 19575568, 18035607, 11407115, 9767581 20658979 </pubmed>

==Control of SigB activity by protein-protein interactions==
<pubmed> 11377871, 12270815, 15312768, 8460143, 8682769, 8002610, 11591687, 7601843, 17498739, 15342582, </pubmed>

==Identification of the SigB regulon==
<pubmed> 11544224, 11532142, 11717291, 10482513, 10220166,22174379 </pubmed>

==Other publications==
<big>''Locke JC, Young JW, Fontes M, Hernández Jiménez MJ, Elowitz MB'' </big>
<big>'''Stochastic pulse regulation in bacterial stress response.''' </big>
<big>Science. 2011 334:366-369. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21979936 PubMed:21979936]
<pubmed> 22210769, 8655572, 3123466, 10369900,3112122, 8468294,8458834, 13129942, 6784117, 12867438, 3100810, 8253681, 12486038, 8764398,3027048, 15342585,17575448, 17586624,,3016731,11902719,14651641,10503549,15205443,6405278, 10383961, 15805528 6790515 116131, 39767581 19948797 </pubmed>

[[Category:Protein-coding genes]]

SigB

2012-01-03T13:32:54Z

MLehnik: Undo revision 148109 by MLehnik (talk)

* '''Description:''' [[RNA polymerase]] [[sigma factor]] SigB 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rpoF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNA polymerase]] [[sigma factor]] SigB
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || general stress response
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SigB SigB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.418
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbW]]'', ''[[rsbX]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12280]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sigB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription]]}},
{{SubtiWiki category|[[sigma factors and their control]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[SigB regulon]]}}

=The [[SigB regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04730

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10735]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' SigB subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[SigB]]-[[RsbW]] {{PubMed|12270815}}
** [[SigB]]-[[RpoB]]-[[RpoC]]

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P06574 P06574]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04730]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[rsbR]]-[[rsbS]]-[[rsbT]]-[[rsbU]]-[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
** ''[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2170324 PubMed]

* '''[[Sigma factor]]:'''
** ''[[rsbR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
** ''[[rsbV]]:'' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]

* '''Regulation:'''
** ''[[rsbV]]:'' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' QB5344 (cat), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

* [[Bill Haldenwang]], San Antonio, USA
* [[Chet Price]], Davis, USA [http://foodscience.ucdavis.edu/price_lab/pricelab.html homepage]

=Your additional remarks=

=References=

==Reviews==
<pubmed> 19575568, 18035607, 11407115, 9767581 20658979 </pubmed>

==Control of SigB activity by protein-protein interactions==
<pubmed> 11377871, 12270815, 15312768, 8460143, 8682769, 8002610, 11591687, 7601843, 17498739, 15342582, </pubmed>

==Identification of the SigB regulon==
<pubmed> 11544224, 11532142, 11717291, 10482513, 10220166,22174379 </pubmed>

==Other publications==
<big>''Locke JC, Young JW, Fontes M, Hernández Jiménez MJ, Elowitz MB'' </big>
<big>'''Stochastic pulse regulation in bacterial stress response.''' </big>
<big>Science. 2011 334:366-369. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21979936 PubMed:21979936]
<pubmed> 8655572, 22210769, 3123466, 10369900,3112122, 8468294,8458834, 13129942, 6784117, 12867438, 3100810, 8253681, 12486038, 8764398,3027048, 15342585,17575448, 17586624,,3016731,11902719,14651641,10503549,15205443,6405278, 10383961, 15805528 6790515 116131, 39767581 19948797 </pubmed>

[[Category:Protein-coding genes]]

SigB

2012-01-03T13:30:33Z

MLehnik: /* Other publications */

* '''Description:''' [[RNA polymerase]] [[sigma factor]] SigB 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rpoF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNA polymerase]] [[sigma factor]] SigB
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || general stress response
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SigB SigB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.418
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbW]]'', ''[[rsbX]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12280]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sigB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription]]}},
{{SubtiWiki category|[[sigma factors and their control]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[SigB regulon]]}}

=The [[SigB regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04730

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10735]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' SigB subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[SigB]]-[[RsbW]] {{PubMed|12270815}}
** [[SigB]]-[[RpoB]]-[[RpoC]]

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P06574 P06574]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04730]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[rsbR]]-[[rsbS]]-[[rsbT]]-[[rsbU]]-[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
** ''[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2170324 PubMed]

* '''[[Sigma factor]]:'''
** ''[[rsbR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
** ''[[rsbV]]:'' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]

* '''Regulation:'''
** ''[[rsbV]]:'' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' QB5344 (cat), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

* [[Bill Haldenwang]], San Antonio, USA
* [[Chet Price]], Davis, USA [http://foodscience.ucdavis.edu/price_lab/pricelab.html homepage]

=Your additional remarks=

=References=

==Reviews==
<pubmed> 19575568, 18035607, 11407115, 9767581 20658979 </pubmed>

==Control of SigB activity by protein-protein interactions==
<pubmed> 11377871, 12270815, 15312768, 8460143, 8682769, 8002610, 11591687, 7601843, 17498739, 15342582, </pubmed>

==Identification of the SigB regulon==
<pubmed> 11544224, 11532142, 11717291, 10482513, 10220166,22174379 </pubmed>

==Other publications==
<big>''Locke JC, Young JW, Fontes M, Hernández Jiménez MJ, Elowitz MB'' </big>
<big>'''Stochastic pulse regulation in bacterial stress response.''' </big>
<big>Science. 2011 334:366-369. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21979936 PubMed:21979936]
<pubmed> 22210769, 8655572, 3123466, 10369900,3112122, 8468294,8458834, 13129942, 6784117, 12867438, 3100810, 8253681, 12486038, 8764398,3027048, 15342585,17575448, 17586624,,3016731,11902719,14651641,10503549,15205443,6405278, 10383961, 15805528 6790515 116131, 39767581 19948797 </pubmed>

[[Category:Protein-coding genes]]

File:PGP1871.png

2011-11-03T12:34:51Z

MLehnik: uploaded a new version of "File:PGP1871.png"

PGP1871

2011-11-03T12:33:05Z

MLehnik: Created page with "'''pGP1871: click to enlarge''' '''General comments''' Integrative plasmid for the fusion of GFP tag to the C-terminus of a protein, ..."

[[File:PGP1871.png|250px|thumb|right|'''pGP1871: click to enlarge''']]

'''General comments'''

Integrative [[plasmid]] for the fusion of GFP tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor
* ''E.coli'': multicopy plasmid, select for ampicillin
* ''B. subtilis'': no ori, select for spectinomycin

'''Hints for the usage'''
* amplify the last 600bp of your gene of interest,
* skip the Stopp-Codon of the gene in the reverse primer
* take care that the integration is in-frame
* do not use the HindIII site for cloning, as GFP is inserted via this restriction site

PGP1870

2011-11-03T12:32:45Z

MLehnik:

[[File:PGP1870.png|250px|thumb|right|'''pGP1870: click to enlarge''']]

'''General comments'''

Integrative [[plasmid]] for the fusion of GFP tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor
* ''E.coli'': multicopy plasmid, select for ampicillin
* ''B. subtilis'': no ori, select for spectinomycin

'''Hints for the usage'''
* amplify the last 600bp of your gene of interest,
* skip the Stopp-Codon of the gene in the reverse primer
* take care that the integration is in-frame
* do not use the HindIII site for cloning, as GFP is inserted via this restriction site

File:PGP1871.png

2011-11-03T12:31:39Z

MLehnik:

PGP1870

2011-11-03T12:29:31Z

MLehnik:

PGP1870

2011-11-03T12:28:48Z

MLehnik: Created page with "'''pGP1870: click to enlarge''' '''General comments''' Integrative plasmid for the fusion of 3x FLAG tag to the C-terminus of a prote..."

[[File:PGP1870.png|250px|thumb|right|'''pGP1870: click to enlarge''']]

'''General comments'''

Integrative [[plasmid]] for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor
* ''E.coli'': multicopy plasmid, select for ampicillin
* ''B. subtilis'': no ori, select for spectinomycin

'''Hints for the usage'''
* amplify the last 600bp of your gene of interest,
* skip the Stopp-Codon of the gene in the reverse primer
* take care that the integration is in-frame
* do not use the HindIII site for cloning, as GFP is inserted via this restriction site

'''Antibody'''
*dilute the anitbody 1:10000 (you can freeze the Blotto solution and reuse it)

File:PGP1870.png

2011-11-03T12:24:37Z

MLehnik:

YfmL

2011-03-25T11:50:15Z

MLehnik: /* Biological materials */

* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yfmL''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 9.602
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1128 bp, 376 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yfmM]]'', ''[[yfmK]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12572]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yfmL_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DEAD-box RNA helicases]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07430

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yfmL.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12963]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' helicase C-terminal domain (according to Swiss-Prot) [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
* '''Paralogous protein(s):''' [[CshA]], [[CshB]], [[DeaD]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34750 O34750]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07430]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''yfmL'' (according to [http://dbtbs.hgc.jp/COG/prom/yfmL.html DBTBS])

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' B. subtilis GP1081 yfmL-yfp spc, available in [[Stülke]] lab,

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YfmL

2011-03-25T11:50:01Z

MLehnik: /* Biological materials */

* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yfmL''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 9.602
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1128 bp, 376 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yfmM]]'', ''[[yfmK]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12572]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yfmL_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DEAD-box RNA helicases]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07430

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yfmL.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12963]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' helicase C-terminal domain (according to Swiss-Prot) [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
* '''Paralogous protein(s):''' [[CshA]], [[CshB]], [[DeaD]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34750 O34750]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07430]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''yfmL'' (according to [http://dbtbs.hgc.jp/COG/prom/yfmL.html DBTBS])

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''B. subtilis GP1081 yfmL-yfp spc, available in [[Stülke]] lab,

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YfmL

2011-03-25T11:49:04Z

MLehnik: /* Biological materials */

* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yfmL''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 9.602
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1128 bp, 376 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yfmM]]'', ''[[yfmK]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12572]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yfmL_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DEAD-box RNA helicases]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07430

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yfmL.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12963]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' helicase C-terminal domain (according to Swiss-Prot) [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
* '''Paralogous protein(s):''' [[CshA]], [[CshB]], [[DeaD]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34750 O34750]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07430]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''yfmL'' (according to [http://dbtbs.hgc.jp/COG/prom/yfmL.html DBTBS])

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''
** B. subtilis GP1081 yfmL-yfp spc, available in [[Stülke]] lab,

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

CshA

2011-03-25T11:48:12Z

MLehnik: /* Biological materials */

* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]], important for adaptation to low temperatures 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cshA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.89
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murF]]'', ''[[ydbS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12265]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ydbR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DEAD-box RNA helicases]]}},
{{SubtiWiki category|[[cold stress proteins]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04580

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12085]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' helicase C-terminal domain (according to Swiss-Prot) [[DEAD-box RNA helicases|DEAD-box RNA helicase]]

* '''Paralogous protein(s):''' [[CshB]], [[DeaD]], [[YfmL]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[Interactions]]:''' part of the [[RNA degradosome]]
** [[CshA]]-[[CshA]] {{PubMed|20572937}}
** [[CshA]]-[[CspB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
** [[CshA]]-[[PnpA]] {{PubMed|20572937}}, [[CshA]]-[[Rny]] {{PubMed|20572937}}, [[CshA]]-[[RnjA]] {{PubMed|20572937}}, [[CshA]]-[[Eno]] {{PubMed|20572937}}, [[CshA]]-[[PfkA]] {{PubMed|20572937}}
** [[DeaD]]-[[CshA]] {{PubMed|20572937}}

* '''Localization:''' cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed], cell membrane {{PubMed|20572937}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96614 P96614]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04580]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''
** induced by cold shock {{PubMed|12399512}}
** constitutive, similar expression at high and low temperatures, throughout growth and in both minimal and complex medium {{PubMed|20572937}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1035 (aphA3), available in [[Stülke]] lab
** GP1083 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1387, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], expression from the native chromomsomal site: GP1026, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1386, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pGP1369 for chromosomal expression of CshA-YFP, available in Stülke lab
** B. subtilis GP1081 cshA-gfp spc, available in [[Stülke]] lab,

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''FLAG-tag construct:''' GP1010 (spc, based on [[pGP1331]]), available in the [[Stülke]] labs

* '''Antibody:'''

=Labs working on this gene/protein=

[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]

=Your additional remarks=

=References=

<pubmed>16352840,20572937 , 12399512 16861794, </pubmed>
'''Additional publications:''' {{PubMed|20709848}}
[[Category:Protein-coding genes]]

CshA

2011-03-25T11:47:23Z

MLehnik: /* Biological materials */

* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]], important for adaptation to low temperatures 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cshA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.89
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murF]]'', ''[[ydbS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12265]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ydbR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DEAD-box RNA helicases]]}},
{{SubtiWiki category|[[cold stress proteins]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04580

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12085]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' helicase C-terminal domain (according to Swiss-Prot) [[DEAD-box RNA helicases|DEAD-box RNA helicase]]

* '''Paralogous protein(s):''' [[CshB]], [[DeaD]], [[YfmL]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[Interactions]]:''' part of the [[RNA degradosome]]
** [[CshA]]-[[CshA]] {{PubMed|20572937}}
** [[CshA]]-[[CspB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
** [[CshA]]-[[PnpA]] {{PubMed|20572937}}, [[CshA]]-[[Rny]] {{PubMed|20572937}}, [[CshA]]-[[RnjA]] {{PubMed|20572937}}, [[CshA]]-[[Eno]] {{PubMed|20572937}}, [[CshA]]-[[PfkA]] {{PubMed|20572937}}
** [[DeaD]]-[[CshA]] {{PubMed|20572937}}

* '''Localization:''' cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed], cell membrane {{PubMed|20572937}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96614 P96614]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04580]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''
** induced by cold shock {{PubMed|12399512}}
** constitutive, similar expression at high and low temperatures, throughout growth and in both minimal and complex medium {{PubMed|20572937}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1035 (aphA3), available in [[Stülke]] lab
** GP1083 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1387, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], expression from the native chromomsomal site: GP1026, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1386, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pGP1369 for chromosomal expression of CshA-YFP, available in Stülke lab
B. subtilis GP1081 cshA-gfp spc, available in [[Stülke]] lab,

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''FLAG-tag construct:''' GP1010 (spc, based on [[pGP1331]]), available in the [[Stülke]] labs

* '''Antibody:'''

=Labs working on this gene/protein=

[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]

=Your additional remarks=

=References=

<pubmed>16352840,20572937 , 12399512 16861794, </pubmed>
'''Additional publications:''' {{PubMed|20709848}}
[[Category:Protein-coding genes]]

CshA

2011-03-25T11:46:53Z

MLehnik: /* Biological materials */

* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]], important for adaptation to low temperatures 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cshA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.89
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murF]]'', ''[[ydbS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12265]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ydbR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DEAD-box RNA helicases]]}},
{{SubtiWiki category|[[cold stress proteins]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04580

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12085]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' helicase C-terminal domain (according to Swiss-Prot) [[DEAD-box RNA helicases|DEAD-box RNA helicase]]

* '''Paralogous protein(s):''' [[CshB]], [[DeaD]], [[YfmL]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[Interactions]]:''' part of the [[RNA degradosome]]
** [[CshA]]-[[CshA]] {{PubMed|20572937}}
** [[CshA]]-[[CspB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
** [[CshA]]-[[PnpA]] {{PubMed|20572937}}, [[CshA]]-[[Rny]] {{PubMed|20572937}}, [[CshA]]-[[RnjA]] {{PubMed|20572937}}, [[CshA]]-[[Eno]] {{PubMed|20572937}}, [[CshA]]-[[PfkA]] {{PubMed|20572937}}
** [[DeaD]]-[[CshA]] {{PubMed|20572937}}

* '''Localization:''' cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed], cell membrane {{PubMed|20572937}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96614 P96614]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04580]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''
** induced by cold shock {{PubMed|12399512}}
** constitutive, similar expression at high and low temperatures, throughout growth and in both minimal and complex medium {{PubMed|20572937}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1035 (aphA3), available in [[Stülke]] lab
** GP1083 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1387, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], expression from the native chromomsomal site: GP1026, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1386, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pGP1369 for chromosomal expression of CshA-YFP, available in Stülke lab
''' B. subtilis GP1081 cshA-gfp spc, available in [[Stülke]] lab,

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''FLAG-tag construct:''' GP1010 (spc, based on [[pGP1331]]), available in the [[Stülke]] labs

* '''Antibody:'''

=Labs working on this gene/protein=

[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]

=Your additional remarks=

=References=

<pubmed>16352840,20572937 , 12399512 16861794, </pubmed>
'''Additional publications:''' {{PubMed|20709848}}
[[Category:Protein-coding genes]]

CshA

2011-03-25T11:43:49Z

MLehnik: /* Biological materials */

* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]], important for adaptation to low temperatures 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cshA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.89
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murF]]'', ''[[ydbS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12265]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ydbR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DEAD-box RNA helicases]]}},
{{SubtiWiki category|[[cold stress proteins]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04580

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12085]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' helicase C-terminal domain (according to Swiss-Prot) [[DEAD-box RNA helicases|DEAD-box RNA helicase]]

* '''Paralogous protein(s):''' [[CshB]], [[DeaD]], [[YfmL]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[Interactions]]:''' part of the [[RNA degradosome]]
** [[CshA]]-[[CshA]] {{PubMed|20572937}}
** [[CshA]]-[[CspB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
** [[CshA]]-[[PnpA]] {{PubMed|20572937}}, [[CshA]]-[[Rny]] {{PubMed|20572937}}, [[CshA]]-[[RnjA]] {{PubMed|20572937}}, [[CshA]]-[[Eno]] {{PubMed|20572937}}, [[CshA]]-[[PfkA]] {{PubMed|20572937}}
** [[DeaD]]-[[CshA]] {{PubMed|20572937}}

* '''Localization:''' cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed], cell membrane {{PubMed|20572937}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96614 P96614]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04580]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''
** induced by cold shock {{PubMed|12399512}}
** constitutive, similar expression at high and low temperatures, throughout growth and in both minimal and complex medium {{PubMed|20572937}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1035 (aphA3), available in [[Stülke]] lab
** GP1083 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1387, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], expression from the native chromomsomal site: GP1026, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1386, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pGP1369 for chromosomal expression of CshA-YFP, available in Stülke lab

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''FLAG-tag construct:''' GP1010 (spc, based on [[pGP1331]]), available in the [[Stülke]] labs

* '''Antibody:'''

=Labs working on this gene/protein=

[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]

=Your additional remarks=

=References=

<pubmed>16352840,20572937 , 12399512 16861794, </pubmed>
'''Additional publications:''' {{PubMed|20709848}}
[[Category:Protein-coding genes]]

CshA

2011-03-25T11:42:58Z

MLehnik: /* Biological materials */

* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]], important for adaptation to low temperatures 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cshA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.89
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murF]]'', ''[[ydbS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12265]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ydbR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DEAD-box RNA helicases]]}},
{{SubtiWiki category|[[cold stress proteins]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04580

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12085]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' helicase C-terminal domain (according to Swiss-Prot) [[DEAD-box RNA helicases|DEAD-box RNA helicase]]

* '''Paralogous protein(s):''' [[CshB]], [[DeaD]], [[YfmL]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[Interactions]]:''' part of the [[RNA degradosome]]
** [[CshA]]-[[CshA]] {{PubMed|20572937}}
** [[CshA]]-[[CspB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
** [[CshA]]-[[PnpA]] {{PubMed|20572937}}, [[CshA]]-[[Rny]] {{PubMed|20572937}}, [[CshA]]-[[RnjA]] {{PubMed|20572937}}, [[CshA]]-[[Eno]] {{PubMed|20572937}}, [[CshA]]-[[PfkA]] {{PubMed|20572937}}
** [[DeaD]]-[[CshA]] {{PubMed|20572937}}

* '''Localization:''' cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed], cell membrane {{PubMed|20572937}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96614 P96614]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04580]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''
** induced by cold shock {{PubMed|12399512}}
** constitutive, similar expression at high and low temperatures, throughout growth and in both minimal and complex medium {{PubMed|20572937}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1035 (aphA3), available in [[Stülke]] lab
** GP1081 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1387, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], expression from the native chromomsomal site: GP1026, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1386, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pGP1369 for chromosomal expression of CshA-YFP, available in Stülke lab

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''FLAG-tag construct:''' GP1010 (spc, based on [[pGP1331]]), available in the [[Stülke]] labs

* '''Antibody:'''

=Labs working on this gene/protein=

[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]

=Your additional remarks=

=References=

<pubmed>16352840,20572937 , 12399512 16861794, </pubmed>
'''Additional publications:''' {{PubMed|20709848}}
[[Category:Protein-coding genes]]

CshA

2011-03-25T11:42:25Z

MLehnik: /* Biological materials */

* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]], important for adaptation to low temperatures 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cshA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.89
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murF]]'', ''[[ydbS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12265]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ydbR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DEAD-box RNA helicases]]}},
{{SubtiWiki category|[[cold stress proteins]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04580

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12085]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' helicase C-terminal domain (according to Swiss-Prot) [[DEAD-box RNA helicases|DEAD-box RNA helicase]]

* '''Paralogous protein(s):''' [[CshB]], [[DeaD]], [[YfmL]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[Interactions]]:''' part of the [[RNA degradosome]]
** [[CshA]]-[[CshA]] {{PubMed|20572937}}
** [[CshA]]-[[CspB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
** [[CshA]]-[[PnpA]] {{PubMed|20572937}}, [[CshA]]-[[Rny]] {{PubMed|20572937}}, [[CshA]]-[[RnjA]] {{PubMed|20572937}}, [[CshA]]-[[Eno]] {{PubMed|20572937}}, [[CshA]]-[[PfkA]] {{PubMed|20572937}}
** [[DeaD]]-[[CshA]] {{PubMed|20572937}}

* '''Localization:''' cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed], cell membrane {{PubMed|20572937}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96614 P96614]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04580]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''
** induced by cold shock {{PubMed|12399512}}
** constitutive, similar expression at high and low temperatures, throughout growth and in both minimal and complex medium {{PubMed|20572937}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1035 (aphA3), available in [[Stülke]] lab
** GP922 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1387, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], expression from the native chromomsomal site: GP1026, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1386, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pGP1369 for chromosomal expression of CshA-YFP, available in Stülke lab

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''FLAG-tag construct:''' GP1010 (spc, based on [[pGP1331]]), available in the [[Stülke]] labs

* '''Antibody:'''

=Labs working on this gene/protein=

[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]

=Your additional remarks=

=References=

<pubmed>16352840,20572937 , 12399512 16861794, </pubmed>
'''Additional publications:''' {{PubMed|20709848}}
[[Category:Protein-coding genes]]

CspD

2011-03-24T10:12:56Z

MLehnik: /* Biological materials */

* '''Description:''' cold shock protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cspD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || cold shock protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA chaperone
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.31
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 198 bp, 66 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ugtP]]'', ''[[degR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14111]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:cspD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[RNA chaperones]]}},
{{SubtiWiki category|[[cold stress proteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU21930

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11531]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

* '''Paralogous protein(s):''' [[CspB]], [[CspC]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P51777 P51777]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU21930]

* '''E.C. number:'''

=== Additional information===

:* subject to Clp-dependent proteolysis upon glucose starvation {{PubMed|17981983}}
=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:'''
** weakly induced by cold shock {{PubMed|12399512}}

* '''Regulatory mechanism:'''

* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation {{PubMed|17981983}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>12171653,12838604,</pubmed>
==Original publications==
<pubmed>12399512,11752341,11717297,9920884,12427936,11591689,9379903,17981983, </pubmed>
[[Category:Protein-coding genes]]

CspC

2011-03-24T10:12:02Z

MLehnik: /* Biological materials */

* '''Description:''' cold shock protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cspC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || cold shock protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA chaperone
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.518
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 198 bp, 66 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydeA]]'', ''[[ydeB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12319]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:cspC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[RNA chaperones]]}},
{{SubtiWiki category|[[cold stress proteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU05120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11024]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

* '''Paralogous protein(s):''' [[CspB]], [[CspD]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39158 P39158]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU05120]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:'''
** induced by cold shock (9-fold) {{PubMed|12399512}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12399512,12171653,11752341,11717297,12838604,9379903,9914312,11591689,9920884,12427936,, </pubmed>

[[Category:Protein-coding genes]]

CspB

2011-03-24T10:11:11Z

MLehnik: /* Biological materials */

* '''Description:''' major cold-shock protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cspB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || major cold-shock protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA chaperone
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.341
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 201 bp, 67 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhcI]]'', ''[[yhcJ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12738]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:cspB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[RNA chaperones]]}},
{{SubtiWiki category|[[cold stress proteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09100

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cspB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10824]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

* '''Paralogous protein(s):''' [[CspC]], [[CspD]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[CshB]]-[[CspB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1CSQ 1CSQ], [http://www.rcsb.org/pdb/explore.do?structureId=1NMG 1NMG] (NMR)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P32081 P32081]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09100]

* '''E.C. number:'''

=== Additional information===

:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
=Expression and regulation=

* '''Operon:''' ''cspB'' {{PubMed|1400185}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|1400185}}

* '''Regulation:'''
** induced upon cold shock {{PubMed|12399512}}

* '''Regulatory mechanism:'''

* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation {{PubMed|17981983}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]

=Your additional remarks=

=References=

<pubmed>12399512,12171653,11752341,11717297,12838604,8321288,8321289,9533624,9379903,8294017,8755892,9914312,11591689,7476164,1409560,16352840,9920884,1400185,12427936,8307174,7703860,16352840, </pubmed>
'''Additional publications:''' {{PubMed|21124848}}
[[Category:Protein-coding genes]]

PGP1389

2010-10-18T06:41:51Z

MLehnik:

[[File:PGP1389 Subtiwiki.png|250px|thumb|right|'''pGP1331: click to enlarge''']]

'''General comments'''

Integrative plasmid for the fusion of Streptag tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor
* ''E.coli'': multicopy plasmid, select for ampicillin
* ''B. subtilis'': no ori, select for spectinomycin

'''Hints for the usage'''
* amplify the last 600bp of your gene of interest,
* skip the Stopp-Codon of the gene in the reverse primer
* take care that the integration is in-frame

PGP1389

2010-10-18T06:40:38Z

MLehnik: Created page with "File:PGP1389 Subtiwiki.png '''General comments''' Integrative plasmid for the fusion of Streptag tag to the C-terminus of a protein, keeping the control of the expression u..."

[[File:PGP1389 Subtiwiki.png]]

'''General comments'''

Integrative plasmid for the fusion of Streptag tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor
* ''E.coli'': multicopy plasmid, select for ampicillin
* ''B. subtilis'': no ori, select for spectinomycin

'''Hints for the usage'''
* amplify the last 600bp of your gene of interest,
* skip the Stopp-Codon of the gene in the reverse primer
* take care that the integration is in-frame

File:PGP1389 Subtiwiki.png

2010-10-18T06:38:49Z

MLehnik:

CshA

2010-07-21T09:39:37Z

MLehnik:

* '''Description:''' DEAD-box RNA helicase, important for adaptation to low temperatures 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cshA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || DEAD-box RNA helicase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.89
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murF]]'', ''[[ydbS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12265]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ydbR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04580

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12085]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' helicase C-terminal domain (according to Swiss-Prot) DEAD-box RNA helicase

* '''Paralogous protein(s):''' [[CshB]], [[DeaD]], [[YfmL]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[CshA]]-[[CshA]] {{PubMed|20572937}}, [[CshA]]-[[CspB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed], [[CshA]]-[[PnpA]] {{PubMed|20572937}}, [[CshA]]-[[Rny]] {{PubMed|20572937}}, [[CshA]]-[[RnjA]] {{PubMed|20572937}}, [[CshA]]-[[Eno]] {{PubMed|20572937}}, [[CshA]]-[[PfkA]] {{PubMed|20572937}}, [[DeaD]]-[[CshA]] {{PubMed|20572937}}

* '''Localization:''' cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed], cell membrane {{PubMed|20572937}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96614 P96614]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04580]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''
** induced by cold shock {{PubMed|12399512}}
** constitutive, similar expression at high and low temperatures, throughout growth and in both minimal and complex medium {{PubMed|20572937}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1035 (aphA3), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1387, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], expression from the native chromomsomal site: GP1026, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1386, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pGP1369 for chromosomal expression of CshA-YFP, available in Stülke lab

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''FLAG-tag construct:''' GP1010 (spc, based on [[pGP1331]]), available in the [[Stülke]] labs

* '''Antibody:'''

=Labs working on this gene/protein=

[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]

=Your additional remarks=

=References=

<pubmed>16352840,20572937 , 12399512 16861794, </pubmed>

[[Category:Protein-coding genes]]

Rny

2010-07-21T09:38:17Z

MLehnik:

* '''Description:''' [[RNase]] Y, 5' end sensitive endoribonuclease, involved in the degradation/processing of mRNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rny''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymdA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] Y
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || Initiates [[S-box]] [[riboswitch]] RNA turnover, required for the processing of the ''[[gapA]]'' operon mRNA, depletion of [[RNase]] Y increases bulk mRNA stability.
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,7 kDa, 5.39
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1560 bp, 520 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpX]]'', ''[[ymdB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13569]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:rny_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16960

===Phenotypes of a mutant ===

essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13420]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** [[RNase]] Y cleaves [[S-box]] [[riboswitch]] RNAs ''in vivo'' and ''in vitro'' {{PubMed|19779461}}
** preference for 5' monophosphorylated substrate ''in vitro'' {{PubMed|19779461}}
** endonucleolytic cleavage {{PubMed|19779461}}
** required for the processing of the ''[[gapA]]'' operon mRNA {{PubMed|19193632}}
** cleavage activity appears sensitive to downstream secondary structure {{PubMed|19779461}}
** [[RNase]] Y initiates the degradation of ''[[rpsO]]'' mRNA {{PubMed|20418391}}

* '''Protein family:''' Member of the HD superfamily of metal-dependent phosphohydrolases; 2',3' cyclic nucleotide phosphodiesterase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** transmembrane domain (4–24)
** KH domain (210–273)
** HD domain (336–429)

* '''Modification:'''

* '''Cofactor(s):''' requires Mg+2, which can be replaced by Zn+2 or Mn+2 ions, [http://www.ncbi.nlm.nih.gov/pubmed/19779461 PubMed]

* '''Effectors of protein activity:''' appears sensitive to downstream secondary structure, [http://www.ncbi.nlm.nih.gov/pubmed/19779461 PubMed]

* '''Interactions:''' [[Rny]]-[[PfkA]] {{PubMed|19193632}}, [[Rny]]-[[Eno]] {{PubMed|19193632}}, [[Rny]]-[[PnpA]] {{PubMed|19193632}}, [[Rny]]-[[RnjA]] {{PubMed|19193632}}, [[Rny]]-[[CshA]] {{PubMed|20572937}}

* '''Localization:''' cell membrane, single-pass membrane protein {{PubMed|18763711,17005971,19820159}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31774 O31774]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16960]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.4.16 3.1.4.16]

=== Additional information===

required for the processing of the ''[[gapA]]'' operon mRNA
=Expression and regulation=

* '''Operon:''' ''[[rny]]-[[ymdB]]''

* '''Sigma factor:'''

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''
** there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there
** The mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed|20525796}}

=Biological materials =

* '''Mutant:''' essential!!!!, 4043 (''rny'' under p-spac control, ''cat''), GP193 (''rny'' under p-xyl control, ''cat''), both available in [[Stülke]] lab; SSB447 (rny under P-spac control, "erm") available in [[Putzer]] lab.

* '''Expression vector:'''
** N-terminal Strep-tag, expression in ''E. coli'', in [[pGP172]]: pGP441, available in [[Stülke]] lab
** N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]: pGP775 , available in [[Stülke]] lab
**Expression of RNase Y missing the N-terminal transmembrane domain (25aa) as an intein fusion in E. coli (no tag left in the purified protein) available in the [[Putzer]] lab
** wild type ''rny'', expression in ''B. subtilis'', in [[pBQ200]]: pGP1201, available in [[Stülke]] lab
** there is also a series of domain constructs present in [[pBQ200]], all available in [[Stülke]] lab

* '''lacZ fusion:''' pGP459 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:''' B. subtilis 3569 (amyE:: (p-xyl rny-gfpmut1-spc)), available in [[Errington]] lab, pGP1368 for chromosomal expression of rny-YFP, available in Stülke lab

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''FLAG-tag construct:''' GP1030 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:''' available in [[van Dijl]] and [[Stülke]] labs

=Labs working on this gene/protein=

[[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=
<pubmed>18763711,19193632,17005971 19779461 19820159 20418391 20525796 20572937</pubmed>
[[Category:Protein-coding genes]]

Rny

2010-07-21T09:37:18Z

MLehnik:

* '''Description:''' [[RNase]] Y, 5' end sensitive endoribonuclease, involved in the degradation/processing of mRNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rny''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymdA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] Y
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || Initiates [[S-box]] [[riboswitch]] RNA turnover, required for the processing of the ''[[gapA]]'' operon mRNA, depletion of [[RNase]] Y increases bulk mRNA stability.
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,7 kDa, 5.39
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1560 bp, 520 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpX]]'', ''[[ymdB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13569]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:rny_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16960

===Phenotypes of a mutant ===

essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13420]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** [[RNase]] Y cleaves [[S-box]] [[riboswitch]] RNAs ''in vivo'' and ''in vitro'' {{PubMed|19779461}}
** preference for 5' monophosphorylated substrate ''in vitro'' {{PubMed|19779461}}
** endonucleolytic cleavage {{PubMed|19779461}}
** required for the processing of the ''[[gapA]]'' operon mRNA {{PubMed|19193632}}
** cleavage activity appears sensitive to downstream secondary structure {{PubMed|19779461}}
** [[RNase]] Y initiates the degradation of ''[[rpsO]]'' mRNA {{PubMed|20418391}}

* '''Protein family:''' Member of the HD superfamily of metal-dependent phosphohydrolases; 2',3' cyclic nucleotide phosphodiesterase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** transmembrane domain (4–24)
** KH domain (210–273)
** HD domain (336–429)

* '''Modification:'''

* '''Cofactor(s):''' requires Mg+2, which can be replaced by Zn+2 or Mn+2 ions, [http://www.ncbi.nlm.nih.gov/pubmed/19779461 PubMed]

* '''Effectors of protein activity:''' appears sensitive to downstream secondary structure, [http://www.ncbi.nlm.nih.gov/pubmed/19779461 PubMed]

* '''Interactions:''' [[Rny]]-[[PfkA]] {{PubMed|19193632}}, [[Rny]]-[[Eno]] {{PubMed|19193632}}, [[Rny]]-[[PnpA]] {{PubMed|19193632}}, [[Rny]]-[[RnjA]] {{PubMed|19193632}}, [[Rny]]-[[CshA]] {{PubMed|20572937}}

* '''Localization:''' cell membrane, single-pass membrane protein {{PubMed|18763711,17005971,19820159}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31774 O31774]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16960]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.4.16 3.1.4.16]

=== Additional information===

required for the processing of the ''[[gapA]]'' operon mRNA
=Expression and regulation=

* '''Operon:''' ''[[rny]]-[[ymdB]]''

* '''Sigma factor:'''

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''
** there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there
** The mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed|20525796}}

=Biological materials =

* '''Mutant:''' essential!!!!, 4043 (''rny'' under p-spac control, ''cat''), GP193 (''rny'' under p-xyl control, ''cat''), both available in [[Stülke]] lab; SSB447 (rny under P-spac control, "erm") available in [[Putzer]] lab.

* '''Expression vector:'''
** N-terminal Strep-tag, expression in ''E. coli'', in [[pGP172]]: pGP441, available in [[Stülke]] lab
** N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]: pGP775 , available in [[Stülke]] lab
**Expression of RNase Y missing the N-terminal transmembrane domain (25aa) as an intein fusion in E. coli (no tag left in the purified protein) available in the [[Putzer]] lab
** wild type ''rny'', expression in ''B. subtilis'', in [[pBQ200]]: pGP1201, available in [[Stülke]] lab
** there is also a series of domain constructs present in [[pBQ200]], all available in [[Stülke]] lab

* '''lacZ fusion:''' pGP459 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:''' B. subtilis 3569 (amyE:: (p-xyl rny-gfpmut1-spc)), available in [[Errington]] lab, pGP1368 for chromosomal expression of rny-YFP

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''FLAG-tag construct:''' GP1030 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:''' available in [[van Dijl]] and [[Stülke]] labs

=Labs working on this gene/protein=

[[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=
<pubmed>18763711,19193632,17005971 19779461 19820159 20418391 20525796 20572937</pubmed>
[[Category:Protein-coding genes]]

RplD

2010-07-14T09:28:29Z

MLehnik:

* '''Description:''' [[ribosomal protein]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rplD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[ribosomal protein]] L4
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 10.498
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 621 bp, 207 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rplC]]'', ''[[rplW]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11893]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:rplD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01170

===Phenotypes of a mutant ===

essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11219]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' [[ribosomal protein]] L4P family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42921 P42921]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01170]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[rpsJ]]-[[rplC]]-[[rplD]]-[[rplW]]-[[rplB]]-[[rpsS]]-[[rplV]]-[[rpsC]]-[[rplP]]-[[rpmC]]-[[rpsQ]]-[[rplN]]-[[rplX]]-[[rplE]]-[[rpsN]]-[[rpsH]]-[[rplF]]-[[rplR]]-[[rpsE]]-[[rpmD]]-[[rplO]]'' {{PubMed|9371452}}

* '''Sigma factor:'''
** [[SigA]] two promoters, about 140bp and 200bp upstream of the start codon {{PubMed|9371452}}

* '''Regulation:'''
** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed|11948165}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 19653700 9371452 11948165</pubmed>
[[Category:Protein-coding genes]]

RplC

2010-07-14T09:27:25Z

MLehnik:

* '''Description:''' [[ribosomal protein]] L3 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rplC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[ribosomal protein]] L3 (BL3)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 10.31
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 627 bp, 209 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpsJ]]'', ''[[rplD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11892]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:rplC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01160

===Phenotypes of a mutant ===

essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11218]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' [[RplC]] binding to the precursor 23S rRNA stimulates [[MrnC]] activity [http://www.ncbi.nlm.nih.gov/sites/entrez/19154332 PubMed]

* '''Protein family:''' [[ribosomal protein]] L3P family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[YsxC]]-[[RplC]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17981968 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42920 P42920]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01160]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[rpsJ]]-[[rplC]]-[[rplD]]-[[rplW]]-[[rplB]]-[[rpsS]]-[[rplV]]-[[rpsC]]-[[rplP]]-[[rpmC]]-[[rpsQ]]-[[rplN]]-[[rplX]]-[[rplE]]-[[rpsN]]-[[rpsH]]-[[rplF]]-[[rplR]]-[[rpsE]]-[[rpmD]]-[[rplO]]'' {{PubMed|9371452}}

* '''Sigma factor:'''
** [[SigA]] two promoters, about 140bp and 200bp upstream of the start codon {{PubMed|9371452}}

* '''Regulation:'''
** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed|11948165}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17981968,9371452,19154332, 19653700 11948165</pubmed>

[[Category:Protein-coding genes]]

RplA

2010-07-14T09:26:53Z

MLehnik:

* '''Description:''' [[ribosomal protein]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rplA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[ribosomal protein]] L1 (BL1)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 9.732
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 696 bp, 232 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rplK]]'', ''[[rplJ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11879]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:rplA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01030

===Phenotypes of a mutant ===

essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10164]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' ribosomal protein L1P family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[YsxC]]-[[RplA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17981968 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q06797 Q06797]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01030]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''
** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed|11948165}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17981968,19653700 , </pubmed>

[[Category:Protein-coding genes]]

DgcW

2010-07-14T09:26:21Z

MLehnik:

* '''Description:''' similar to ''E. coli'' CsrD 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ykoW''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 84 kDa, 6.823
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2247 bp, 749 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykoV]]'', ''[[ykoX]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13199]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ykoW_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU13420

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13266]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' aa 290-735 are similar to ''E. coli'' CsrD (18% identity, 43% similarity)

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:''' cell membrane (according to Swiss-Prot)

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34311 O34311]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13420]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>11728710,16980588 , </pubmed>

[[Category:Protein-coding genes]]

DnaK

2010-07-14T09:25:45Z

MLehnik:

* '''Description:''' class I heat-shock protein (molecular chaperone) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''dnaK''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || class I heat-shock protein (molecular chaperone)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein quality control
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.571
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1833 bp, 611 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[surC]]'', ''[[grpE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14489]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:dnaK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25470

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lepA-hemN-hrcA-grpE-dnaKJ-yqeTUV.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10664]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' heat shock protein 70 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[DnaK]]-[[DnaJ]]

* '''Localization:''' cytoplasm (according to Swiss-Prot), Membrane-proximal (Spotty) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P17820 P17820]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25470]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[hrcA]]-[[grpE]]-[[dnaK]]-[[dnaJ]]-[[yqeT]]-[[yqeU]]-[[yqeV]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9023197 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|1339421}}

* '''Regulation:'''
** induced by heat shock ([[HrcA]]) {{PubMed|1339421}}

* '''Regulatory mechanism:'''
** [[HrcA]]: transcription repression {{PubMed|1339421}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

[[Wolfgang Schumann]], Bayreuth University, Germany [http://www.genetik.uni-bayreuth.de/LSGenetik1/schumann_research.htm Homepage]

=Your additional remarks=

=References=

<pubmed>1339421,12224648,10383760,9023197,7540247,7592421 ,16479537, 1339421 ,17726680 </pubmed>

[[Category:Protein-coding genes]]

Hfq

2010-07-14T09:25:07Z

MLehnik:

* '''Description:''' RNA chaperone 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hfq ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymaH''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA chaperone
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 8.698
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 219 bp, 73 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[miaA]]'', ''[[ymzC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13618]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ymaH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU17340

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13416]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' hfq family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3HSB 3HSB] (complex with an RNA aptamer)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31796 O31796]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU17340]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:''' repressed by glucose (7.7-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP22 (cat), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:''' pGP460 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 17395525 15009882 </pubmed>
==Original publications==
<pubmed>12850135, 20445260 </pubmed>
[[Category:Protein-coding genes]]

Tkt

2010-07-14T09:24:01Z

MLehnik:

* '''Description:''' transketolase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tkt''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tktA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transketolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 72 kDa, 4.803
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2001 bp, 667 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ynzC]]'', ''[[sirA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13673]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:tkt_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU17890

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tkt.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11247]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate (according to Swiss-Prot)

* '''Protein family:''' transketolase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3K95 3K95]], complex with thiamine diphosphate, from ''B. anthracis''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P45694 P45694]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU17890]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.2.1.1 2.2.1.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''tkt'' {{PubMed|9068642}}

* '''[[Sigma factor]]:'''

* '''Regulation:'''
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' BS4530 (aphA3), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP94 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis, in [[pGP380]]), available in [[Stülke]] lab
** for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP820, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>14651647,16493705, 19603213 9068642 </pubmed>

[[Category:Protein-coding genes]]

File:PGP1331.jpg

2010-03-16T13:35:11Z

MLehnik:

PGP1331

2010-03-16T13:20:53Z

MLehnik:

[[File:PGP1331.png|250px|thumb|right|'''pBQ200: click to enlarge''']]

'''General comments'''

Integrative Plasmid for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor
*E.coli: multicopy plasmid, select for ampicillin
*B. subtilis: no ori, select for spectinomycin

'''Hints for the usage'''
*amplify the last 600bp of your gene of interest,
*skip the Stopp-Codon of the gene in the revers primer
*take care that the integration is in-frame

'''Antibody'''
*dilute the anitbody 1:10000 (you can freeze the Blotto solution and reuse it)

PGP1331

2010-03-16T13:20:07Z

MLehnik:

[[File:PGP1331.png]]

'''General comments'''

Integrative Plasmid for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor
*E.coli: multicopy plasmid, select for ampicillin
*B. subtilis: no ori, select for spectinomycin

'''Hints for the usage'''
*amplify the last 600bp of your gene of interest,
*skip the Stopp-Codon of the gene in the revers primer
*take care that the integration is in-frame

'''Antibody'''
*dilute the anitbody 1:10000 (you can freeze the Blotto solution and reuse it)

File:PGP1331.png

2010-03-16T13:19:19Z

MLehnik:

PGP1331

2010-03-16T13:16:41Z

MLehnik:

'''General comments'''

Integrative Plasmid for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor
*E.coli: multicopy plasmid, select for ampicillin
*B. subtilis: no ori, select for spectinomycin

'''Hints for the usage'''
*amplify the last 600bp of your gene of interest,
*skip the Stopp-Codon of the gene in the revers primer
*take care that the integration is in-frame

'''Antibody'''
*dilute the anitbody 1:10000 (you can freeze the Blotto solution and reuse it)

PGP1331

2010-03-16T13:16:03Z

MLehnik:

'''General comments'''

Integrative Plasmid for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor
*E.coli: multicopy plasmid, select for ampicillin
*B. subtilis: no ori, select for spectinomycin

'''Hints for the usage'''
amplify the last 600bp of your gene of interest,
skip the Stopp-Codon of the gene in the revers primer
take care that the integration is in-frame

'''Antibody'''
dilute the anitbody 1:10000 (you can freeze the Blotto solution and reuse it)

PGP1331

2010-03-16T13:14:49Z

MLehnik:

'''General comments'''

Integrative Plasmid for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor
E.coli: multicopy plasmid, select for ampicillin
B. subtilis: no ori, select for spectinomycin

'''Hints for the usage'''
amplify the last 600bp of your gene of interest,
skip the Stopp-Codon of the gene in the revers primer
take care that the integration is in-frame

'''Antibody'''
dilute the anitbody 1:10000 (you can freeze the Blotto solution and reuse it)

PGP1331

2010-03-16T13:06:47Z

MLehnik: Created page with ' '''general comments''' Integrative Plasmid for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor E.col…'

'''general comments'''

Integrative Plasmid for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor
E.coli: multicopy plasmid, select for ampicillin
B. subtilis: no ori, select for spectinomycin

'''Hints for the usage'''
amplify the last 600bp of your gene of interest,
skip the Stopp-Codon of the gene in the revers primer
take care that the integration is in-frame

'''Antibody'''
dilute the anitbody 1:10000 (you can freeze the Blotto solution and reuse it)