SubtiWiki - User contributions [en]

Spo0A

2014-05-09T12:26:53Z

Kgunka: /* Biological materials */

* '''Description:''' [[phosphorelay]] regulator, initiation of sporulation, coordinates [[DNA replication]] and initiation of [[sporulation]] by binding to sites close to the ''oriC'' 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''spo0A''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0C, spo0G, spoIIL, sof-1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[phosphorelay]] response regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24220 spo0A]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=Spo0A Spo0A]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=spo0A spo0A] '''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 801 bp, 267 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqiG]]'', ''[[spoIVB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24220 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24220 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24220 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:spo0A_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=spo0A_2518023_2518826_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:spo0A_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24220]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[phosphorelay]]}},
{{SubtiWiki category|[[biofilm formation]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[SigH regulon]]}},
{{SubtiWiki regulon|[[Spo0A regulon]]}}

=The [[Spo0A regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24220

===Phenotypes of a mutant ===
* inactivation of ''[[spo0A]]'' restores beta-lactam resistance in a ''[[sigM]]'' mutant {{PubMed|22211522}}
* altered cell death pattern in colonies {{PubMed|23012477}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24220&redirect=T BSU24220]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/spo0A.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10765]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** activation of gene expression at the onset of [[sporulation]] ([[Spo0A regulon]])
** coordination between DNA replication and initiation of [[sporulation]] by binding to sites close to the ''oriC'' (this limits re-initiation of replication) {{PubMed|23301687}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' receives phosphorylation from [[Spo0B]], dephosphorylation by [[Spo0E]], direct phosphorylation by [[KinC]] upon potassium leakage {{PubMed|19114652}}

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

* '''Effectors of protein activity:'''
** the phosphorylation state affects DNA binding activity
** interaction with [[MecA]] inhibits the transcriptional activity of [[Spo0A]]∼P {{PubMed|21435029}}

* '''[[SubtInteract|Interactions]]:'''
** [[KinC]]-[[Spo0A]] {{PubMed|19114652}}
** [[Spo0A]]-[[Spo0E]] {{PubMed|12067336}}
** [[Spo0A]]-[[SigA]] {{PubMed|14976210}}
** [[Spo0A]]-[[Spo0B]]
** [[SinI]]-[[Spo0A]] {{PubMed|21326214}}
** [[MecA]]-[[Spo0A]] {{PubMed|21435029}}

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24220&redirect=T BSU24220]

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1QMP 1QMP] (with phosphorylated aspartate, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/explore.do?structureId=1FC3 1FC3] (trans-activation domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/explore.do?structureId=1LQ1 1LQ1] (complex with DNA)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P06534 P06534]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24220]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''spo0A'' {{PubMed|11254139}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=spo0A_2518023_2518826_-1 spo0A] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|11254139,1569009}}, [[SigH]] {{PubMed|11254139,1569009}}

* '''Regulation:'''
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]
** repressed by casamino acids {{PubMed|15060025}}
** repressed by [[SinR]] overexpression {{PubMed|9685500}}
** repressed by [[soj]] {{PubMed|10852876}}
** expression increases when drowth rate declines {{PubMed|21552330}}

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]
** [[Spo0A]] synthesis is subject to a post-transcriptional control mechanism such that translation of mRNAs originating from the [[SigA]]-dependent promoter is impeded due to RNA secondary structure {{PubMed|21949067}}

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 394 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 358 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 1763 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:'''
** BKG9 (''[[spo0A]]''::''aphA3''), available in [[Jörg Stülke]]'s lab
* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

* [[Tony Wilkinson]], York University, U.K. [http://www.york.ac.uk/depts/chem/staff/ajw.html homepage]
* [[Imrich Barak]], Slovak Academy of Science, Bratislava, Slovakia [http://imb.savba.sk/~barak/ homepage]
* [[Charles Moran]], Emory University, NC, USA [http://www.microbiology.emory.edu/moran_c.html homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed>19995980 20030732 20157337 11286862 20833318 20955377 22303284 </pubmed>
==The [[Spo0A regulon]]==
<pubmed>14651647,15687200, </pubmed>
==Other original Publications==
<pubmed>14679239, 1569009 20413551 20404177 19528067, 19581368 , 8730857,2106683,3157992, 11254139, 12067336, 10869437, 16385044,9287005, 8127878,9287022, 8231806, 1905258,16452424,2118505,8207022, 12176382, 9733708, 11069677,1391039,12730135, 2437099,8288522, 16166384, 9495766,2118512,1556084, 18296515,7768874, 3145384, 19114652 20689749 1537790,9658000, 8509330,14762002, 1846779, 2981817, 9477965,8600030, 18840696, 1391039, 14976210, 19207565 11679073 12270811 11112444 18978066 20154131 14712656 17157871 15060025 9685500 10852876 21552330 22303282 22745669 23301687 23335417 23660663 23012477,23170957,23169620,22412392,21326214,21435029,21478340,21622736,21949067,21980382,22211522 23927765 24123822 </pubmed>

[[Category:Protein-coding genes]]

RadA

2014-01-24T19:10:16Z

Kgunka: /* Biological materials */

* '''Description:''' negative effector of [[DisA]] activity, suppressor of ''[[recU]]'' and ''[[recB]]'' mutations, participates in the stabilization and or processing of holliday junction intermediates 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''radA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sms, yacJ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA repair protein homolog
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || homologous recombination , control of c-di-AMP formation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00870 radA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=RadA RadA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=radA radA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 8.128
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1374 bp, 458 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[clpC]]'', ''[[disA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00870 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00870 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00870 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:radA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=radA_106096_107472_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:radA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00870]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[metabolism of signalling nucleotides]]}},
{{SubtiWiki category|[[DNA repair/ recombination]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[heat shock proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00870

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10149]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' RadA 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]]:'''
** [[RadA]]-[[DisA]] {{PubMed|23760274}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37572 P37572]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00870]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=radA_106096_107472_1 radA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]

* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed], induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Regulatory mechanism:''' [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** BKG1 (''[[radA]]''::''spc''), available in [[Stülke]] lab
** BKG2 (''[[radA]]-[[disA]]::spc''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>8793870,9987115,15317759,23760274,11544224, </pubmed>

[[Category:Protein-coding genes]]

DisA

2014-01-24T19:08:15Z

Kgunka: /* Biological materials */

* '''Description:''' DNA integrity scanning protein,diadenylate cyclase, delays sporulation in the case of chromosome damage, the DisA-dependent checkpoint arrests [[DNA replication]] during ''B. subtilis'' spore outgrowth until the germinating spore's genome is free of damage 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''disA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yacK''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA integrity scanning protein, has diadenylate cyclase activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[sporulation]] initiation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00880 disA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=DisA DisA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=disA disA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.569
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1080 bp, 360 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[radA]]'', ''[[yacL]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00880 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00880 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00880 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yacK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=disA_107476_108558_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:disA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00880]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell division]]}},
{{SubtiWiki category|[[metabolism of signalling nucleotides]]}},
{{SubtiWiki category|[[sporulation/ other]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},
{{SubtiWiki category|[[heat shock proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00880

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10150]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** synthesis of c-di-AMP from two molecules of ATP {{PubMed|23192352,21566650}}

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:'''
** contains a [[DAC domain]] for the synthesis of c-di-AMP {{PubMed|18439896}}

* '''Modification:'''

* '''[[Cofactors]]:'''

* '''Effectors of protein activity:'''
** [[RadA]] is an inhibitor of [[DisA]] activity {{PubMed|23760274}}

* '''[[SubtInteract|Interactions]]:'''
** forms octamers
** [[RacA]]-[[DisA]] {{PubMed|12493822}}
** [[RadA]]-[[DisA]] {{PubMed|23760274}}, this interaction result in the inhibition of [[DisA]] activity {{PubMed|23760274}}

* '''[[Localization]]:'''
** see a [http://download.cell.com/mmcs/journals/0092-8674/PIIS0092867406005034.mmc12.avi video] showing the movement of DisA in the cell (in real time) [http://www.ncbi.nlm.nih.gov/pubmed/16713562 PubMed]
** forms discrete globular foci in germinating spres that colocalize with the nucleoid {{PubMed|24244006}}

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3C23 3C23] {{PubMed|18439896}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37573 P37573]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00880]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]
** ''disA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=disA_107476_108558_1 disA] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''
** ''[[ctsR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]
** ''disA'': [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]

* '''Regulation:'''
** induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed], induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]
** expressed during [[sporulation]] in the mother cell {{PubMed|24244006}}
** expressed during germination and spore outgrowth {{PubMed|24244006}}

* '''Regulatory mechanism:''' [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' YA5 ''[[disA]]::tet'', available in [[Stülke]] lab
** GP987 (''[[disA]]''::''tet''), available in [[Stülke]] lab
** BKG2 (''[[radA]]-[[disA]]::spc''), available in [[Stülke]] lab
** 1A939 ( ''disA''::''tet''), {{PubMed|16713562}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A939&Search=1A939 BGSC]

* '''Expression vector:'''
** IPTG inducible expression of His-''disA'' in ''E. coli'': pGP2563 (in [http://biochem.web.utah.edu/hill/links/pET19b.pdf pET19b]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 22933559 18714086</pubmed>
== Original publications ==
<pubmed>24244006,8793870,9987115,16713562, 23760274,11544224 17434969 18439896 16713555 12493822 21566650 23192352 23608499 </pubmed>

[[Category:Protein-coding genes]]

RadA

2014-01-24T19:00:57Z

Kgunka: /* Biological materials */

* '''Description:''' negative effector of [[DisA]] activity, suppressor of ''[[recU]]'' and ''[[recB]]'' mutations, participates in the stabilization and or processing of holliday junction intermediates 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''radA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sms, yacJ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA repair protein homolog
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || homologous recombination , control of c-di-AMP formation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00870 radA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=RadA RadA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=radA radA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 8.128
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1374 bp, 458 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[clpC]]'', ''[[disA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00870 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00870 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00870 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:radA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=radA_106096_107472_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:radA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00870]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[metabolism of signalling nucleotides]]}},
{{SubtiWiki category|[[DNA repair/ recombination]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[heat shock proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00870

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10149]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' RadA 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]]:'''
** [[RadA]]-[[DisA]] {{PubMed|23760274}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37572 P37572]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00870]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=radA_106096_107472_1 radA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]

* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed], induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Regulatory mechanism:''' [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** BKG1 (''[[radA]]''::''spc''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>8793870,9987115,15317759,23760274,11544224, </pubmed>

[[Category:Protein-coding genes]]

File:Map pBP137.png

2013-10-29T16:18:02Z

Kgunka: Kgunka uploaded a new version of "File:Map pBP137.png"

File:PBP137 MCS.png

2013-10-29T16:16:15Z

Kgunka:

PBP137

2013-10-29T16:15:54Z

Kgunka:

[[File:Map_pBP137.png|250px|thumb|right|'''pBP137: click to enlarge''']]
[[File:PBP137_MCS.png|250px|thumb|right|'''pBP137 cloning region: click to enlarge''']]

Vector for the construction of translational ''gfp'' fusions that can be integrated at the ''amyE'' site

Does not replicate in ''B. subtilis'', integrates into the ''amyE'' site

Constructed in [[Fabian Commichau]]'s lab

* in ''E. coli'': ampicillin resistance

* in ''B. subtilis'': chloramphenicol resistance

* similar vectors: [[pAC6]], [[pAC7]]

sequencing primers:
*'''KG307:''' 5’-CACCTTCACCCTCTCCACTGACAG -3’
*'''PAC5F:''' 5’-GCGTAGCGAAAAATCCTTTTC-3‘

PBP137

2013-10-29T16:14:32Z

Kgunka:

[[File:Map_pBP137.png|250px|thumb|right|'''pBP137: click to enlarge''']]
[[File:PAC5_cloning_region.jpeg|250px|thumb|right|'''pBP137 cloning region: click to enlarge''']]

Vector for the construction of translational ''gfp'' fusions that can be integrated at the ''amyE'' site

Does not replicate in ''B. subtilis'', integrates into the ''amyE'' site

Constructed in [[Fabian Commichau]]'s lab

* in ''E. coli'': ampicillin resistance

* in ''B. subtilis'': chloramphenicol resistance

* similar vectors: [[pAC6]], [[pAC7]]

sequencing primers:
*'''KG307:''' 5’-CACCTTCACCCTCTCCACTGACAG -3’
*'''PAC5F:''' 5’-GCGTAGCGAAAAATCCTTTTC-3‘

PBP137

2013-10-29T16:12:39Z

Kgunka:

[[File:Map_pBP137.png|250px|thumb|right|'''pBP137: click to enlarge''']]

Vector for the construction of translational ''gfp'' fusions that can be integrated at the ''amyE'' site

Does not replicate in ''B. subtilis'', integrates into the ''amyE'' site

Constructed in [[Fabian Commichau]]'s lab

* in ''E. coli'': ampicillin resistance

* in ''B. subtilis'': chloramphenicol resistance

* similar vectors: [[pAC6]], [[pAC7]]

sequencing primers:
*'''KG307:''' 5’-CACCTTCACCCTCTCCACTGACAG -3’
*'''PAC5F:''' 5’-GCGTAGCGAAAAATCCTTTTC-3‘

File:Map pBP137.png

2013-10-29T16:00:31Z

Kgunka:

PBP137

2013-10-29T15:59:13Z

Kgunka: Created page with "Vector for the construction of translational ''gfp'' fusions that can be integrated at the ''amyE'' site Does not replicate in ''B. subtilis'', integrates into the ''amyE'' s..."

Vector for the construction of translational ''gfp'' fusions that can be integrated at the ''amyE'' site

Does not replicate in ''B. subtilis'', integrates into the ''amyE'' site

Constructed in [[Fabian Commichau]]'s lab

* in ''E. coli'': ampicillin resistance

* in ''B. subtilis'': chloramphenicol resistance

* similar vectors: [[pAC6]], [[pAC7]]

sequencing primers:
*'''KG307:''' 5’-CACCTTCACCCTCTCCACTGACAG -3’
*'''PAC5F:''' 5’-GCGTAGCGAAAAATCCTTTTC-3‘

SigM

2013-10-28T12:05:51Z

Kgunka: /* Biological materials */

* '''Description:''' [[RNA polymerase]] ECF-type [[sigma factor]] [[SigM]] 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yhdM ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNA polymerase]] ECF-type [[sigma factor]] [[SigM]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || responsible for intrinsic resistance against beta-lactam antibiotics
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09520 sigM]
|-
|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/SigM SigM]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 6.77
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 489 bp, 163 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhdL]]'', ''[[yhdN]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09520 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09520 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09520 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:sigM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sigM_1029577_1030068_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sigM_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09520]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription]]}},
{{SubtiWiki category|[[sigma factors and their control]]}},
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},
{{SubtiWiki category|[[resistance against toxins/ antibiotics]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[SigM regulon]]}}
=The [[SigM regulon]]=
=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09520

===Phenotypes of a mutant ===
* SigM is essential for growth and survival in nutrient broth (NB) containing 1.4 M NaCl {{PubMed|10216858}}
* ''sigM'' mutants form aberrantly shaped cells, which swell and lyse spontaneously during growth in NB medium containing increased levels (0.35-0.7 M) of a wide range of different salts {{PubMed|10216858}}
* increased sensitivity towards beta-lactam antibiotics {{PubMed|22211522}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13019]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' sigma-70 factor family, ECF subfamily (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** expression of [[CsbB]] in the absence of [[YfhO]] causes constitutive activation of [[SigM]] {{PubMed|23632331}}
** shortage of available bactoprenol causes [[SigM]] activation {{PubMed|23632331}}

* '''[[SubtInteract|Interactions]]:'''
** [[SigM]]-[[YhdK]]-[[YhdL]] {{PubMed|14993308}}
** [[SigM]]-[[RpoB]]-[[RpoC]]

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07582 O07582]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09520]

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

=== Additional information===
* Expression of the [[SigM regulon]] in increased in ''[[ugtP]]'' mutants {{PubMed|22362028}}

=Expression and regulation=

* '''Operon:''' ''[[sigM]]-[[yhdL]]-[[yhdK]]'' {{PubMed|9573210}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sigM_1029577_1030068_-1 sigM] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|9573210}}, [[SigM]] {{PubMed|9573210,18179421}}

* '''Regulation:'''
** induced by paraquat ([[SigM]]) {{PubMed|12775685}}

* '''Regulatory mechanism:'''

* '''Additional information:'''
** expression of [[CsbB]] in the absence of [[YfhO]] causes constitutive activation of [[SigM]] {{PubMed|23632331}}
** shortage of available bactoprenol causes [[SigM]] activation {{PubMed|23632331}}

=Biological materials =

* '''Mutant:'''
** 1A906 (''sigM''::''kan''), {{PubMed|12207695}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A906&Search=1A906 BGSC]
** BP129 (''sigM::aphA3''), available in [[Fabian Commichau]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]

=Your additional remarks=

=References=
==The [[SigM regulon]]==
<pubmed>18179421,17675383,17434969,</pubmed>
==Other original publications==
<pubmed>22362028 18394148,14993308,12399481,12775685,12207695,18820022,15838020,19047346,14651641,16151214 ,19465659 19745567 10216858 20057163 23103977 23632331 23070162,22211522,20817771</pubmed>

[[Category:Protein-coding genes]]

SigM

2013-10-23T13:28:30Z

Kgunka: /* Biological materials */

* '''Description:''' [[RNA polymerase]] ECF-type [[sigma factor]] [[SigM]] 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yhdM ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNA polymerase]] ECF-type [[sigma factor]] [[SigM]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || responsible for intrinsic resistance against beta-lactam antibiotics
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09520 sigM]
|-
|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/SigM SigM]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 6.77
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 489 bp, 163 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhdL]]'', ''[[yhdN]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09520 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09520 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09520 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:sigM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sigM_1029577_1030068_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sigM_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09520]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription]]}},
{{SubtiWiki category|[[sigma factors and their control]]}},
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},
{{SubtiWiki category|[[resistance against toxins/ antibiotics]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[SigM regulon]]}}
=The [[SigM regulon]]=
=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09520

===Phenotypes of a mutant ===
* SigM is essential for growth and survival in nutrient broth (NB) containing 1.4 M NaCl {{PubMed|10216858}}
* ''sigM'' mutants form aberrantly shaped cells, which swell and lyse spontaneously during growth in NB medium containing increased levels (0.35-0.7 M) of a wide range of different salts {{PubMed|10216858}}
* increased sensitivity towards beta-lactam antibiotics {{PubMed|22211522}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13019]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' sigma-70 factor family, ECF subfamily (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** expression of [[CsbB]] in the absence of [[YfhO]] causes constitutive activation of [[SigM]] {{PubMed|23632331}}
** shortage of available bactoprenol causes [[SigM]] activation {{PubMed|23632331}}

* '''[[SubtInteract|Interactions]]:'''
** [[SigM]]-[[YhdK]]-[[YhdL]] {{PubMed|14993308}}
** [[SigM]]-[[RpoB]]-[[RpoC]]

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07582 O07582]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09520]

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

=== Additional information===
* Expression of the [[SigM regulon]] in increased in ''[[ugtP]]'' mutants {{PubMed|22362028}}

=Expression and regulation=

* '''Operon:''' ''[[sigM]]-[[yhdL]]-[[yhdK]]'' {{PubMed|9573210}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sigM_1029577_1030068_-1 sigM] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|9573210}}, [[SigM]] {{PubMed|9573210,18179421}}

* '''Regulation:'''
** induced by paraquat ([[SigM]]) {{PubMed|12775685}}

* '''Regulatory mechanism:'''

* '''Additional information:'''
** expression of [[CsbB]] in the absence of [[YfhO]] causes constitutive activation of [[SigM]] {{PubMed|23632331}}
** shortage of available bactoprenol causes [[SigM]] activation {{PubMed|23632331}}

=Biological materials =

* '''Mutant:'''
** 1A906 ( ''sigM''::''kan''), {{PubMed|12207695}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A906&Search=1A906 BGSC]
** BP97 (D(''sigM'')::''aphA3''), available in [[Fabian Commichau]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]

=Your additional remarks=

=References=
==The [[SigM regulon]]==
<pubmed>18179421,17675383,17434969,</pubmed>
==Other original publications==
<pubmed>22362028 18394148,14993308,12399481,12775685,12207695,18820022,15838020,19047346,14651641,16151214 ,19465659 19745567 10216858 20057163 23103977 23632331 23070162,22211522,20817771</pubmed>

[[Category:Protein-coding genes]]

YhdK

2013-10-23T13:26:39Z

Kgunka: /* Biological materials */

* '''Description:''' anti-[[SigM]] protein 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhdK''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-[[SigM]] protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[SigM]] activity
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09500 yhdK]
|-
|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/YhdK YhdK]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 8.134
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 288 bp, 96 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhdJ]]'', ''[[yhdL]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09500 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09500 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09500 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yhdK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yhdK_1028233_1028523_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yhdK_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09500]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[sigma factors and their control]]}},
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09500

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13017]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[SigM]]-[[YhdK]]-[[YhdL]] {{PubMed|14993308}}

* '''[[Localization]]:''' cell membrane {{PubMed|14993308}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07580 O07580]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09500]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[sigM]]-[[yhdL]]-[[yhdK]]'' {{PubMed|9573210}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yhdK_1028233_1028523_-1 yhdK] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|9573210}}, [[SigM]] {{PubMed|9573210,18179421}}

* '''Regulation:'''
** induced by paraquat ([[SigM]]) {{PubMed|12775685}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** BP97 (D(''[[sigM]]-[[yhdL]]-[[yhdK]]'')::''aphA3''), available in [[Fabian Commichau]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18179421,14993308,9573210, </pubmed>

[[Category:Protein-coding genes]]

YhdL

2013-10-23T13:24:16Z

Kgunka: /* Biological materials */

* '''Description:''' anti-[[SigM]] protein 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhdL''
|-
|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''' || anti-[[SigM]] protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[SigM]] activity
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09510 yhdL]
|-
|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/YhdL YhdL]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 6.182
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1074 bp, 358 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhdK]]'', ''[[sigM]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09510 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09510 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09510 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yhdL_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yhdL_1028511_1029587_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yhdL_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09510]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[sigma factors and their control]]}},
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09510

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13018]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[SigM]]-[[YhdK]]-[[YhdL]] {{PubMed|14993308}}

* '''[[Localization]]:''' cell membrane {{PubMed|14993308}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07581 O07581]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09510]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[sigM]]-[[yhdL]]-[[yhdK]]'' {{PubMed|9573210}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yhdL_1028511_1029587_-1 yhdL] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|9573210}}, [[SigM]] {{PubMed|9573210,18179421}}

* '''Regulation:'''
** induced by paraquat ([[SigM]]) {{PubMed|12775685}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** BP97 (D(''[[sigM]]-[[yhdL]]-[[yhdK]]'')::''aphA3''), available in [[Fabian Commichau]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18179421,14993308,10216858, </pubmed>

[[Category:Protein-coding genes]]

YjcL

2013-07-11T13:48:59Z

Kgunka: /* Biological materials */

* '''Description:''' unknown 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yjcL''
|-
|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
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU11900 yjcL]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 9.381
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1188 bp, 396 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yjcK]]'', ''[[trnSL-Val2]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU11900 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU11900 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU11900 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yjcL_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yjcL_1261426_1262616_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yjcL_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU11900]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[proteins of unknown function]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU11900

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13165]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31634 O31634]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU11900]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yjcL_1261426_1262616_-1 yjcL] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** BP138 (spc) available in [[Fabian Commichau]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

SspA

2013-07-11T13:48:03Z

Kgunka: /* Biological materials */

* '''Description:''' small acid-soluble spore protein (major alpha-type SASP) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sspA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small acid-soluble spore protein (major alpha-type SASP)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protection of spore DNA
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29570 sspA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 4.731
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 207 bp, 69 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytcI]]'', ''[[thiI]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29570 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29570 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29570 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:sspA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sspA_3025445_3025654_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sspA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29570]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29570

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10786]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' alpha/beta-type SASP family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?pdbId=2BZ0 2BZ0] (82% identity, 89% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P04831 P04831]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29570]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[sspA]]'' {{PubMed|3009398}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sspA_3025445_3025654_-1 sspA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigG]] {{PubMed|15699190}}

* '''Regulation:'''
** expressed late during sporulation in the forespore ([[SigG]], [[SpoVT]]) {{PubMed|15699190,8755877}}

* '''Regulatory mechanism:'''
** [[SpoVT]]: transcription activation {{PubMed|8755877}}

* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]

=Biological materials =

* '''Mutant:'''
** BP137 (cat) available in [[Fabian Commichau]]'s lab
** 1S109 (no resistance), available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S109&Search=1S109 BGSC]
** 1S111 (no resistance), {{PubMed|3087950}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S111&Search=1S111 BGSC]
** 1S112 (no resistance), {{PubMed|3125155}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S112&Search=1S112 BGSC]
** 1S113 (no resistance), {{PubMed|3125155}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S113&Search=1S113 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>16707666,2456528,3009398,12884008,11092849,7608092,15458366, 19542328 15699190,8755877 23064347 3087950 3125155</pubmed>

[[Category:Protein-coding genes]]

SspA

2013-07-11T13:47:44Z

Kgunka: /* Biological materials */

* '''Description:''' small acid-soluble spore protein (major alpha-type SASP) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sspA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small acid-soluble spore protein (major alpha-type SASP)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protection of spore DNA
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29570 sspA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 4.731
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 207 bp, 69 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytcI]]'', ''[[thiI]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29570 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29570 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29570 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:sspA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sspA_3025445_3025654_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sspA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29570]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29570

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10786]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' alpha/beta-type SASP family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?pdbId=2BZ0 2BZ0] (82% identity, 89% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P04831 P04831]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29570]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[sspA]]'' {{PubMed|3009398}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sspA_3025445_3025654_-1 sspA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigG]] {{PubMed|15699190}}

* '''Regulation:'''
** expressed late during sporulation in the forespore ([[SigG]], [[SpoVT]]) {{PubMed|15699190,8755877}}

* '''Regulatory mechanism:'''
** [[SpoVT]]: transcription activation {{PubMed|8755877}}

* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]

=Biological materials =

* '''Mutant:'''
** BP137 (cat)available in [[Fabian Commichau]]'s lab
** 1S109 (no resistance), available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S109&Search=1S109 BGSC]
** 1S111 (no resistance), {{PubMed|3087950}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S111&Search=1S111 BGSC]
** 1S112 (no resistance), {{PubMed|3125155}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S112&Search=1S112 BGSC]
** 1S113 (no resistance), {{PubMed|3125155}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S113&Search=1S113 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>16707666,2456528,3009398,12884008,11092849,7608092,15458366, 19542328 15699190,8755877 23064347 3087950 3125155</pubmed>

[[Category:Protein-coding genes]]

DgcW

2013-07-11T12:40:01Z

Kgunka: /* Biological materials */

* '''Description:''' potential diguanylate cyclase and phosphodiesterase 

{| 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''' || potential diguanylate cyclase and phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13420 ykoW]
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13420 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13420 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13420 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ykoW_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykoW_1407329_1409578_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ykoW_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13420]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[metabolism of signalling nucleotides]]}}

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

=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:'''
** contains a central GGDEF domain and a C-terminal EAL domain {{PubMed|22821967}}
** aa 290-735 are similar to ''E. coli'' CsrD (18% identity, 43% similarity)

* '''Modification:'''

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

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

* '''[[SubtInteract|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:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykoW_1407329_1409578_-1 ykoW] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP850 (''[[ykoW]]''::''cat''), available in [[Jörg Stülke]]'s lab
** BP140 (ermC) available in [[Fabian Commichau]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>11728710,16980588 , 22821967</pubmed>

[[Category:Protein-coding genes]]

YddT

2013-05-08T14:11:44Z

Kgunka: /* Biological materials */

* '''Description:''' unknown essential gene 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yddT''
|-
|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''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU05100 yddT]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 9.546
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 684 bp, 228 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydzM]]'', ''[[ydzN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12317]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yddT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU05100 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yddT_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[proteins of unknown function]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU05100

===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+BG12127]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

* '''Paralogous protein(s):''' almost identical to the protein [[YomL]] encoded by the prophage SPß (the two proteins differ in only 4 out of 228 amino acids)

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96657 P96657]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU05100]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''''' [[yddT]]'' {{PubMed|20817675}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU05100 yddT] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
**BP116 (spc), available in [[Fabian Commichau]]'s lab
* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|20817675}}

<pubmed>17114254 23420519 </pubmed>
[[Category:Protein-coding genes]]

YdzM

2013-05-08T14:11:06Z

Kgunka: /* Biological materials */

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ydzM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || -
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU05099 ydzM]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6.5 kDa, 9.101
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 174 bp, 58 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yddS]]'','' [[yddT]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:ydzM_context.gif]]
|-
|colspan="2" |'''[None Expression at a glance]'''   {{PubMed|22383849}} [[Image:ydzM_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[proteins of unknown function]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU05099

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' no entry

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

* '''Paralogous protein(s):''' identical to the protein [[YouB]] encoded by the prophage SPß

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q9K3A9 Q9K3A9]

* '''KEGG entry:'''

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
**BP115 (spc), available in [[Fabian Commichau]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=subtilis+ydzM&log$=activity search PubMed]

[[Category:Protein-coding genes]]

YomL

2013-05-08T14:08:05Z

Kgunka: /* Biological materials */

* '''Description:''' unknown essential protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yomL''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes {{PubMed|17114254}}
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU21320 yomL]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 9.357
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 684 bp, 228 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yozP]]'', ''[[youB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14050]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yomL_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU21320 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yomL_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[proteins of unknown function]]}},
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[SPß prophage]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU21320

===Phenotypes of a mutant ===
essential {{PubMed|17114254}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13599]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

* '''Paralogous protein(s):''' [[YddT]] (the two proteins differ in only 4 out of 228 amino acids)

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31973 O31973]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU21320]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU21320 yomL] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
**BP118 (kan), available in [[Fabian Commichau]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>17114254 23420519 </pubmed>
[[Category:Protein-coding genes]]

PGP1459

2013-05-02T14:25:58Z

Kgunka:

[[File:PGP1459.png|250px|thumb|right|'''PGP1459: click to enlarge''']]
[[File:PGP380_cloning_region.jpeg|250px|thumb|right|'''pGP380 cloning region: click to enlarge''']]

The vector was constructed in the [[Stülke]] lab and it is suitable for constitutive expression of N-terminally Strep-tagged proteins in ''B. subtilis''. The plasmid confers resistance to ampicillin and kanamycin in ''E. coli'' and ''B. subtilis'', respectively. To transform ''B. subtilis'', the plasmid has to be linearized with ScaI. The plasmid will integrate into the ''[[ganA]]'' gene. Just like [[pGP380]] it can be used for the [[SPINE]] method.

The cloning region of [[pGP380]] is shown for detailed information.

Sequencing primers:
*'''KG64:''' 5‘-TATCAGGGCCTCGACTACA-3‘
*'''ML107:''' 5‘-GCTTCATAGAGTAATTCTGTAAAGG-3‘

Similar plasmid: [[pGP1460]] (for C-terminal Strep-tags)

<pubmed> </pubmed>

PGP1460

2013-05-02T13:46:30Z

Kgunka:

[[File:PGP1460.png|250px|thumb|right|'''pGP1460: click to enlarge''']]
[[File:PGP382_cloning_region.jpeg|250px|thumb|right|'''pGP382 cloning region: click to enlarge''']]

The vector was constructed in the [[Stülke]] lab and it is suitable for constitutive expression of C-terminally Strep-tagged proteins in ''B. subtilis''. The plasmid confers resistance to ampicillin and kanamycin in ''E. coli'' and ''B. subtilis'', respectively. To transform ''B. subtilis'', the plasmid has to be linearized with ScaI. The plasmid will integrate into the ''[[ganA]]'' gene. Just like [[pGP382]] it can be used for the [[SPINE]] method.

The cloning region of [[pGP382]] is shown for detailed information.

'''Genes cloned into this vector require a Shine-Dalgarno sequence.'''

Sequencing primers:
*'''KG64:''' 5‘-TATCAGGGCCTCGACTACA-3‘
*'''ML107:''' 5‘-GCTTCATAGAGTAATTCTGTAAAGG-3‘

Similar plasmid: [[pGP1459]] (for N-terminal Strep-tags)

<pubmed> </pubmed>

List of plasmids

2013-04-29T11:48:25Z

Kgunka: /* Expression/ purification in B. subtilis */

Here you can find a list of ''Bacillus subtilis'' plasmids:

==Fusion to reporter genes==
*[[pAC5]]: translational ''lacZ''-fusions (chloramphenicol resistence)
*[[pAC6]]: transcriptional ''lacZ''-fusions (cat resistence)
*[[pAC7]]: translational ''lacZ''-fusions (kanamycin resistence)
* pBaSysBioII: gfp transcriptional fusions for high-throughput analysis of gene expression {{PubMed|20150235}}
* a suite of vectors for ectopic insertion of GFP, CFP and IYFP transcriptional fusions in single copy at the ''amyE'' and ''bglS'' loci {{PubMed|20600285}}

==Labelling of a protein with a flourescent tag==
* [[pBP43]]: integrative plasmid for the fusion of monomeric GFP tag to the C-terminus of a protein, keeping the control of the expression under its natural promoter, '''this is the preferred plasmid for constructing GFP fusions!'''
* [[pGP1871]]: integrative plasmid for the fusion of YFP tag to the C-terminus of a protein, keeping the control of the expression under its natural promoter
* [[pGP1080]]: integrative plasmid for the fusion of GFP tag to the C-terminus of a protein, keeping the control of the expression under its natural promoter, allows express of the downstream gene by the P(spac) promoter, '''ATTENTION: This plasmid encodes the dimeric GFP that tends to produce artifacts!!!'''
* [[pGP1870]]: integrative plasmid for the fusion of GFP tag to the C-terminus of a protein, keeping the control of the expression under its natural promoter, '''ATTENTION: This plasmid encodes the dimeric GFP that tends to produce artifacts!!!'''

==Labelling of a protein with a triple FLAG tag==
* [[pGP1331]]: integrative plasmid for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping expression under the control of the natural promoter
* [[pGP1087]]: integrative plasmid for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping expression under the control of the natural promoter, allowing the expression of downstream genes under the control of the IPTG-inducible Pspac promoter

==Expression/ purification in ''B. subtilis''==
*[[pBP26]]: expression of YFP in ''B. subtilis'' and in ''E. coli''
*[[pBP27]]: expression of CFP in ''B. subtilis'' and in ''E. coli''
*[[pBQ200]]: overexpression of proteins in ''B. subtilis'' under control of a strong ''degQ36'' promoter
*[[pGP380]]: expression of proteins in ''B. subtilis'' allows fusion to a Strep-tag at the N-terminus of the protein
*[[pGP382]]: expression of proteins in ''B. subtilis'' allows fusion to a Strep-tag at the C-terminus of the protein
*[[pGP886]]: integration vector (integrates in ''[[xkdE]]''); allowing the expression of genes under the control of the xylose-inducible PxylA promoter in ''B. subtilis''
*[[pGP888]]: integration vector (integrates in ''[[ganA]]''); allowing the expression of genes under the control of the xylose-inducible PxylA promoter in ''B. subtilis''
*[[pGP1459]]: integration vector (integrates in ''[[ganA]]'') analogous to [[pGP380]]; expression of proteins in ''B. subtilis'' allows fusion to a Strep-tag at the N-terminus of the protein
*[[pGP1460]]: integration vector (integrates in ''[[ganA]]'') analogous to [[pGP382]]; expression of proteins in ''B. subtilis'' allows fusion to a Strep-tag at the C-terminus of the protein
* [[pGP1389]]: integrative plasmid for the fusion of a Strep-tag to the C-terminus of a protein, keeping expression under the control of the natural promoter

==Expression/ purification in ''E. coli''==
*[[pWH844]]: expression of proteins in ''E. coli'', allows fusion to a N-terminal His-tag
*[[pGP570]]: expression of proteins in ''E. coli'', allows fusion to a N-terminal His-tag that can be cleaved off
*[[pGP172]]: expression of proteins in ''E. coli'' allows fusion to a Strep-tag at the N-terminus of the protein
*[[pGP574]]: expression of proteins in ''E. coli'' allows fusion to a Strep-tag at the C-terminus of the protein

== Construction of (markerless) deletions ==
*[[pMAD]]: construction of markerless KOs in Gram-positive bacteria

File:PBP26.png

2013-04-29T11:39:58Z

Kgunka:

File:PBP27.png

2013-04-29T11:31:31Z

Kgunka:

PBP27

2013-04-29T11:31:09Z

Kgunka: Created page with "'''pBP27: click to enlarge''' vector for the integration of a constitutively expressed ''cfp'' gene at the ''amyE'' site does not repl..."

[[File:PBP27.png|250px|thumb|right|'''pBP27: click to enlarge''']]

vector for the integration of a constitutively expressed ''cfp'' gene at the ''amyE'' site

does not replicate in ''B. subtilis'' but in ''E. coli''

constructed in [[Fabian Commichau]]'s lab

in ''E. coli'': ampicillin resistance

in ''B. subtilis'': chloramphenicol resistance

similar vectors: [[pBP26]]

File:Abb. pBP26.png

2013-04-29T11:22:03Z

Kgunka: Kgunka uploaded a new version of "File:Abb. pBP26.png"

PBP26

2013-04-29T11:18:53Z

Kgunka:

[[File:PBP26.png|250px|thumb|right|'''pBP26: click to enlarge''']]

vector for the integration of a constitutively expressed ''yfp'' gene at the ''amyE'' site

does not replicate in ''B. subtilis'' but in ''E. coli''

constructed in [[Fabian Commichau]]'s lab

in ''E. coli'': ampicillin resistance

in ''B. subtilis'': chloramphenicol resistance

similar vectors: [[pBP27]]

PBP26

2013-04-29T11:17:42Z

Kgunka: Created page with "'''pBP26: click to enlarge''' vector for the integration of a constitutively expressed ''yfp'' gene at the ''amyE'' site does not repl..."

[[File:PBP26.png|250px|thumb|right|'''pBP26: click to enlarge''']]

vector for the integration of a constitutively expressed ''yfp'' gene at the ''amyE'' site

does not replicate in ''B. subtilis'' but in ''E. coli''

constructed in the Commichau lab

in ''E. coli'': ampicillin resistance

in ''B. subtilis'': chloramphenicol resistance

similar vectors: [[pBP27]]

File:Abb. pBP26.png

2013-04-29T11:16:43Z

Kgunka:

DgcW

2013-04-19T07:23:09Z

Kgunka: /* Biological materials */

* '''Description:''' potential diguanylate cyclase and phosphodiesterase 

{| 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''' || potential diguanylate cyclase and phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU13420 ykoW]
|-
|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>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykoW_1407329_1409578_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ykoW_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[metabolism of signalling nucleotides]]}}

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

=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:'''
** contains a central GGDEF domain and a C-terminal EAL domain {{PubMed|22821967}}
** aa 290-735 are similar to ''E. coli'' CsrD (18% identity, 43% similarity)

* '''Modification:'''

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

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

* '''[[SubtInteract|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:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykoW_1407329_1409578_-1 ykoW] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP850 (''[[ykoW]]''::''cat''), available in [[Stülke]] lab

* '''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=
'''Additional publications:''' {{PubMed|22821967}}
<pubmed>11728710,16980588 , </pubmed>

[[Category:Protein-coding genes]]

DgcW

2013-04-19T07:22:00Z

Kgunka: /* Biological materials */

* '''Description:''' potential diguanylate cyclase and phosphodiesterase 

{| 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''' || potential diguanylate cyclase and phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU13420 ykoW]
|-
|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>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykoW_1407329_1409578_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ykoW_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[metabolism of signalling nucleotides]]}}

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

=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:'''
** contains a central GGDEF domain and a C-terminal EAL domain {{PubMed|22821967}}
** aa 290-735 are similar to ''E. coli'' CsrD (18% identity, 43% similarity)

* '''Modification:'''

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

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

* '''[[SubtInteract|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:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykoW_1407329_1409578_-1 ykoW] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP850 (''[[ykoW]]''::''cat''), available in [[Stülke]] lab

* '''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=
'''Additional publications:''' {{PubMed|22821967}}
<pubmed>11728710,16980588 , </pubmed>

[[Category:Protein-coding genes]]

DgcK

2013-04-19T07:21:02Z

Kgunka: /* Biological materials */

* '''Description:''' potential c-di-GMP synthase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhcK''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || potential diguanylate cyclase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU09120 yhcK]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 8.571
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1077 bp, 359 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhcJ]]'', ''[[tcyP]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12740]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yhcK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yhcK_985734_986813_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yhcK_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[metabolism of signalling nucleotides]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09120

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11589]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** contains a C-terminal GGDEF domain {{PubMed|22821967}}

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54595 P54595]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09120]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yhcK_985734_986813_-1 yhcK] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP848 (''[[yhcK]]''::''ermC''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22821967}}
[[Category:Protein-coding genes]]

PBP43

2013-03-01T12:12:44Z

Kgunka:

[[File:pBP43.png|250px|thumb|right|'''pBP43: click to enlarge''']]

'''General comments'''

Integrative [[plasmid]] for the fusion of the monomeric variant of GFP A206K to the C-terminus of a protein, keeping the control of the expression under its natural promoter
* ''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
* Don't use XbaI and KpnI for cloning. They cut the vector twice!

PBP43

2013-03-01T12:11:26Z

Kgunka: Created page with "'''pBP43: click to enlarge''' '''General comments''' Integrative plasmid for the fusion of the monomeric variant of GFP A206K to the C-..."

File:PBP43.png

2013-03-01T12:09:28Z

Kgunka: uploaded a new version of "File:PBP43.png"

File:PBP43.png

2013-03-01T12:07:27Z

Kgunka:

List of plasmids

2013-02-01T07:39:32Z

Kgunka: /* Expression/ purification in B. subtilis */

Here you can find a list of ''Bacillus subtilis'' plasmids:

==Fusion to reporter genes==
*[[pAC5]]: translational ''lacZ''-fusions (chloramphenicol resistence)
*[[pAC6]]: transcriptional ''lacZ''-fusions (cat resistence)
*[[pAC7]]: translational ''lacZ''-fusions (kanamycin resistence)
* pBaSysBioII: gfp transcriptional fusions for high-throughput analysis of gene expression {{PubMed|20150235}}
* a suite of vectors for ectopic insertion of GFP, CFP and IYFP transcriptional fusions in single copy at the ''amyE'' and ''bglS'' loci {{PubMed|20600285}}

==Labelling of a protein with a flourescent tag==
* [[pGP1080]]: integrative plasmid for the fusion of GFP tag to the C-terminus of a protein, keeping the control of the expression under its natural promoter, allows express of the downstream gene by the P(spac) promoter
* [[pGP1870]]: integrative plasmid for the fusion of GFP tag to the C-terminus of a protein, keeping the control of the expression under its natural promoter
* [[pGP1871]]: integrative plasmid for the fusion of YFP tag to the C-terminus of a protein, keeping the control of the expression under its natural promoter

==Labelling of a protein with a triple FLAG tag==
* [[pGP1331]]: integrative plasmid for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping expression under the control of the natural promoter
* [[pGP1087]]: integrative plasmid for the fusion of 3x FLAG tag to the C-terminus of a protein, keeping expression under the control of the natural promoter, allowing the expression of downstream genes under the control of the IPTG-inducible Pspac promoter

==Expression/ purification in ''B. subtilis''==
*[[pBQ200]]: overexpression of proteins in ''B. subtilis'' under control of a strong ''degQ36'' promoter
*[[pGP380]]: expression of proteins in ''B. subtilis'' allows fusion to a Strep-tag at the N-terminus of the protein
*[[pGP382]]: expression of proteins in ''B. subtilis'' allows fusion to a Strep-tag at the C-terminus of the protein
*[[pGP886]]: integration vector (integrates in ''[[xkdE]]''); allowing the expression of genes under the control of the xylose-inducible PxylA promoter in ''B. subtilis''
*[[pGP888]]: integration vector (integrates in ''[[ganA]]''); allowing the expression of genes under the control of the xylose-inducible PxylA promoter in ''B. subtilis''
*[[pGP1459]]: integration vector (integrates in ''[[ganA]]'') analogous to [[pGP380]]; expression of proteins in ''B. subtilis'' allows fusion to a Strep-tag at the N-terminus of the protein
*[[pGP1460]]: integration vector (integrates in ''[[ganA]]'') analogous to [[pGP382]]; expression of proteins in ''B. subtilis'' allows fusion to a Strep-tag at the C-terminus of the protein
* [[pGP1389]]: integrative plasmid for the fusion of a Strep-tag to the C-terminus of a protein, keeping expression under the control of the natural promoter

==Expression/ purification in ''E. coli''==
*[[pWH844]]: expression of proteins in ''E. coli'', allows fusion to a N-terminal His-tag
*[[pGP570]]: expression of proteins in ''E. coli'', allows fusion to a N-terminal His-tag that can be cleaved off
*[[pGP172]]: expression of proteins in ''E. coli'' allows fusion to a Strep-tag at the N-terminus of the protein
*[[pGP574]]: expression of proteins in ''E. coli'' allows fusion to a Strep-tag at the C-terminus of the protein

== Construction of (markerless) deletions ==
*[[pMAD]]: construction of markerless KOs in Gram-positive bacteria

File:PGP886.png

2013-01-31T13:29:48Z

Kgunka:

PGP886

2013-01-31T13:29:05Z

Kgunka: Created page with "'''pGP886: click to enlarge''' The vector was constructed in Jörg Stülke's lab and it is suitable for the xylose-inducible expression..."

[[File:pGP886.png|250px|thumb|right|'''pGP886: click to enlarge''']]

The vector was constructed in [[Jörg Stülke]]'s lab and it is suitable for the xylose-inducible expression of proteins in ''B. subtilis''. The plasmid confers resistance to ampicillin and erythromycin/lincomycin in ''E. coli'' and ''B. subtilis'', respectively. To transform ''B. subtilis'', the plasmid has to be linearized with ScaI or NotI. The plasmid will integrate into the ''[[xkdE]]'' gene.

''' Hints for usage'''
*An additional base has to be inserted in the forward primer to restore the frame.
*Don't forget a stop codon in the reverse primer.

TreR

2012-12-12T14:12:26Z

Kgunka:

* '''Description:''' transcription repressor of the ''[[treP]]-[[treA]]-[[treR]]'' operon, ([[GntR family]]) 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''treR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yfxA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription repressor, ([[GntR family]])
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of trehalose utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU07820 treR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 6.82
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 714 bp, 238 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[treA]]'', ''[[hypO]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12611]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:treR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=treR_853556_854272_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:treR_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of specific carbon sources]]}},
{{SubtiWiki category|[[transcription factors and their control]]}}

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

=The [[TreR regulon]]=
* ''[[treP]]-[[treA]]-[[treR]]''

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07820

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11011]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2OGG 2OGG] (effector binding domain) {{PubMed|17705272}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39796 P39796]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07820]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[treP]]-[[treA]]-[[treR]]'' {{PubMed|8755887}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=treR_853556_854272_1 treR] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|8755887}}

* '''Regulation:'''
** induced by trehalose ([[TreR]]) {{PubMed|8755887}}
** repressed by glucose ([[CcpA]]) {{PubMed|18977770}}
** expressed under conditions of phosphate limitation ([[PhoP]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/21636651 PubMed]

* '''Regulatory mechanism:'''
** [[TreR]]: transcription repression {{PubMed|8755887}}
** [[CcpA]]: transcription repression {{PubMed|18977770}}
** [[PhoP]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/21636651 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|21636651}}

<pubmed>8755887,9829827,8917076, 17705272,18977770, </pubmed>

[[Category:Protein-coding genes]]

McsB

2012-12-05T12:36:33Z

Kgunka: /* Biological materials */

* '''Description:''' [[protein kinases and phosphatases|protein arginine kinase]], adaptor protein, modulator of [[CtsR]]-dependent repression 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mcsB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yacI ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[protein kinases and phosphatases|protein arginine kinase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[CtsR]] activity
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU00850 mcsB]
|-
|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/McsB McsB]
|-
|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''' || 40 kDa, 5.068
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1089 bp, 363 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mcsA]]'', ''[[clpC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11861]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mcsB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mcsB_102484_103575_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mcsB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00850

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10147]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' targets non-functional CtsR for degradation by [[ClpP]]/[[ClpC]] {{PubMed|20852588}}

* '''Protein family:''' ATP:guanido phosphotransferase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** autophosphorylation on specific arginine residues {{PubMed|20852588,21622759}}, dephosphorylation by [[YwlE]] {{PubMed|20852588,21622759}}
** autophosphorylation stimulates McsB activity as adaptor protein for [[ClpC]] {{PubMed|21622759}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[McsA]]-[[McsB]]-[[CtsR]], [[McsB]]-[[CtsR]] {{PubMed|20852588}}, [[McsA]]-[[McsB]]
** [[McsB]]-[[YwlE]] {{PubMed|20852588}}
** [[McsB]]-[[ClpP]]/[[ClpC]] (rapid degradation of phosphorylated McsB) {{PubMed|20852588}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37570 P37570]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00850]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mcsB_102484_103575_1 mcsB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2], [[SigF]] {{PubMed|16497325}}

* '''Regulation:'''
** expressed early during sporulation in the forespore ([[SigF]]) {{PubMed|16497325}}
** induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
** induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Regulatory mechanism:'''
** [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/9987115 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
**''mcsB::aphA3'' availbale from the Gerth lab
**mcsBC167S::spec available from the Gerth lab
**GP1457 (''mcsB''::''aphA3''), available in [[Stülke]] lab
**BP69 (spc), available in [[Fabian Commichau]]'s lab
* '''Expression vector:''' for expression, purification in E. coli with N-terminal His-tag, pRSETA available in Gerth lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:''' available in Gerth lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

==Reviews==
{{PubMed|19609260}}
==Original Publications==
<pubmed> 11179229,9987115, 8793870, 16497325,19226326, 9987115, 11544224, 20852588 21622759 22517742</pubmed>
'''Additional publications:''' {{PubMed|17380125,16163393,19498169}}
[[Category:Protein-coding genes]]

MdtP

2012-12-05T12:34:19Z

Kgunka: /* Biological materials */

* '''Description:''' multidrug-efflux transporter 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdtP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yusP ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || multidrug-efflux transporter
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || multidrug resistance
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32880 mdtP]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.836
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1623 bp, 541 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mdtR]]'', ''[[yusQ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15277]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yusP_context.gif]]
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transporters/ other]]}},
{{SubtiWiki category|[[resistance against toxins/ antibiotics]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14028]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''
** cell membrane (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32182 O32182]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32880]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[mdtR]]-[[mdtP]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19286808 PubMed]

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

* '''Regulation:'''

* '''Regulatory mechanism:''' repression by [[MdtR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19286808 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' BP70 (spc) available in [[Fabian Commichau]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711 19286808, </pubmed>

[[Category:Protein-coding genes]]

OppC

2012-12-05T12:33:51Z

Kgunka: /* Biological materials */

* '''Description:''' oligopeptide [[ABC transporter]] (permease) 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''oppC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0KC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || oligopeptide [[ABC transporter]] (permease)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation, competence development
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU11450 oppC]
|-
|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/OppC OppC]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Alternative nitrogen sources]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 10.107
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 915 bp, 305 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[oppB]]'', ''[[oppD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13002]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:oppC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=oppC_1222533_1223450_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:oppC_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ABC transporters]]}},
{{SubtiWiki category|[[utilization of nitrogen sources other than amino acids]]}},
{{SubtiWiki category|[[genetic competence]]}},
{{SubtiWiki category|[[phosphorelay]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU11450

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10773]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** required for the uptake of quorum sensing peptides such as [[PhrH]] {{PubMed|21908671}}

* '''Protein family:''' ABC transmembrane type-1 domain (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** ([[OppD]]-[[OppF]])-([[OppB]]-[[OppC]])-[[OppA]] {{PubMed|10092453}}

* '''[[Localization]]:''' cell membrane {{PubMed|10092453}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P24139 P24139]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU11450]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[oppA]]-[[oppB]]-[[oppC]]-[[oppD]]-[[oppF]]'' {{PubMed|1901616}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=oppC_1222533_1223450_1 oppC] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''
** expressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
** repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 PubMed]

* '''Regulatory mechanism:'''
** [[TnrA]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' BP68 (spc) available in [[Fabian Commichau]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|21908671}}
<pubmed>12823818,1901616,10092453,9252573,,12823818,10383984, 7997159 </pubmed>

[[Category:Protein-coding genes]]

OppA

2012-12-05T12:33:20Z

Kgunka: /* Biological materials */

* '''Description:''' oligopeptide [[ABC transporter]] (binding protein) 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''oppA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0KA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || oligopeptide [[ABC transporter]] (binding protein)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation, competence development
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU11430 oppA]
|-
|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/OppA OppA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.722
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1635 bp, 545 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trpS]]'', ''[[oppB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13000]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:oppA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=oppA_1219849_1221486_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:oppA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ABC transporters]]}},
{{SubtiWiki category|[[utilization of nitrogen sources other than amino acids]]}},
{{SubtiWiki category|[[genetic competence]]}},
{{SubtiWiki category|[[phosphorelay]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU11430

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10771]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** required for the uptake of quorum sensing peptides such as [[PhrH]] {{PubMed|21908671}}

* '''Protein family:''' bacterial solute-binding protein 5 family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[DppE]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on (Tyr-301 OR Tyr-303) AND Thr-470 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

* '''[[SubtInteract|Interactions]]:'''
** ([[OppD]]-[[OppF]])-([[OppB]]-[[OppC]])-[[OppA]] {{PubMed|10092453}}

* '''[[Localization]]:'''
** attached to the cell membrane (via [[OppB]]-[[OppC]]) {{PubMed|10092453}}
** at the outer side of the cell: extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], lipid modification as retention signal [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P24141 P24141]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU11430]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[oppA]]-[[oppB]]-[[oppC]]-[[oppD]]-[[oppF]]'' {{PubMed|1901616}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=oppA_1219849_1221486_1 oppA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''
** expressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
** repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 PubMed]

* '''Regulatory mechanism:'''
** [[TnrA]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 PubMed]

* '''Additional information:'''
** A [[ncRNA]] is predicted between ''[[trpS]]'' and ''[[oppA]]'' {{PubMed|20525796}}

=Biological materials =

* '''Mutant:''' BP67 (spc) available in [[Fabian Commichau]]'s lab
** 1S118 ( ''oppA''::''spec''), {{PubMed|11267663}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S118&Search=1S118 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|21908671}}
<pubmed>1901616,10092453,12823818,11267663,9252573,10960106,,12823818,10383984,18957862 18763711 17218307, 7997159 20525796</pubmed>

[[Category:Protein-coding genes]]

MdtP

2012-12-05T12:28:34Z

Kgunka: /* Biological materials */

* '''Description:''' multidrug-efflux transporter 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdtP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yusP ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || multidrug-efflux transporter
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || multidrug resistance
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32880 mdtP]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.836
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1623 bp, 541 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mdtR]]'', ''[[yusQ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15277]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yusP_context.gif]]
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transporters/ other]]}},
{{SubtiWiki category|[[resistance against toxins/ antibiotics]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14028]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''
** cell membrane (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32182 O32182]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32880]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[mdtR]]-[[mdtP]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19286808 PubMed]

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

* '''Regulation:'''

* '''Regulatory mechanism:''' repression by [[MdtR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19286808 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' BP70 (spc) available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711 19286808, </pubmed>

[[Category:Protein-coding genes]]

McsB

2012-12-05T12:27:25Z

Kgunka: /* Biological materials */

* '''Description:''' [[protein kinases and phosphatases|protein arginine kinase]], adaptor protein, modulator of [[CtsR]]-dependent repression 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mcsB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yacI ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[protein kinases and phosphatases|protein arginine kinase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[CtsR]] activity
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU00850 mcsB]
|-
|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/McsB McsB]
|-
|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''' || 40 kDa, 5.068
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1089 bp, 363 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mcsA]]'', ''[[clpC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11861]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mcsB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mcsB_102484_103575_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mcsB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00850

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10147]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' targets non-functional CtsR for degradation by [[ClpP]]/[[ClpC]] {{PubMed|20852588}}

* '''Protein family:''' ATP:guanido phosphotransferase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** autophosphorylation on specific arginine residues {{PubMed|20852588,21622759}}, dephosphorylation by [[YwlE]] {{PubMed|20852588,21622759}}
** autophosphorylation stimulates McsB activity as adaptor protein for [[ClpC]] {{PubMed|21622759}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[McsA]]-[[McsB]]-[[CtsR]], [[McsB]]-[[CtsR]] {{PubMed|20852588}}, [[McsA]]-[[McsB]]
** [[McsB]]-[[YwlE]] {{PubMed|20852588}}
** [[McsB]]-[[ClpP]]/[[ClpC]] (rapid degradation of phosphorylated McsB) {{PubMed|20852588}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37570 P37570]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00850]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mcsB_102484_103575_1 mcsB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2], [[SigF]] {{PubMed|16497325}}

* '''Regulation:'''
** expressed early during sporulation in the forespore ([[SigF]]) {{PubMed|16497325}}
** induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
** induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Regulatory mechanism:'''
** [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/9987115 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
**''mcsB::aphA3'' availbale from the Gerth lab
**mcsBC167S::spec available from the Gerth lab
**GP1457 (''mcsB''::''aphA3''), BP69 (spc), all available in [[Stülke]] lab

* '''Expression vector:''' for expression, purification in E. coli with N-terminal His-tag, pRSETA available in Gerth lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:''' available in Gerth lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

==Reviews==
{{PubMed|19609260}}
==Original Publications==
<pubmed> 11179229,9987115, 8793870, 16497325,19226326, 9987115, 11544224, 20852588 21622759 22517742</pubmed>
'''Additional publications:''' {{PubMed|17380125,16163393,19498169}}
[[Category:Protein-coding genes]]

OppC

2012-12-05T12:25:12Z

Kgunka: /* Biological materials */

* '''Description:''' oligopeptide [[ABC transporter]] (permease) 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''oppC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0KC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || oligopeptide [[ABC transporter]] (permease)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation, competence development
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU11450 oppC]
|-
|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/OppC OppC]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Alternative nitrogen sources]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 10.107
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 915 bp, 305 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[oppB]]'', ''[[oppD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13002]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:oppC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=oppC_1222533_1223450_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:oppC_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ABC transporters]]}},
{{SubtiWiki category|[[utilization of nitrogen sources other than amino acids]]}},
{{SubtiWiki category|[[genetic competence]]}},
{{SubtiWiki category|[[phosphorelay]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU11450

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10773]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** required for the uptake of quorum sensing peptides such as [[PhrH]] {{PubMed|21908671}}

* '''Protein family:''' ABC transmembrane type-1 domain (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** ([[OppD]]-[[OppF]])-([[OppB]]-[[OppC]])-[[OppA]] {{PubMed|10092453}}

* '''[[Localization]]:''' cell membrane {{PubMed|10092453}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P24139 P24139]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU11450]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[oppA]]-[[oppB]]-[[oppC]]-[[oppD]]-[[oppF]]'' {{PubMed|1901616}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=oppC_1222533_1223450_1 oppC] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''
** expressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
** repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 PubMed]

* '''Regulatory mechanism:'''
** [[TnrA]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' BP68 (spc) available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|21908671}}
<pubmed>12823818,1901616,10092453,9252573,,12823818,10383984, 7997159 </pubmed>

[[Category:Protein-coding genes]]