SubtiWiki - User contributions [en]

DisA

2013-11-27T11:08:06Z

Fmehne: /* Original publications */

* '''Description:''' DNA integrity scanning protein, delays sporulation in the case of chromosome damage, has diadenylate cyclase activity 

{| 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/pathways/stress_response.html Stress]'''
|-
|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:'''

* '''Modification:'''

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

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

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

=== Database entries ===

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

* '''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]

* '''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
** 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, 18714086, 23760274,11544224 17434969 18439896 16713555 12493822 21566650 23192352 23608499 </pubmed>

[[Category:Protein-coding genes]]

ExoA

2013-11-27T11:07:14Z

Fmehne: /* Original publications */

* '''Description:''' apurinic/apyrimidinic endonuclease, multifunctional DNA-repair enzyme, important for spore dormance 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''exoA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || apurinic/apyrimidinic endonuclease
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || repair of oxidative DNA damage in spores
|-
|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=BSU40880 exoA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 4.592
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 756 bp, 252 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ccpB]]'', ''[[rpsR]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40880 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40880 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40880 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:exoA_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=exoAA_4197780_4198538_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:exoA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40880]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40880

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10046]

=== Additional information===
* [[ExoA]] is functionally redundant with [[Nfo]]

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates (according to Swiss-Prot)

* '''Protein family:''' DNA repair enzymes AP/exoA 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]]:'''
** cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37454 P37454]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40880]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[exoA]]-[[ccpB]]'' (according to [http://dbtbs.hgc.jp/COG/prom/exoA-ccpA.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=exoAA_4197780_4198538_-1 exoA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigG]] {{PubMed|16237020}}

* '''Regulation:'''
** expressed late during sporulation in the forespore ([[SigG]]) {{PubMed|16237020}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP898 (''exoA''::''kan''), available in [[Jörg Stülke]]'s lab
** GP1503 (''exoA''::''kan'', ''nfo''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 22933559 </pubmed>
== Original publications ==
<pubmed>24244006,18203828,16237020, 19930460, 10540738 21441501 24123749 </pubmed>

[[Category:Protein-coding genes]]

Nfo

2013-11-27T11:06:38Z

Fmehne: /* Original publications */

* '''Description:''' type IV apurinic/apyrimidinic endonuclease 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''nfo ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqfS''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || type IV apurinic/apyrimidinic endonuclease
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || repair of oxidative DNA damage in spores
|-
|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=BSU25130 nfo]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 5.371
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 891 bp, 297 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfT]]'', ''[[cshB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU25130 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU25130 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU25130 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yqfS_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=nfo_2593281_2594174_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:nfo_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU25130]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25130

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11665]

=== Additional information===
* Nfo is functionally redundant with [[ExoA]]
=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products (according to Swiss-Prot)

* '''Protein family:''' AP endonuclease 2 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:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54476 P54476]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25130]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[nfo]]-[[yqfU]]'' {{PubMed|12486072}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=nfo_2593281_2594174_-1 nfo] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigG]] {{PubMed|12486072}}

* '''Regulation:'''
** expressed late during sporulation in the forespore ([[SigG]]) {{PubMed|12486072}}

* '''Regulatory mechanism:'''

* '''Additional information:'''
The gene ''[[yqfT]]'' is located between ''[[nfo]]'' and ''[[yqfU]]'', but is transcribed in the opposite direction.

=Biological materials =

* '''Mutant:'''
** available in [[Mario Pedraza-Reyes]]' lab
** GP899 (''nfo''::''kan'') and GP1502 (''nfo''::''cat''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 22933559 </pubmed>
== Original publications ==
<pubmed>24244006,18203828,16237020,12949090, 19930460,12486072, 21441501 24123749 </pubmed>

[[Category:Protein-coding genes]]

HemE

2013-10-23T19:24:53Z

Fmehne: /* References */

* '''Description:''' uroporphyrinogen decarboxylase (uroporphyrinogen III) 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hemE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || uroporphyrinogen decarboxylase (uroporphyrinogen III)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || heme biosynthesis
|-
|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=BSU10120 hemE]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 5.262
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1059 bp, 353 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpF]]'', ''[[hemH]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU10120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU10120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU10120 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:hemE_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=hemE_1086117_1087178_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:hemE_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU10120]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[biosynthesis of cofactors]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU10120

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10429]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Uroporphyrinogen III = coproporphyrinogen + 4 CO2 (according to Swiss-Prot)

* '''Protein family:''' uroporphyrinogen decarboxylase 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]]:'''
** cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2INF 2INF]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P32395 P32395]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU10120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.37 4.1.1.37]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[hemE]]-[[hemH]]-[[hemY]]'' {{PubMed|1459957}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hemE_1086117_1087178_1 hemE] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''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=

<pubmed>17122346,, </pubmed>

[[Category:Protein-coding genes]]
<pubmed>1459957,, </pubmed>

[[Category:Protein-coding genes]]

HemE

2013-10-23T19:24:23Z

Fmehne: /* References */

* '''Description:''' uroporphyrinogen decarboxylase (uroporphyrinogen III) 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hemE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || uroporphyrinogen decarboxylase (uroporphyrinogen III)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || heme biosynthesis
|-
|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=BSU10120 hemE]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 5.262
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1059 bp, 353 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpF]]'', ''[[hemH]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU10120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU10120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU10120 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:hemE_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=hemE_1086117_1087178_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:hemE_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU10120]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[biosynthesis of cofactors]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU10120

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10429]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Uroporphyrinogen III = coproporphyrinogen + 4 CO2 (according to Swiss-Prot)

* '''Protein family:''' uroporphyrinogen decarboxylase 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]]:'''
** cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2INF 2INF]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P32395 P32395]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU10120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.37 4.1.1.37]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[hemE]]-[[hemH]]-[[hemY]]'' {{PubMed|1459957}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hemE_1086117_1087178_1 hemE] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''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=

<pubmed>17122346,, </pubmed>

[[Category:Protein-coding genes]]

<pubmed>1459957,, </pubmed>

[[Category:Protein-coding genes]]

CdaS

2013-08-13T16:45:15Z

Fmehne: /* Biological materials */

* '''Description:''' sporulation-specific diadenylate cyclase, synthesis of c-di-AMP 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cdaS''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yojJ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || sporulation-specific diadenylate cyclase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of c-di-AMP
|-
|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=BSU19430 cdaS]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.367
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 621 bp, 207 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yojK]]'', ''[[yojI]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU19430 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU19430 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU19430 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yojJ_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=yojJ_2118504_2119127_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yojJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU19430]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19430

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13562]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=2FB5 2FB5] (the protein of ''B. cereus'', 48% identity, 81% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31854 O31854]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19430]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaS]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yojJ_2118504_2119127_-1 cdaS] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigG]] {{PubMed|22383849}}

* '''Regulation:'''
** expressed late during sporulation in the forespore ([[SigG]]) {{PubMed|22383849}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP983 (''[[cdaS]]''::''ermC''), available in [[Jörg Stülke]]'s lab
** GP1360 (''[[cdaS]]''::''spc''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** IPTG inducible expression of '''''B. cereus''''' Strep-''cdaS'' in ''E. coli'': pGP2593 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''His-tag fusion:'''
**pGP2591 10xHis-''cdaS'' under the control of native promoter (based on [[pAC7]]), available in [[Jörg Stülke]]'s lab**
**pGP2592 10xHis-''cdaS-L44F'' under the control of native promoter (based on [[pAC7]]), available in [[Jörg Stülke]]'s lab**

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
<pubmed>21566650, 23192352 22383849</pubmed>
[[Category:Protein-coding genes]]

CdaS

2013-08-13T16:42:42Z

Fmehne: /* Biological materials */

* '''Description:''' sporulation-specific diadenylate cyclase, synthesis of c-di-AMP 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cdaS''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yojJ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || sporulation-specific diadenylate cyclase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of c-di-AMP
|-
|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=BSU19430 cdaS]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.367
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 621 bp, 207 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yojK]]'', ''[[yojI]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU19430 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU19430 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU19430 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yojJ_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=yojJ_2118504_2119127_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yojJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU19430]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19430

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13562]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=2FB5 2FB5] (the protein of ''B. cereus'', 48% identity, 81% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31854 O31854]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19430]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaS]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yojJ_2118504_2119127_-1 cdaS] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigG]] {{PubMed|22383849}}

* '''Regulation:'''
** expressed late during sporulation in the forespore ([[SigG]]) {{PubMed|22383849}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP983 (''[[cdaS]]''::''ermC''), available in [[Jörg Stülke]]'s lab
** GP1360 (''[[cdaS]]''::''spc''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''His-tag fusion:'''
**pGP2591 10xHis-''cdaS'' under the control of native promoter (based on [[pAC7]]), available in [[Jörg Stülke]]'s lab**
**pGP2592 10xHis-''cdaS-L44F'' under the control of native promoter (based on [[pAC7]]), available in [[Jörg Stülke]]'s lab**

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
<pubmed>21566650, 23192352 22383849</pubmed>
[[Category:Protein-coding genes]]

CdaS

2013-08-13T16:41:48Z

Fmehne: /* Biological materials */

* '''Description:''' sporulation-specific diadenylate cyclase, synthesis of c-di-AMP 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cdaS''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yojJ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || sporulation-specific diadenylate cyclase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of c-di-AMP
|-
|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=BSU19430 cdaS]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.367
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 621 bp, 207 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yojK]]'', ''[[yojI]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU19430 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU19430 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU19430 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yojJ_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=yojJ_2118504_2119127_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yojJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU19430]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19430

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13562]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=2FB5 2FB5] (the protein of ''B. cereus'', 48% identity, 81% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31854 O31854]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19430]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaS]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yojJ_2118504_2119127_-1 cdaS] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigG]] {{PubMed|22383849}}

* '''Regulation:'''
** expressed late during sporulation in the forespore ([[SigG]]) {{PubMed|22383849}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP983 (''[[yojJ]]''::''ermC''), available in [[Jörg Stülke]]'s lab
** GP1360 (''[[yojJ]]''::''spc''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''His-tag fusion:'''
**pGP2591 10xHis-''cdaS'' under the control of native promoter (based on [[pAC7]]), available in [[Jörg Stülke]]'s lab**
**pGP2592 10xHis-''cdaS-L44F'' under the control of native promoter (based on [[pAC7]]), available in [[Jörg Stülke]]'s lab**

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
<pubmed>21566650, 23192352 22383849</pubmed>
[[Category:Protein-coding genes]]

YddT

2013-08-13T16:36:45Z

Fmehne: /* 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://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU05100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU05100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU05100 DNA_with_flanks]
|-
|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|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU05100]]
|-
|}

__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:'''
** IPTG inducible expression of Strep-''yddT'' in ''E. coli'': pGP2581 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>17114254 23420519 20817675</pubmed>
[[Category:Protein-coding genes]]

YomL

2013-08-13T16:35:56Z

Fmehne: /* 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://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU21320 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU21320 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU21320 DNA_with_flanks]
|-
|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|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU21320]]
|-
|}

__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:'''
** IPTG inducible expression of Strep-''yomL'' in ''E. coli'': pGP2580 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab

* '''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]]

GlmM

2013-08-13T16:34:42Z

Fmehne: /* Biological materials */

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|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=BSU01770 glmM]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cdaR]]'', ''[[glmS]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01770 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01770 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01770 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_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=glmM_198497_199843_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:glmM_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01770]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===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+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3PDK 3PDK] (from ''B. anthracis'') {{PubMed|21685296}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmM_198497_199843_1 glmM] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
**pGP400: (expression in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1401: (expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab
**pGP1402: (cloning vector for glmM (GlmM S100A) in ''E. coli'', in [[pBlueskript KS]]), available in [[Jörg Stülke]]'s lab
**pGP1403: (expression of GlmM (S100A) in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1405: (expression, purification of GlmM (S100A) in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''
** GP1340 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''
** GP1382 ''glmM-gfp ermC'' (based on [[pGP1080]]), available in [[Jörg Stülke]]'s lab

* '''two-hybrid system:'''
**pGP2576 (glmM in p25N), available in [[Jörg Stülke]]'s lab

* '''FLAG-tag construct:'''
** GP1380 ''lacA::cdaR-Strep aphA3 glmM-3xFLAG ermC'' (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Strep-tag construct:'''
** GP1388 ''lacA::glmM-Strep aphA3 cdaA-3xFLAG ermC'' (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:''' available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522}}
<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 20525796 21685296 23192352</pubmed>

[[Category:Protein-coding genes]]

CdaR

2013-08-13T16:34:10Z

Fmehne: /* Biological materials */

* '''Description:''' effector protein controlling [[CdaA]] diadenylate cyclase activity 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cdaR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ybbR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || effector protein controlling [[CdaA]] diadenylate cyclase activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of c-di-AMP synthesis
|-
|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=BSU01760 cdaR]
|-
|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/CdaR CdaR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 4.719
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1449 bp, 483 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cdaA]]'', ''[[glmM]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01760 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01760 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01760 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ybbR_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=ybbR_197027_198478_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01760]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01760

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12703]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** stimulates [[CdaA]] activity upon protein-protein interaction {{PubMed|23192352}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed|23192352}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34659 O34659]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01760]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbR_197027_198478_1 cdaR] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP999 (''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[cdaA]]''-''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** IPTG inducible expression of Strep-''cdaR'' in ''E. coli'': pGP2565 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab
** IPTG inducible expression of His-''cdaR'' in ''E. coli'': pGP2557 (in [http://biochem.web.utah.edu/hill/links/pET19b.pdf pET19b]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmids: pGP1989 and pGP1992.

* '''Strep-tag construct:'''
** GP1330 (aphA3, based on [[pGP1460]]), available in [[Jörg Stülke]]'s lab
** GP1380 ''lacA::cdaR-Strep aphA3 glmM-3xFLAG ermC'' (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:''' available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522,21154411}}
<pubmed>12884008, 16236721, 23192352 </pubmed>

[[Category:Protein-coding genes]]

YlaN

2013-08-13T16:33:54Z

Fmehne: /* Biological materials */

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ylaN''
|-
|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://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14840 ylaN]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 4.615
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 279 bp, 93 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylaM]]'', ''[[ftsW]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14840 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14840 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14840 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ylaN_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=ylaN_1552412_1552693_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ylaN_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14840]]
|-
|}

__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]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14840

===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+BG13351]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0358 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?structureId=2ODM 2ODM] {{PubMed|17469204}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07638 O07638]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14840]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ylaN]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ylaN_1552412_1552693_1 ylaN] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** IPTG inducible expression of Strep-''ylaN'' in ''E. coli'': pGP2579 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab
** IPTG inducible expression of His-''ylaN'' in ''E. coli'': pGP2583 (in [[pWH844]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:''' available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17005971 17469204 22383849 22383849 23420519 </pubmed>

[[Category:Protein-coding genes]]

YcgG

2013-08-13T16:30:22Z

Fmehne: /* Biological materials */

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ycgG''
|-
|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://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU03100 ycgG]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 9.185
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ycgF]]'', ''[[ycgH]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU03100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU03100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU03100 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ycgG_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=ycgG_335329_336090_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ycgG_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU03100]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU03100

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12005]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== 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/P94382 P94382]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU03100]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ycgF]]-[[ycgG]]'' {{PubMed|12662922}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ycgG_335329_336090_1 ycgG] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigE]] {{PubMed|12662922}}

* '''Regulation:''' subject to negative regulation by [[SpoIIID]] {{PubMed|15383836}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** IPTG inducible expression of Strep-''ycgG'' in ''E. coli'': pGP2578 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>12662922, 15383836 23420519 </pubmed>

[[Category:Protein-coding genes]]

UgtP

2013-08-13T16:27:52Z

Fmehne: /* Biological materials */

* '''Description:''' UDP-glucose diacylglycerol glucosyltransferase, growth-rate dependent inhibitor of [[cell division]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ugtP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypfP ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || UDP-glucose diacylglycerol glucosyltransferase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of glycolipids and anchoring of lipoteichoic acid, inhibition of [[FtsZ]] assembly
|-
|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=BSU21920 ugtP]
|-
|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/UgtP UgtP]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 8.398
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1146 bp, 382 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[metA]]'', ''[[cspD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU21920 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU21920 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU21920 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ugtP_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=ugtP_2306514_2307662_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ugtP_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU21920]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell division]]}},
{{SubtiWiki category|[[lipid metabolism/ other]]}},
{{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:''' BSU21920

===Phenotypes of a mutant ===
** cells are bent and distended {{PubMed|22362028}}
** increased expression of the [[SigM]], [[SigV]], and [[SigX]] regulons {{PubMed|22362028}}
** altered [[localization]] of [[MreB]] (irregular clusters instead of helical dots) {{PubMed|22362028}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11611]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** UDP-glucose + 1,2-diacylglycerol = UDP + 1,2-diacyl-3-(O-beta-D-glucopyranosyl)-sn-glycerol (according to Swiss-Prot)
** the interaction with [[FtsZ]] results in inhibition of [[cell division]] and an increase of cell size {{PubMed|22931116}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** oligomerization of [[UgtP]] is inhibited by UDP-Glc and by interaction with [[FtsZ]] {{PubMed|22931116}}

* '''[[SubtInteract|Interactions]]:'''
** [[EzrA]]-[[UgtP]] {{PubMed|17662947}}
** [[UgtP]]-[[UgtP]] {{PubMed|17662947}}, forms oligomers {{PubMed|22931116}}
** [[UgtP]]-[[FtsZ]] (under nutrient rich conditions) {{PubMed|22931116}}

* '''[[Localization]]:'''
** membrane-bound protein, self-assembles into tightly wound spirals ''in vitro'' {{PubMed|17662947}}
** under nutrient rich conditions (increased concentration of UDP-Glc): throughout the cell, concentrated at the cell poles and/or the cytokinetic ring, interaction with [[FtsZ]] {{PubMed|22931116}}
** under nutrient poor conditions: forms punctate foci (oligomers), no interaction with [[FtsZ]] {{PubMed|22931116}}
=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54166 P54166]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU21920]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ugtP_2306514_2307662_1 ugtP] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18179421 PubMed]

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1369 (''[[ugtP]]''::''spc''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
**pGP2571 (based on [[pBQ200]], 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> 19680248 17662935 22575476 </pubmed>

==Original Publications==
<pubmed>9244290,18820022,17662947,9720862 22362028 15640167 23935518 22931116</pubmed>

[[Category:Protein-coding genes]]

CdaA

2013-08-13T16:24:23Z

Fmehne: /* Biological materials */

* '''Description:''' diadenylate cyclase, synthesis of c-di-AMP in vegetative cells 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cdaA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbP, ybbQ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || diadenylate cyclase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of c-di-AMP
|-
|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=BSU01750 cdaA]
|-
|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/CdaA CdaA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 8.074
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 819 bp, 273 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsiW]]'', ''[[cdaR]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01750 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01750 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01750 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbP_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=ybbP_196213_197034_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbP_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01750]]
|-
|}

__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:''' BSU01750

===Phenotypes of a mutant ===
* inactivation of ''[[cdaA]]'' results in severe beta-lactam sensitivity {{PubMed|22211522}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11577]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** the interaction with [[CdaR]] stimulates the diadenylate cyclase activity of [[CdaA]] {{PubMed|23192352}}

* '''[[SubtInteract|Interactions]]:'''
** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed|23192352}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45589 Q45589]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbP_196213_197034_1 cdaA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP94 (D''[[cdaA]]''::''spc''), available in [[Jörg Stülke]]'s lab
** GP997 (''[[cdaA]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[cdaA]]''-''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** expression of native ''cdaA'' in ''B. subtilis'': pGP1960 (in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
** expression of ''cdaA''-Strep in ''B. subtilis'' suitable for [[SPINE]]: pGP1986 (in [[pGP382]]), available in [[Jörg Stülke]]'s lab
** IPTG inducible expression of ''cdaA''-Strep in ''E. coli'': pGP2564 (in [[pGP574]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:''' GP1339 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmid: pGP1990.

* '''FLAG-tag construct:'''
** GP1381 ''cdaA-3xFLAG ermC'' (based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
<pubmed>12884008,21566650, 23192352 22211522</pubmed>

[[Category:Protein-coding genes]]

DisA

2013-08-13T16:22:08Z

Fmehne: /* Biological materials */

* '''Description:''' DNA integrity scanning protein, delays sporulation in the case of chromosome damage, has diadenylate cyclase activity 

{| 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://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/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/pathways/stress_response.html Stress]'''
|-
|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:'''

* '''Modification:'''

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

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

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

=== Database entries ===

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

* '''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]

* '''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
** 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=

<pubmed>8793870,9987115,16713562,17434969,18714086,16713555,18439896,23760274,11544224 17434969 18714086 18439896 16713562 16713555 12493822 21566650 23192352 23608499 </pubmed>

[[Category:Protein-coding genes]]

CdaR

2013-08-13T16:20:33Z

Fmehne: /* Biological materials */

* '''Description:''' effector protein controlling [[CdaA]] diadenylate cyclase activity 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cdaR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ybbR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || effector protein controlling [[CdaA]] diadenylate cyclase activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of c-di-AMP synthesis
|-
|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=BSU01760 cdaR]
|-
|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/CdaR CdaR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 4.719
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1449 bp, 483 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cdaA]]'', ''[[glmM]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01760 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01760 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01760 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ybbR_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=ybbR_197027_198478_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01760]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01760

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12703]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** stimulates [[CdaA]] activity upon protein-protein interaction {{PubMed|23192352}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed|23192352}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34659 O34659]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01760]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbR_197027_198478_1 cdaR] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP999 (''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[cdaA]]''-''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** IPTG inducible expression of Strep-''cdaR'' in ''E. coli'': pGP2565 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab
** IPTG inducible expression of His-''cdaR'' in ''E. coli'': pGP2557 (in [http://biochem.web.utah.edu/hill/links/pET19b.pdf pET19b]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmids: pGP1989 and pGP1992.

* '''Strep-tag construct:'''
** GP1330 (aphA3, based on [[pGP1460]]), available in [[Jörg Stülke]]'s lab
** GP1380 ''lacA::cdaR-Strep aphA3 glmM-3xFLAG ermC'' (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522,21154411}}
<pubmed>12884008, 16236721, 23192352 </pubmed>

[[Category:Protein-coding genes]]

YfnI

2013-08-13T16:14:36Z

Fmehne: /* Biological materials */

* '''Description:''' polyglycerolphosphate lipoteichoic acid synthase, general stress protein, major secreted protein, required for survival at low temperature (4°C) 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yfnI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yetP, ltaSA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || minor lipoteichoic acid synthetase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of lipoteichoic acid
|-
|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=BSU07260 yfnI]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 73 kDa, 5.951
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1917 bp, 639 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yetO]]'', ''[[yfnH]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07260 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07260 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07260 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yfnI_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=ltaSA_796314_798233_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yfnI_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07260]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07260

===Phenotypes of a mutant ===
* induction of [[SigM]] and [[SigX]] activities {{PubMed|23103977}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12980]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

* '''Paralogous protein(s):''' [[LtaS]], [[YqgS]], [[YvgJ]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on (Thr-311 OR Ser-312) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

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

* '''[[Localization]]:'''
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q797B3 Q797B3]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07260]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ltaSA_796314_798233_1 yfnI] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** SM-NB (''yfnI-spc''), available in [[Anne Galinier]]'s and [[Boris Görke]]'s labs
** GP1390 ''yfnI::spc'', available in [[Jörg Stülke]]'s lab
** GP1397 ''yfnI::ermC'', available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
'''Additional reviews:''' {{PubMed|21255102}}
<pubmed> 21388439 </pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|23103977}}
<pubmed>17434969, 18957862 17218307 19229300 21255105, </pubmed>

[[Category:Protein-coding genes]]

YfnI

2013-08-13T16:14:17Z

Fmehne: /* Biological materials */

LtaS

2013-08-13T16:12:23Z

Fmehne: /* Biological materials */

* '''Description:''' polyglycerolphosphate lipoteichoic acid synthase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ltaS''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yflE''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || major lipoteichoic acid synthase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of lipoteichoic acid
|-
|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=BSU07710 ltaS]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 74 kDa, 5.202
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1947 bp, 649 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nagP]]'', ''[[yflD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07710 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07710 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07710 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yflE_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/index.py?detailname=&locustag=BSU07710 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ltaS_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07710]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===
* induction of [[SigM]] and [[SigX]] activities {{PubMed|23103977}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12940]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

* '''Paralogous protein(s):''' [[YfnI]], [[YqgS]], [[YvgJ]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated on Thr-297 {{PubMed|19229300}}

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

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

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

* '''[[Localization]]:'''
** cell membrane, at the septum of the cell {{PubMed|15743965}}
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=69910&ordinalpos=1&log$=structuread_title 2W8D]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34952 O34952]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07710]

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1389 ''ltaS::aphA3'', available in [[Jörg Stülke]]'s lab
** GP1396 ''ltaS::tet'', available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews: {{PubMed|21255102}}==
<pubmed> 21388439 </pubmed>
==Original publications==
<pubmed>19229300,17483484 21255105, 19168632 15743965 23103977 </pubmed>

[[Category:Protein-coding genes]]

DgkB

2013-08-13T16:06:42Z

Fmehne: /* Biological materials */

* '''Description:''' diacylglycerol kinase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''dgkB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yerQ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' ||yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || diacylglycerol kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of lipoteichoic acid
|-
|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=BSU06720 dgkB]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 5.635
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 909 bp, 303 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yerP]]'', ''[[rlmCD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06720 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06720 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06720 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yerQ_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=dagK_736436_737347_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:dgkB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU06720]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[essential genes]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU06720

===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+BG12843]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3S40 3S40] (from ''B. anthracis'', 32% identity, 68% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31502 O31502]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU06720]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dagK_736436_737347_1 dgkB] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1391 ''dgkB::cat ltaS::aphA3'', available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17535816,, 22451476</pubmed>

[[Category:Protein-coding genes]]

DgkB

2013-08-13T16:05:16Z

Fmehne: /* Biological materials */

* '''Description:''' diacylglycerol kinase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''dgkB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yerQ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' ||yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || diacylglycerol kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of lipoteichoic acid
|-
|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=BSU06720 dgkB]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 5.635
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 909 bp, 303 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yerP]]'', ''[[rlmCD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06720 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06720 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06720 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yerQ_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=dagK_736436_737347_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:dgkB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU06720]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[essential genes]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU06720

===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+BG12843]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3S40 3S40] (from ''B. anthracis'', 32% identity, 68% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31502 O31502]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU06720]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dagK_736436_737347_1 dgkB] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1391 ''dgkB::cat'', available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17535816,, 22451476</pubmed>

[[Category:Protein-coding genes]]

YfnI

2013-08-13T16:04:13Z

Fmehne: /* Biological materials */

* '''Description:''' polyglycerolphosphate lipoteichoic acid synthase, general stress protein, major secreted protein, required for survival at low temperature (4°C) 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yfnI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yetP, ltaSA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || minor lipoteichoic acid synthetase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of lipoteichoic acid
|-
|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=BSU07260 yfnI]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 73 kDa, 5.951
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1917 bp, 639 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yetO]]'', ''[[yfnH]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07260 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07260 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07260 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yfnI_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=ltaSA_796314_798233_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yfnI_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07260]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07260

===Phenotypes of a mutant ===
* induction of [[SigM]] and [[SigX]] activities {{PubMed|23103977}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12980]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

* '''Paralogous protein(s):''' [[LtaS]], [[YqgS]], [[YvgJ]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on (Thr-311 OR Ser-312) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

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

* '''[[Localization]]:'''
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q797B3 Q797B3]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07260]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ltaSA_796314_798233_1 yfnI] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** SM-NB (''yfnI-spc''), available in [[Anne Galinier]]'s and [[Boris Görke]]'s labs
** GP1390 ''yfnI::spc'', available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
'''Additional reviews:''' {{PubMed|21255102}}
<pubmed> 21388439 </pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|23103977}}
<pubmed>17434969, 18957862 17218307 19229300 21255105, </pubmed>

[[Category:Protein-coding genes]]

LtaS

2013-08-13T16:02:54Z

Fmehne: /* Biological materials */

* '''Description:''' polyglycerolphosphate lipoteichoic acid synthase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ltaS''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yflE''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || major lipoteichoic acid synthase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of lipoteichoic acid
|-
|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=BSU07710 ltaS]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 74 kDa, 5.202
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1947 bp, 649 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nagP]]'', ''[[yflD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07710 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07710 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07710 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yflE_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/index.py?detailname=&locustag=BSU07710 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ltaS_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07710]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===
* induction of [[SigM]] and [[SigX]] activities {{PubMed|23103977}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12940]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

* '''Paralogous protein(s):''' [[YfnI]], [[YqgS]], [[YvgJ]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated on Thr-297 {{PubMed|19229300}}

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

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

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

* '''[[Localization]]:'''
** cell membrane, at the septum of the cell {{PubMed|15743965}}
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=69910&ordinalpos=1&log$=structuread_title 2W8D]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34952 O34952]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07710]

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1389 ''ltaS::aphA3'', available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews: {{PubMed|21255102}}==
<pubmed> 21388439 </pubmed>
==Original publications==
<pubmed>19229300,17483484 21255105, 19168632 15743965 23103977 </pubmed>

[[Category:Protein-coding genes]]

FtsZ

2013-08-13T15:54:56Z

Fmehne: /* Biological materials */

* '''Description:''' cell-division initiation protein (septum formation) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ftsZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ts-1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || cell-division initiation protein (septum formation)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || formation of Z-ring
|-
|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=BSU15290 ftsZ]
|-
|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/FtsZ FtsZ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 4.814
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1146 bp, 382 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ftsA]]'', ''[[bpr]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15290 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ftsZ_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=ftsZ_1597832_1598980_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ftsZ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU15290]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell division]]}},
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU15290

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10232]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** Z ring formation is inhibited upon binding of [[MciZ]] to FtsZ
** bundling of FtsZ protofilaments into strikingly long and regular tubular structures reminiscent of eukaryotic microtubules requires the prior formation of large ring polymers of [[SepF]] {{PubMed|21224850}}
** interaction with [[UgtP]] inhibits [[FtsZ]] filament formation {{PubMed|22931116}}
** FtsZ polymerization is inhibited by interaction with [[MinC]] {{PubMed|23577149}}

* '''[[SubtInteract|Interactions]]:'''
** [[FtsZ]]-[[ZapA]] {{PubMed|19843223}}
** [[FtsZ]]-[[EzrA]] {{PubMed|10449747}}
** [[FtsZ]]-[[SpoIIE]]
** [[FtsZ]]-[[FtsA]]
** [[FtsZ]]-[[FtsZ]] {{PubMed|17662947}}
** [[MciZ]]-[[FtsZ]] {{PubMed|18284588}}
** [[FtsZ]] (extreme C terminus of [[FtsZ]])-[[SepF]] {{PubMed|22912848,16420366}}
** [[RefZ]]-[[FtsZ]] {{PubMed|22730127}}
** [[FtsZ]]-[[LytE]] {{PubMed|16950129}}
** [[UgtP]]-[[FtsZ]], this interaction inhibits [[FtsZ]] filament formation {{PubMed|22931116}}
** [[FtsZ]] (C-terminal domain)-[[MinC]] {{PubMed|23577149}}

* '''[[Localization]]:'''
** septal at the cell membrane {{PubMed|20566861}}
** septal localization partially depends on the proton motive force {{PubMed|20566861}}
** [[Noc]] and the Min system ensure the efficient utilization of the division site at midcell in by ensuring [[FtsZ|Z ring]] placement {{PubMed|22457634}}
=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2VAM 2VAM], [http://www.rcsb.org/pdb/explore.do?structureId=2RHL 2RHL] (dimer with GDP)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P17865 P17865]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU15290]

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

=== Additional information===
** the novel antibiotic ADEP (acyldepsipeptides) causes [[FtsZ]] degradation via dysregulation [[ClpP]] activity (activity occurs even in the absence of an ATPase subunit ([[ClpC]], [[ClpE]], or [[ClpX]])) {{PubMed|21969594}}

=Expression and regulation=

* '''Operon:''' ''[[ftsA]]-[[ftsZ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1569582 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ftsZ_1597832_1598980_1 ftsZ] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1569582 PubMed], [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1569582 PubMed]

* '''Regulation:'''
** activated by [[WalR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10878122 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''strains:'''
** GP1372 ''(Pxyl ftsZ aphA3) disA::tet cdaS::ermC'' for xylose inducible expression of ''ftsZ'', available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:''' available in the [[Jeff Errington]] lab

=Labs working on this gene/protein=

* [[Imrich Barak]], Slovak Academy of Science, Bratislava, Slovakia [http://imb.savba.sk/~barak/ homepage]
* [[Leendert Hamoen]], CBCB, Newcastle University, UK

=Your additional remarks=

=References=

==Reviews==
<pubmed>22047950 22575476 21119015 19680248 19884039 17506674 15037301 21047262 21981908</pubmed>

==FtsZ as antibacterial drug target==
<pubmed> 19583568 20410587 ,16174771, 20212044 20615583 21276094 23841620 23855511 </pubmed>

==Other original Publications==
<pubmed> 15288790, 15317782,12180929, 9364910,10323866, 19212404,15942012, 12007411,16420366, 16159787,10747015, 16950129, 16796675,10322023, 9495766,9287012,1569582,10878122, 11395470,10449747,17662947, 12368265,18284588,8600030,18588879,7592498, 19136590 , 19429628, 19141479 19843223 16484179 20199598 20566861 20711458 20807205 20933427 15948963 12700262 22298780 22457634 22730127 22984350 23577149 22931116,22912848,21224850 23692518 23701187 23836667 </pubmed>
[[Category:Protein-coding genes]]

GlmM

2013-08-13T15:50:23Z

Fmehne: /* Biological materials */

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|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=BSU01770 glmM]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cdaR]]'', ''[[glmS]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01770 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01770 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01770 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_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=glmM_198497_199843_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:glmM_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01770]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===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+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3PDK 3PDK] (from ''B. anthracis'') {{PubMed|21685296}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmM_198497_199843_1 glmM] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
**pGP400: (expression in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1401: (expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab
**pGP1402: (cloning vector for glmM (GlmM S100A) in ''E. coli'', in [[pBlueskript KS]]), available in [[Jörg Stülke]]'s lab
**pGP1403: (expression of GlmM (S100A) in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1405: (expression, purification of GlmM (S100A) in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''
** GP1340 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''
** GP1382 ''glmM-gfp ermC'' (based on [[pGP1080]]), available in [[Jörg Stülke]]'s lab

* '''two-hybrid system:'''
**pGP2576 (glmM in p25N), available in [[Jörg Stülke]]'s lab

* '''FLAG-tag construct:'''
** GP1380 ''lacA::cdaR-Strep aphA3 glmM-3xFLAG ermC'' (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Strep-tag construct:'''
** GP1388 ''lacA::glmM-Strep aphA3 cdaA-3xFLAG ermC'' (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522}}
<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 20525796 21685296 23192352</pubmed>

[[Category:Protein-coding genes]]

UgtP

2013-08-13T15:43:09Z

Fmehne: /* Biological materials */

* '''Description:''' UDP-glucose diacylglycerol glucosyltransferase, growth-rate dependent inhibitor of [[cell division]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ugtP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypfP ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || UDP-glucose diacylglycerol glucosyltransferase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of glycolipids and anchoring of lipoteichoic acid, inhibition of [[FtsZ]] assembly
|-
|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=BSU21920 ugtP]
|-
|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/UgtP UgtP]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 8.398
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1146 bp, 382 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[metA]]'', ''[[cspD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU21920 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU21920 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU21920 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ugtP_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=ugtP_2306514_2307662_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ugtP_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU21920]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell division]]}},
{{SubtiWiki category|[[lipid metabolism/ other]]}},
{{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:''' BSU21920

===Phenotypes of a mutant ===
** cells are bent and distended {{PubMed|22362028}}
** increased expression of the [[SigM]], [[SigV]], and [[SigX]] regulons {{PubMed|22362028}}
** altered [[localization]] of [[MreB]] (irregular clusters instead of helical dots) {{PubMed|22362028}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11611]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** UDP-glucose + 1,2-diacylglycerol = UDP + 1,2-diacyl-3-(O-beta-D-glucopyranosyl)-sn-glycerol (according to Swiss-Prot)
** the interaction with [[FtsZ]] results in inhibition of [[cell division]] and an increase of cell size {{PubMed|22931116}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** oligomerization of [[UgtP]] is inhibited by UDP-Glc and by interaction with [[FtsZ]] {{PubMed|22931116}}

* '''[[SubtInteract|Interactions]]:'''
** [[EzrA]]-[[UgtP]] {{PubMed|17662947}}
** [[UgtP]]-[[UgtP]] {{PubMed|17662947}}, forms oligomers {{PubMed|22931116}}
** [[UgtP]]-[[FtsZ]] (under nutrient rich conditions) {{PubMed|22931116}}

* '''[[Localization]]:'''
** membrane-bound protein, self-assembles into tightly wound spirals ''in vitro'' {{PubMed|17662947}}
** under nutrient rich conditions (increased concentration of UDP-Glc): throughout the cell, concentrated at the cell poles and/or the cytokinetic ring, interaction with [[FtsZ]] {{PubMed|22931116}}
** under nutrient poor conditions: forms punctate foci (oligomers), no interaction with [[FtsZ]] {{PubMed|22931116}}
=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54166 P54166]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU21920]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ugtP_2306514_2307662_1 ugtP] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18179421 PubMed]

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1369 (''[[ugtP]]''::''spc''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

==Reviews==
<pubmed> 19680248 17662935 22575476 </pubmed>

==Original Publications==
<pubmed>9244290,18820022,17662947,9720862 22362028 15640167 23935518 22931116</pubmed>

[[Category:Protein-coding genes]]

PGP172

2013-04-16T06:56:18Z

Fmehne:

[[File:PGP172.jpeg|250px|thumb|right|'''pGP172: click to enlarge''']]
[[File:PGP172_cloning_region.jpeg|250px|thumb|right|'''pGP172 cloning region: click to enlarge''']]

* vector for the expression of proteins in ''E. coli'', the [[plasmid]] allows to fuse a Strep-tag to the N-terminus of the expressed protein

* host: ''E. coli'' BL21(DE3)/pLysS, expression of the desired protein is induced by the addition of 1 mM IPTG to the culture

* constructed in the [[Stülke]] lab

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

* based on pET3C

* similar [[plasmid]]: [[pGP574]]

* sequencing primer:
**'''CD13:''' 5’-AAACATATGGCTAGCTGGAGCCACCCGCAGTTC -3’
** '''NP20:''' 5’-GCAGCAGCCAACTCAGCTTCCTTTCGGGC-3’

* important: ''Eco''RI, although mentioned in the MCS, is not unique!

<pubmed> 14717704 </pubmed>

PGP172

2013-04-16T06:55:57Z

Fmehne:

[[File:PGP172.jpeg|250px|thumb|right|'''pGP172: click to enlarge''']]
[[File:PGP172_cloning_region.jpeg|250px|thumb|right|'''pGP172 cloning region: click to enlarge''']]

* vector for the expression of proteins in ''E. coli'', the [[plasmid]] allows to fuse a Strep-tag to the N-terminus of the expressed protein

* host: ''E. coli'' BL21(DE3)/pLysS, expression of the desired protein is induced by the addition of 1 mM IPTG to the culture

* constructed in the [[Stülke]] lab

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

* based on pET3C

* similar [[plasmid]]: [[pGP574]]

* sequencing primer:
**'''CD13:''' 5’-AAACATATGGCTAGCTGGAGCCACCCGCAGTTC -3’
** '''NP20:''' 5’-GCAGCAGCCAACTCAGCTTCCTTTCGGGC-3’

* important: EcoRI, although mentioned in the MCS, is not unique!

<pubmed> 14717704 </pubmed>

CdaA

2012-12-18T13:54:14Z

Fmehne: /* Biological materials */

* '''Description:''' diadenylate cyclase, synthesis of c-di-AMP in vegetative cells 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cdaA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbP, ybbQ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || diadenylate cyclase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of c-di-AMP
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01750 cdaA]
|-
|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/CdaA CdaA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 8.074
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 819 bp, 273 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsiW]]'', ''[[cdaR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11951]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbP_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=ybbP_196213_197034_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbP_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:''' BSU01750

===Phenotypes of a mutant ===
* inactivation of ''[[cdaA]]'' results in severe beta-lactam sensitivity {{PubMed|22211522}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11577]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** the interaction with [[CdaR]] stimulates the diadenylate cyclase activity of [[CdaA]] {{PubMed|23192352}}

* '''[[SubtInteract|Interactions]]:'''
** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed|23192352}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45589 Q45589]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbP_196213_197034_1 cdaA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP997 (''[[cdaA]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[cdaA]]''-''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** expression of native ''cdaA'' in ''B. subtilis'': pGP1960 (in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
** expression of ''cdaA''-Strep in ''B. subtilis'' suitable for [[SPINE]]: pGP1986 (in [[pGP382]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:''' GP1339 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmid: pGP1990.

* '''FLAG-tag construct:'''
** GP1331 ''lacA::cdaR-Strep aphA3 cdaA-3xFLAG ermC'' (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab
** GP1381 ''cdaA-3xFLAG ermC'' (based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|22211522}}
<pubmed>12884008,21566650, 23192352 </pubmed>

[[Category:Protein-coding genes]]

CdaR

2012-12-18T13:44:23Z

Fmehne: /* Biological materials */

* '''Description:''' effector protein controlling [[CdaA]] diadenylate cyclase activity 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cdaR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ybbR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || effector protein controlling [[CdaA]] diadenylate cyclase activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of c-di-AMP synthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01760 cdaR]
|-
|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/CdaR CdaR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 4.719
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1449 bp, 483 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cdaA]]'', ''[[glmM]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11952]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ybbR_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=ybbR_197027_198478_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbR_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01760

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12703]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** stimulates [[CdaA]] activity upon protein-protein interaction {{PubMed|23192352}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed|23192352}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34659 O34659]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01760]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbR_197027_198478_1 cdaR] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP999 (''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[cdaA]]''-''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** IPTG inducible expression of Strep-''cdaR'' in ''E. coli'': pGP2565 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmids: pGP1989 and pGP1992.

* '''Strep-tag construct:'''
** GP1330 (aphA3, based on [[pGP1460]]), available in [[Jörg Stülke]]'s lab
** GP1380 ''lacA::cdaR-Strep aphA3 glmM-3xFLAG ermC'' (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522,21154411}}
<pubmed>12884008, 16236721, 23192352 </pubmed>

[[Category:Protein-coding genes]]

GlmM

2012-12-18T13:43:54Z

Fmehne: /* Biological materials */

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01770 glmM]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cdaR]]'', ''[[glmS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11953]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_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=glmM_198497_199843_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:glmM_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===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+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3PDK 3PDK] (from ''B. anthracis'') {{PubMed|21685296}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmM_198497_199843_1 glmM] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
**pGP400: (expression in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1401: (expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab
**pGP1402: (cloning vector for glmM (GlmM S100A) in ''E. coli'', in [[pBlueskript KS]]), available in [[Jörg Stülke]]'s lab
**pGP1403: (expression of GlmM (S100A) in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1405: (expression, purification of GlmM (S100A) in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''
** GP1340 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''
** GP1382 ''glmM-gfp ermC'' (based on [[pGP1080]]), available in [[Jörg Stülke]]'s lab

* '''two-hybrid system:'''
**pGP2576 (glmM in p25N), available in [[Jörg Stülke]]'s lab

* '''FLAG-tag construct:'''
** GP1380 ''lacA::cdaR-Strep aphA3 glmM-3xFLAG ermC'' (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522}}
<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 20525796 21685296 23192352</pubmed>

[[Category:Protein-coding genes]]

CdaA

2012-12-18T13:41:01Z

Fmehne: /* Biological materials */

* '''Description:''' diadenylate cyclase, synthesis of c-di-AMP in vegetative cells 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cdaA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbP, ybbQ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || diadenylate cyclase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of c-di-AMP
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01750 cdaA]
|-
|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/CdaA CdaA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 8.074
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 819 bp, 273 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsiW]]'', ''[[cdaR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11951]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbP_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=ybbP_196213_197034_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbP_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:''' BSU01750

===Phenotypes of a mutant ===
* inactivation of ''[[cdaA]]'' results in severe beta-lactam sensitivity {{PubMed|22211522}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11577]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** the interaction with [[CdaR]] stimulates the diadenylate cyclase activity of [[CdaA]] {{PubMed|23192352}}

* '''[[SubtInteract|Interactions]]:'''
** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed|23192352}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45589 Q45589]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbP_196213_197034_1 cdaA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP997 (''[[cdaA]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[cdaA]]''-''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** expression of native ''cdaA'' in ''B. subtilis'': pGP1960 (in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
** expression of ''cdaA''-Strep in ''B. subtilis'' suitable for [[SPINE]]: pGP1986 (in [[pGP382]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:''' GP1339 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmid: pGP1990.

* '''FLAG-tag construct:'''
** GP1331 (''[[cdaA]]''-3xFLAG ''ermC'', based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab
** GP1381 cdaA-3xFLAG ermC (based on [[pGP1966]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|22211522}}
<pubmed>12884008,21566650, 23192352 </pubmed>

[[Category:Protein-coding genes]]

GlmM

2012-12-18T13:15:54Z

Fmehne: /* Biological materials */

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01770 glmM]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cdaR]]'', ''[[glmS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11953]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_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=glmM_198497_199843_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:glmM_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===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+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3PDK 3PDK] (from ''B. anthracis'') {{PubMed|21685296}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmM_198497_199843_1 glmM] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
**pGP400: (expression in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1401: (expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab
**pGP1402: (cloning vector for glmM (GlmM S100A) in ''E. coli'', in [[pBlueskript KS]]), available in [[Jörg Stülke]]'s lab
**pGP1403: (expression of GlmM (S100A) in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1405: (expression, purification of GlmM (S100A) in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab

* '''FLAG-tag fusion:'''
** GP1380 lacA::cdaR-Strep aphA3 glmM-3xFLAG ermC (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''
** GP1340 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''
** GP1382 glmM-gfp ermC (based on [[pGP1080]]), available in [[Jörg Stülke]]'s lab

* '''two-hybrid system:'''
**pGP2576(glmM in p25N), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522}}
<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 20525796 21685296 23192352</pubmed>

[[Category:Protein-coding genes]]

CdaA

2012-12-18T13:14:15Z

Fmehne: /* Biological materials */

* '''Description:''' diadenylate cyclase, synthesis of c-di-AMP in vegetative cells 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cdaA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbP, ybbQ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || diadenylate cyclase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of c-di-AMP
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01750 cdaA]
|-
|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/CdaA CdaA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 8.074
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 819 bp, 273 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsiW]]'', ''[[cdaR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11951]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbP_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=ybbP_196213_197034_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbP_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:''' BSU01750

===Phenotypes of a mutant ===
* inactivation of ''[[cdaA]]'' results in severe beta-lactam sensitivity {{PubMed|22211522}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11577]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** the interaction with [[CdaR]] stimulates the diadenylate cyclase activity of [[CdaA]] {{PubMed|23192352}}

* '''[[SubtInteract|Interactions]]:'''
** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed|23192352}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45589 Q45589]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbP_196213_197034_1 cdaA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP997 (''[[cdaA]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[cdaA]]''-''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** expression of native ''cdaA'' in ''B. subtilis'': pGP1960 (in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
** expression of ''cdaA''-Strep in ''B. subtilis'' suitable for [[SPINE]]: pGP1986 (in [[pGP382]]), available in [[Jörg Stülke]]'s lab

* '''FLAG-tag fusion:'''
**GP1381 cdaA-3xFLAG ermC (based on [[pGP1966]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:''' GP1339 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmid: pGP1990.

* '''FLAG-tag construct:'''
** GP1331 (''[[cdaA]]''-3xFLAG ''ermC'', based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|22211522}}
<pubmed>12884008,21566650, 23192352 </pubmed>

[[Category:Protein-coding genes]]

GlmM

2012-12-18T13:11:43Z

Fmehne: /* Biological materials */

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01770 glmM]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cdaR]]'', ''[[glmS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11953]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_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=glmM_198497_199843_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:glmM_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===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+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3PDK 3PDK] (from ''B. anthracis'') {{PubMed|21685296}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmM_198497_199843_1 glmM] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
**pGP400: (expression in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1401: (expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab
**pGP1402: (cloning vector for glmM (GlmM S100A) in ''E. coli'', in [[pBlueskript KS]]), available in [[Jörg Stülke]]'s lab
**pGP1403: (expression of GlmM (S100A) in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1405: (expression, purification of GlmM (S100A) in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''
** GP1340 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''
** GP1382 glmM-gfp ermC (based on [[pGP1080]]), available in [[Jörg Stülke]]'s lab

* '''two-hybrid system:'''
**pGP2576(glmM in p25N), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522}}
<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 20525796 21685296 23192352</pubmed>

[[Category:Protein-coding genes]]

GlmM

2012-12-18T12:59:37Z

Fmehne: /* Biological materials */

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01770 glmM]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cdaR]]'', ''[[glmS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11953]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_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=glmM_198497_199843_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:glmM_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===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+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3PDK 3PDK] (from ''B. anthracis'') {{PubMed|21685296}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmM_198497_199843_1 glmM] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP1380 lacA::cdaR-Strep aphA3 glmM-3xFLAG ermC (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
**pGP400: (expression in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1401: (expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab
**pGP1402: (cloning vector for glmM (GlmM S100A) in ''E. coli'', in [[pBlueskript KS]]), available in [[Jörg Stülke]]'s lab
**pGP1403: (expression of GlmM (S100A) in ''B. subtilis'' in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
**pGP1405: (expression, purification of GlmM (S100A) in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''
** GP1340 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522}}
<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 20525796 21685296 23192352</pubmed>

[[Category:Protein-coding genes]]

CdaR

2012-12-18T12:58:41Z

Fmehne: /* Biological materials */

* '''Description:''' effector protein controlling [[CdaA]] diadenylate cyclase activity 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cdaR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ybbR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || effector protein controlling [[CdaA]] diadenylate cyclase activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of c-di-AMP synthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01760 cdaR]
|-
|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/CdaR CdaR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 4.719
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1449 bp, 483 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cdaA]]'', ''[[glmM]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11952]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ybbR_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=ybbR_197027_198478_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbR_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01760

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12703]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** stimulates [[CdaA]] activity upon protein-protein interaction {{PubMed|23192352}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed|23192352}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34659 O34659]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01760]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbR_197027_198478_1 cdaR] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP999 (''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[cdaA]]''-''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** IPTG inducible expression of Strep-''cdaR'' in ''E. coli'': pGP2565 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmids: pGP1989 and pGP1992.

* '''Strep-tag construct:'''
** GP1330 (aphA3, based on [[pGP1460]]), available in [[Jörg Stülke]]'s lab
** GP1380 lacA::cdaR-Strep aphA3 glmM-3xFLAG ermC (based on [[pGP1460]] and [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522,21154411}}
<pubmed>12884008, 16236721, 23192352 </pubmed>

[[Category:Protein-coding genes]]

CdaR

2012-10-31T09:06:48Z

Fmehne: /* Biological materials */

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ybbR''
|-
|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://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01760 ybbR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 4.719
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1449 bp, 483 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbP]]'', ''[[glmM]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11952]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ybbR_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=ybbR_197027_198478_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbR_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:''' BSU01760

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12703]

=== 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/O34659 O34659]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01760]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbR_197027_198478_1 ybbR] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP999 (''[[ybbR]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[ybbP]]''-''[[ybbR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** IPTG inducible expression of Strep-''ybbR'' in ''E. coli'': pGP2565 (in [[pGP172]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmids: pGP1989 and pGP1992.

* '''Strep-tag construct:''' GP1330 (aphA3, based on [[pGP1460]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522,21154411}}
<pubmed>12884008, 16236721, </pubmed>

[[Category:Protein-coding genes]]

CdaA

2012-10-31T09:02:04Z

Fmehne: /* Biological materials */

* '''Description:''' maybe involved in the synthesis of c-di-AMP in vegetative cells 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ybbP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbQ ''
|-
|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://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01750 ybbP]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 8.074
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 819 bp, 273 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbM]]'', ''[[ybbR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11951]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbP_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=ybbP_196213_197034_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbP_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:''' BSU01750

===Phenotypes of a mutant ===
* inactivation of ''[[ybbP]]'' results in severe beta-lactam sensitivity {{PubMed|22211522}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11577]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain potentially involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''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/Q45589 Q45589]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbP_196213_197034_1 ybbP] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP997 (''[[ybbP]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[ybbP]]''-''[[ybbR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** expression of native ''ybbP'' in ''B. subtilis'': pGP1960 (in [[pBQ200]]), available in [[Stülke]] lab
** expression of ''ybbP''-Strep in ''B. subtilis'' suitable for [[SPINE]]: pGP1986 (in [[pGP382]]), available in [[Stülke]] lab

* '''lacZ fusion:''' GP1339 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmid: pGP1990.

* '''FLAG-tag construct:''' GP1331 (''[[ybbP]]''-3xFLAG ermC ''[[ganA]]''::(''[[ybbR]]''-Strep aphA3), based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|22211522}}
<pubmed>12884008,21566650, </pubmed>

[[Category:Protein-coding genes]]

CdaA

2012-10-31T09:01:14Z

Fmehne: /* Biological materials */

* '''Description:''' maybe involved in the synthesis of c-di-AMP in vegetative cells 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ybbP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbQ ''
|-
|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://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01750 ybbP]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 8.074
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 819 bp, 273 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbM]]'', ''[[ybbR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11951]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbP_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=ybbP_196213_197034_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbP_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:''' BSU01750

===Phenotypes of a mutant ===
* inactivation of ''[[ybbP]]'' results in severe beta-lactam sensitivity {{PubMed|22211522}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11577]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain potentially involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''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/Q45589 Q45589]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbP_196213_197034_1 ybbP] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP997 (''[[ybbP]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[ybbP]]''-''[[ybbR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** expression of native ''ybbP'' in ''B. subtilis'': pGP1960 (in [[pBQ200]]), available in [[Stülke]] lab
** expression of ''ybbP''-Strep in ''B. subtilis'' suitable for [[SPINE]]: pGP1986 (in pGP382), available in [[Stülke]] lab

* '''lacZ fusion:''' GP1339 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmid: pGP1990.

* '''FLAG-tag construct:''' GP1331 (''[[ybbP]]''-3xFLAG ermC ''[[ganA]]''::(''[[ybbR]]''-Strep aphA3), based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|22211522}}
<pubmed>12884008,21566650, </pubmed>

[[Category:Protein-coding genes]]

CdaA

2012-10-31T08:55:10Z

Fmehne: /* Biological materials */

* '''Description:''' maybe involved in the synthesis of c-di-AMP in vegetative cells 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ybbP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbQ ''
|-
|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://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01750 ybbP]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 8.074
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 819 bp, 273 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbM]]'', ''[[ybbR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11951]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbP_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=ybbP_196213_197034_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbP_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:''' BSU01750

===Phenotypes of a mutant ===
* inactivation of ''[[ybbP]]'' results in severe beta-lactam sensitivity {{PubMed|22211522}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11577]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain potentially involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''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/Q45589 Q45589]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbP_196213_197034_1 ybbP] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP997 (''[[ybbP]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[ybbP]]''-''[[ybbR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** expression of native ''ybbP'' in ''B. subtilis'': pGP1960 (in pBQ200), available in Stülke lab

* '''lacZ fusion:''' GP1339 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmid: pGP1990.

* '''FLAG-tag construct:''' GP1331 (''[[ybbP]]''-3xFLAG ermC ''[[ganA]]''::(''[[ybbR]]''-Strep aphA3), based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|22211522}}
<pubmed>12884008,21566650, </pubmed>

[[Category:Protein-coding genes]]

CdaS

2012-10-30T12:12:25Z

Fmehne: /* Biological materials */

* '''Description:''' maybe involved in the synthesis of c-di-AMP in vegetative cells 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yojJ''
|-
|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://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU19430 yojJ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.367
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 621 bp, 207 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yojK]]'', ''[[yojI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13835]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yojJ_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=yojJ_2118504_2119127_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yojJ_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19430

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13562]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain potentially involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=2FB5 2FB5] (the protein of ''B. cereus'', 48% identity, 81% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31854 O31854]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19430]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yojJ_2118504_2119127_-1 yojJ] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP983 (''[[yojJ]]''::''ermC''), available in [[Stülke]] lab
** GP1360 (''[[yojJ]]''::''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=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
<pubmed>21566650, </pubmed>
[[Category:Protein-coding genes]]

GlmM

2012-10-30T11:55:20Z

Fmehne: /* Biological materials */

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01770 glmM]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbR]]'', ''[[glmS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11953]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_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=glmM_198497_199843_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:glmM_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===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+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3PDK 3PDK] (from ''B. anthracis'') {{PubMed|21685296}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmM_198497_199843_1 glmM] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
**pGP400: (expression in ''B. subtilis'' in [[pBQ200]]), available in [[Stülke]] lab
**pGP1401: (expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
**pGP1402: (cloning vector for glmM (GlmM S100A) in ''E. coli'', in [[pBlueskript KS]]), available in [[Stülke]] lab
**pGP1403: (expression of GlmM (S100A) in ''B. subtilis'' in [[pBQ200]]), available in [[Stülke]] lab
**pGP1405: (expression, purification of GlmM (S100A) in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab

* '''lacZ fusion:''' GP1340 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22211522}}
<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 20525796 21685296 </pubmed>

[[Category:Protein-coding genes]]

CdaA

2012-10-30T11:54:25Z

Fmehne: /* Biological materials */

* '''Description:''' maybe involved in the synthesis of c-di-AMP in vegetative cells 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ybbP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbQ ''
|-
|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://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01750 ybbP]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 8.074
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 819 bp, 273 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbM]]'', ''[[ybbR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11951]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbP_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=ybbP_196213_197034_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ybbP_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:''' BSU01750

===Phenotypes of a mutant ===
* inactivation of ''[[ybbP]]'' results in severe beta-lactam sensitivity {{PubMed|22211522}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11577]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' contains a DAC domain potentially involved in the synthesis of c-di-AMP {{PubMed|21566650}}

* '''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/Q45589 Q45589]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbP_196213_197034_1 ybbP] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

* '''Mutant:'''
** GP997 (''[[ybbP]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP985 (''[[ybbP]]''-''[[ybbR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:''' GP1339 (cat) based on [[pAC6]], available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab. Respective plasmid: pGP1990.

* '''FLAG-tag construct:''' GP1331 (''[[ybbP]]''-3xFLAG ermC ''[[ganA]]''::(''[[ybbR]]''-Strep aphA3), based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 18714086</pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|22211522}}
<pubmed>12884008,21566650, </pubmed>

[[Category:Protein-coding genes]]

YkuI

2012-10-30T11:38:02Z

Fmehne: /* Biological materials */

* '''Description:''' potential c-di-GMP degrading phosphodiesterase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ykuI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || potential c-di-GMP degrading 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/BSU14090 ykuI]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.462
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1221 bp, 407 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuH]]'', ''[[fsrA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13282]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ykuI_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=ykuI_1482248_1483471_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ykuI_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14090

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13293]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' degradation of cyclic di-GMP [http://www.ncbi.nlm.nih.gov/sites/entrez/19244251 PubMed]

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' EAL domain (aa 1 ... 245, for c-di-GMP hydrolysis), PAS-like domain (aa 300 ... 400) [http://www.ncbi.nlm.nih.gov/sites/entrez/19244251 PubMed]

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2BAS 2BAS], in complex with c-di-GMP [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2W27 2W27] [http://www.ncbi.nlm.nih.gov/sites/entrez/19244251 PubMed]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O35014 O35014]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14090]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykuI_1482248_1483471_1 ykuI] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1324 (tet), 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}}
<pubmed> 19244251 </pubmed>

[[Category:Protein-coding genes]]

YkuI

2012-10-30T11:37:34Z

Fmehne: /* Biological materials */

* '''Description:''' potential c-di-GMP degrading phosphodiesterase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ykuI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || potential c-di-GMP degrading 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/BSU14090 ykuI]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.462
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1221 bp, 407 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuH]]'', ''[[fsrA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13282]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ykuI_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=ykuI_1482248_1483471_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ykuI_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14090

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13293]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' degradation of cyclic di-GMP [http://www.ncbi.nlm.nih.gov/sites/entrez/19244251 PubMed]

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' EAL domain (aa 1 ... 245, for c-di-GMP hydrolysis), PAS-like domain (aa 300 ... 400) [http://www.ncbi.nlm.nih.gov/sites/entrez/19244251 PubMed]

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2BAS 2BAS], in complex with c-di-GMP [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2W27 2W27] [http://www.ncbi.nlm.nih.gov/sites/entrez/19244251 PubMed]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O35014 O35014]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14090]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykuI_1482248_1483471_1 ykuI] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1324 (tet) 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}}
<pubmed> 19244251 </pubmed>

[[Category:Protein-coding genes]]

PGP1389

2012-10-30T11:33:49Z

Fmehne:

[[File:PGP1389 Subtiwiki.png|250px|thumb|right|'''pGP1389: click to enlarge''']]

'''General comments'''

Integrative [[plasmid]] for the fusion of the C-terminus of a protein to a Strep tag, keeping the control of expression under control of the natural promotor of the target gene.

* ''E.coli'': multicopy plasmid, select for ampicillin
* ''B. subtilis'': no ori, select for spectinomycin

'''Hints for the utilisation of the plasmid'''
* 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

'''The reference'''
<pubmed>21803996</pubmed>

CcpA

2012-10-30T11:25:29Z

Fmehne: /* Biological materials */

* '''Description:''' Carbon catabolite control protein A, involved in glucose regulation of many genes; represses catabolic genes and activates genes involved in excretion of excess carbon 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ccpA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''graR, alsA, amyR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator ([[LacI family]])
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates carbon catabolite repression (CCR)
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29740 ccpA]
|-
|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/CcpA CcpA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/nucleosides_catabolism.html Nucleoside catabolism], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/ile_val_leu.html Ile, Leu, Val], [http://subtiwiki.uni-goettingen.de/pathways/histidine.html His], [http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html Coenzyme A], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36,8 kDa, 5.06
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1002 bp, 334 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[motP]]'', ''[[aroA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14952]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ccpA_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=ccpA_3044165_3045169_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ccpA_expression.png|500px]]
|-
|}

__TOC__
 
 
 

 

= [[Categories]] containing this gene/protein =
* {{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[regulators of core metabolism]]}}
* see also: [[glutamate metabolism]]

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

= The [[CcpA regulon]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29740

===Phenotypes of a mutant ===

Loss of carbon catabolite repression.
Loss of [[PTS]]-dependent sugar transport due to excessive phosphorylation of [[PtsH |HPr]] by [[HprK]].
The mutant is unable to grow on a minimal medium with glucose and ammonium as the only sources of carbon and nitrogen, respectively.

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10376]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcriptional regulator of carbon catabolite repression (CCR)

* '''Protein family:''' [[LacI family]]

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** HTH LacI-type Domain (1 – 58)
** DNA binding Domain (6 – 25)

* '''Modification:'''

* '''Cofactor(s):''' [[PtsH |HPr]]-Ser46-P, [[Crh]]-Ser-46-P

* '''Effectors of protein activity:'''glucose-6-phosphate, fructose-1,6-bisphosphate [http://www.ncbi.nlm.nih.gov/pubmed/17376479?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Pubmed]

* '''[[SubtInteract|Interactions]]:'''
** [[CcpA]]-[[PtsH |HPr]] {{PubMed|15369672}}
** [[CcpA]]-[[Crh]] {{PubMed|16316990}}
** [[CcpA]]-[[RpoA]] {{PubMed|22512862}}
** [[CcpA]]-[[CodY]] {{PubMed|22512862}}

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

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2JCG 2JCG] (Apoprotein from ''Bacillus megaterium'')
** CcpA-[[Crh]]-DNA-complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326 NCBI]
** complex with P-Ser-[[PtsH |HPr]] and sulphate ions [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39857 NCBI]
** [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3OQM 3OQM] (complex of ''B. subtilis'' CcpA with P-Ser-[[PtsH |HPr]] and the ''[[ackA]]'' operator site)
** [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3OQN 3OQN] (complex of ''B. subtilis'' CcpA with P-Ser-[[PtsH |HPr]] and the ''[[gntR]]'' operator site)
** [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3OQO 3OQO] (complex of ''B. subtilis'' CcpA with P-Ser-[[PtsH |HPr]] and a optimal synthetic operator site)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P25144 P25144]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29740]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ccpA]]-[[motP]]-[[motS]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16547058 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ccpA_3044165_3045169_-1 ccpA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]

* '''Additional information:''' there are about 3.000 molecules of CcpA per cell [http://www.ncbi.nlm.nih.gov/sites/entrez/8000527 PubMed], this corresponds to a concentration of 3 myM (according to {{PubMed|20408793}})

=Biological materials =

* '''Mutant:''' QB5407 (spc), GP302 (erm), GP300 (an in frame deletion of ''[[ccpA]]''), available in [[Stülke]] lab; WH649 (aphA3), available in [[Gerald Seidel]]'s lab

* '''Expression vector:'''
** pGP643 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pWH940 (C-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP382]]), available in [[Gerald Seidel]]'s lab

* '''Strep-tag construct:''' GP1303 ccpA-Strep (spc) in native locus, based on ([[pGP1389]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''Antibody:''' available in [[Hillen]] and [[Stülke]] labs

=Labs working on this gene/protein=
* [[Gerald Seidel]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]
* [[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]
* [[Milton H. Saier]], University of California at San Diego, USA [http://biology.ucsd.edu/faculty/saier.html Homepage]
* [[Yasutaro Fujita]], University of Fukuyama, Japan
* [[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
* [[Oscar Kuipers]], University of Groningen, The Netherlands [http://molgen.biol.rug.nl/molgen/index.php Homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20408793 8598282 , 19202299,14665673,18628769 ,18359269, 18628769 </pubmed>

==General and physiological studies==
'''Additional publications:''' {{PubMed|22512862}}
<pubmed>1904524 ,10941796 ,12123463,8000527, 18757537,16547058,14523131 22001508</pubmed>

==Global analyses (proteome, transcriptome, ChIP-chip)==
<pubmed>12850135 ,11251851,10559165, 11160890,17183215 22383848 22900538 </pubmed>

==Repression of target genes by CcpA==
'''Additional publications:''' {{PubMed|21398533}}
<pubmed>15150224 ,16166551 ,11929549 , 7913927 ,17827291 ,11985717 ,12100558,7592486 16825793 16491025 </pubmed>

==Positive regulation of gene expression by CcpA==
<pubmed>8226682 ,12193635 ,10559153 ,15916605, 9811655 ,10986270 </pubmed>
==Control of CcpA activity==
<pubmed>7623661 ,9973552 ,9334231 ,12051938, 9689125 </pubmed>
==CcpA-DNA interaction==
<pubmed>8596444 ,10666464 ,15885105,7665492 ,9254709 21106498 </pubmed>
==Functional analysis of CcpA==
<pubmed>10383986 ,10601226 ,11557150,9252590 ,9988473 </pubmed>
==Structural analyses==
<pubmed>15369672 ,16316990 ,17376479 16755587 17500051 17401189 10666630 </pubmed>
[[Category:Protein-coding genes]]