SubtiWiki - User contributions [en]

KimA

2017-04-20T11:17:41Z

Jgundlach: Created page with "{{#bank: kimA}}"

AccB

2015-04-01T12:26:23Z

Jgundlach: /* Biological materials */

* '''Description:''' acetyl-CoA carboxylase (biotin carboxyl carrier subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''accB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fabE, yqhW ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || acetyl-CoA carboxylase (biotin carboxyl carrier subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || production of malonyl-CoA, the substrate for fatty acid 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=BSU24350 accB]
|-
|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=AccB AccB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=accB accB]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.394
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 477 bp, 159 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[accC]]'', ''[[spoIIIAH]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24350 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24350 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24350 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:accB_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=accB_2531718_2532197_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:accB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24350]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[biosynthesis of lipids]]}},
{{SubtiWiki category|[[essential genes]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24350

===Phenotypes of a mutant ===

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24350&redirect=T BSU24350]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11383]

=== 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:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** ([[AccA]]-[[AccD]])-[[AccB]]-[[AccC]] (acetyl-CoA carboxylase complex)

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24350&redirect=T BSU24350]

* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=1BDO 1BDO] (the protein from ''E. coli'') {{PubMed|8747466}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49786 P49786]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24350]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.4.1.2 6.4.1.2]

=== Additional information===

AccB binds to StrepTactin, and may be co-purified when purifying Strep-tagged proteins by [[SPINE]].

=Expression and regulation=

* '''Operon:''' ''[[accB]]-[[accC]]-[[yqhY]]'' {{PubMed|7592499}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=accB_2531718_2532197_-1 accB] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 3355 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 889 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 28 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:'''

* '''Expression vector:'''
** GP1477 (chromosomal ''accB''-Strep fusion, ''aphA''3), purification from ''B. subtilis'', for [[SPINE]], available in [[Jörg Stülke]]'s lab'''
** pGP2649: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab
** pGP2650: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab
** pGP2652: IPTG inducible expression, purification in ''E. coli'' with C-terminal Strep-tag, in [[pGP574]], 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

* '''FLAG-tag construct:'''
** GP1484 (''mls'', based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15952903 12121720 15968460 </pubmed>

==Original Publications==
<pubmed>7592499, 8747466, </pubmed>

[[Category:Protein-coding genes]]

AccB

2015-04-01T12:25:25Z

Jgundlach: /* Biological materials */

* '''Description:''' acetyl-CoA carboxylase (biotin carboxyl carrier subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''accB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fabE, yqhW ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || acetyl-CoA carboxylase (biotin carboxyl carrier subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || production of malonyl-CoA, the substrate for fatty acid 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=BSU24350 accB]
|-
|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=AccB AccB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=accB accB]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.394
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 477 bp, 159 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[accC]]'', ''[[spoIIIAH]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24350 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24350 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24350 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:accB_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=accB_2531718_2532197_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:accB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24350]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[biosynthesis of lipids]]}},
{{SubtiWiki category|[[essential genes]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24350

===Phenotypes of a mutant ===

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24350&redirect=T BSU24350]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11383]

=== 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:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** ([[AccA]]-[[AccD]])-[[AccB]]-[[AccC]] (acetyl-CoA carboxylase complex)

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24350&redirect=T BSU24350]

* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=1BDO 1BDO] (the protein from ''E. coli'') {{PubMed|8747466}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49786 P49786]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24350]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.4.1.2 6.4.1.2]

=== Additional information===

AccB binds to StrepTactin, and may be co-purified when purifying Strep-tagged proteins by [[SPINE]].

=Expression and regulation=

* '''Operon:''' ''[[accB]]-[[accC]]-[[yqhY]]'' {{PubMed|7592499}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=accB_2531718_2532197_-1 accB] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 3355 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 889 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 28 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:'''

* '''Expression vector:'''
** GP1477 (chromosomal ''accB''-Strep fusion, ''aphA''3), purification from ''B. subtilis'', for [[SPINE]], available in [[Jörg Stülke]]'s lab'''
** pGP2649: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab
** pGP2650: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, 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

* '''FLAG-tag construct:'''
** GP1484 (''mls'', based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15952903 12121720 15968460 </pubmed>

==Original Publications==
<pubmed>7592499, 8747466, </pubmed>

[[Category:Protein-coding genes]]

DarA

2015-04-01T12:24:32Z

Jgundlach: /* Biological materials */

* '''Description:''' c-di-AMP-binding PII-like protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''darA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaQ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' ||
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || c-di-AMP-binding PII-like protein
|-
|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=BSU00290 darA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 6.088
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 327 bp, 109 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tmk]]'', ''[[yaaR]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00290 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yaaQ_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=yaaQ_39871_40200_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yaaQ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00290]]
|-
|}

__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:''' BSU00290

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00290&redirect=T BSU00290]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10093]

=== 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:'''

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

* '''Effectors of protein activity:'''
** binds c-di-AMP {{PubMed|25433025}}

* '''[[SubtInteract|Interactions]]:'''
** forms homo-trimers {{PubMed|25433025}}

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00290&redirect=T BSU00290]

* '''Structure:'''
** [http://www.pdb.org/pdb/explore/explore.do?structureId=4RLE 4RLE] (the ''B. subtilis'' protein in complex with c-di-AMP) {{PubMed|25433025}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37538 P37538]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00290]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[darA]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaQ_39871_40200_1 darA] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 1030 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 922 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 894 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:'''
** GP1712 (''[[darA]]''::''cat''), available in [[Jörg Stülke]]'s lab {{PubMed|25433025}}
** GP1713 (''[[darA]]-[[yaaR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP2601: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab {{PubMed|25433025}}
** pGP2624: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab
** pGP2603: expression of ''yaaQ''-Strep by [[pGP382]] in ''B. subtilis'' suitable for [[SPINE]], 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

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

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 22383849 25433025 </pubmed>
[[Category:Protein-coding genes]]

AccB

2015-04-01T12:24:09Z

Jgundlach: /* Biological materials */

* '''Description:''' acetyl-CoA carboxylase (biotin carboxyl carrier subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''accB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fabE, yqhW ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || acetyl-CoA carboxylase (biotin carboxyl carrier subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || production of malonyl-CoA, the substrate for fatty acid 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=BSU24350 accB]
|-
|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=AccB AccB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=accB accB]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.394
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 477 bp, 159 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[accC]]'', ''[[spoIIIAH]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24350 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24350 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24350 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:accB_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=accB_2531718_2532197_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:accB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24350]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[biosynthesis of lipids]]}},
{{SubtiWiki category|[[essential genes]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24350

===Phenotypes of a mutant ===

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24350&redirect=T BSU24350]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11383]

=== 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:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** ([[AccA]]-[[AccD]])-[[AccB]]-[[AccC]] (acetyl-CoA carboxylase complex)

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24350&redirect=T BSU24350]

* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=1BDO 1BDO] (the protein from ''E. coli'') {{PubMed|8747466}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49786 P49786]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24350]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.4.1.2 6.4.1.2]

=== Additional information===

AccB binds to StrepTactin, and may be co-purified when purifying Strep-tagged proteins by [[SPINE]].

=Expression and regulation=

* '''Operon:''' ''[[accB]]-[[accC]]-[[yqhY]]'' {{PubMed|7592499}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=accB_2531718_2532197_-1 accB] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 3355 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 889 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 28 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:'''

* '''Expression vector:'''
** GP1477 (chromosomal ''accB''-Strep fusion, ''aphA''3), purification from ''B. subtilis'', for [[SPINE]], available in [[Jörg Stülke]]'s lab'''
** pGP2649: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], 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

* '''FLAG-tag construct:'''
** GP1484 (''mls'', based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15952903 12121720 15968460 </pubmed>

==Original Publications==
<pubmed>7592499, 8747466, </pubmed>

[[Category:Protein-coding genes]]

PgpH

2015-04-01T12:20:22Z

Jgundlach: /* Biological materials */

* '''Description:''' c-di-AMP specific phosphodiesterase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yqfF''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || c-di-AMP specific phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of c-di-AMP homeostasis
|-
|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=BSU25330 yqfF]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 78 kDa, 7.697
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2133 bp, 711 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfG]]'', ''[[phoH]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU25330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU25330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU25330 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yqfF_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=yqfF_2612282_2614417_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yqfF_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU25330]]
|-
|}

__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:''' BSU25330

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25330&redirect=T BSU25330]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11655]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** hydrolysis of c-di-AMP to 5'-pApA {{PubMed|25583510}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:'''

* '''Modification:'''

* '''Cofactors:''' Mn(2+) {{PubMed|25583510}}

* '''Effectors of protein activity:'''
** ppGpp acts as allosteric inhibitor of phosphodiesterase activity (in ''Listeria monocytogenes'') {{PubMed|25583510}}

* '''[[SubtInteract|Interactions]]:'''
** [[YqfF]] is a member of a suspected group of hubs proteins that were suggested to be involved in a large number of [[SubtInteract|interactions]] {{PubMed|21630458}}

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25330&redirect=T BSU25330]

* '''Structure:'''
** [http://pdb.org/pdb/explore/explore.do?structureId=4S1B 4S1B] (the HD domain of the protein from ''Listeria monocytogenes'' in complex with c-di-AMP, 58% identity, 85% similarity) {{PubMed|25583510}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P46344 P46344]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25330]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqfF_2612282_2614417_-1 yqfF] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** SM-GN1 (''yqfF-spc''), available in [[Anne Galinier]]'s and [[Boris Görke]]'s labs
** BKE25330 (''[[yqfF]]''::''erm'' without terminator, available in the BGSC and in [[Jörg Stülke]]'s lab)
** GP2033 (''[[yqfF]]''::''tet'', available in [[Jörg Stülke]]'s lab)
** GP2034 (''[[yqfF]]''::''erm'' without terminator, available in [[Jörg Stülke]]'s lab)
** GP2049 (''[[yqfF]]''::''cat'' without terminator, available in [[Jörg Stülke]]'s lab)

* '''Expression vector:'''

* '''lacZ fusion:''' pGP190 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>25637595</pubmed>
==Original publications==
<pubmed>21630458 25583510 </pubmed>
[[Category:Protein-coding genes]]

PgpH

2015-04-01T12:18:35Z

Jgundlach: /* Biological materials */

* '''Description:''' c-di-AMP specific phosphodiesterase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yqfF''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || c-di-AMP specific phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of c-di-AMP homeostasis
|-
|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=BSU25330 yqfF]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 78 kDa, 7.697
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2133 bp, 711 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfG]]'', ''[[phoH]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU25330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU25330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU25330 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yqfF_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=yqfF_2612282_2614417_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yqfF_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU25330]]
|-
|}

__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:''' BSU25330

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25330&redirect=T BSU25330]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11655]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** hydrolysis of c-di-AMP to 5'-pApA {{PubMed|25583510}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:'''

* '''Modification:'''

* '''Cofactors:''' Mn(2+) {{PubMed|25583510}}

* '''Effectors of protein activity:'''
** ppGpp acts as allosteric inhibitor of phosphodiesterase activity (in ''Listeria monocytogenes'') {{PubMed|25583510}}

* '''[[SubtInteract|Interactions]]:'''
** [[YqfF]] is a member of a suspected group of hubs proteins that were suggested to be involved in a large number of [[SubtInteract|interactions]] {{PubMed|21630458}}

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25330&redirect=T BSU25330]

* '''Structure:'''
** [http://pdb.org/pdb/explore/explore.do?structureId=4S1B 4S1B] (the HD domain of the protein from ''Listeria monocytogenes'' in complex with c-di-AMP, 58% identity, 85% similarity) {{PubMed|25583510}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P46344 P46344]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25330]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqfF_2612282_2614417_-1 yqfF] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** SM-GN1 (''yqfF-spc''), available in [[Anne Galinier]]'s and [[Boris Görke]]'s labs
** BKE25330 (''[[yqfF]]''::''erm'' without terminator, available in the BGSC and in [[Jörg Stülke]]'s lab)

* '''Expression vector:'''

* '''lacZ fusion:''' pGP190 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>25637595</pubmed>
==Original publications==
<pubmed>21630458 25583510 </pubmed>
[[Category:Protein-coding genes]]

HemQ

2015-04-01T11:40:24Z

Jgundlach: /* Biological materials */

* '''Description:''' heme-binding protein, essential for heme biosynthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hemQ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-87r, ywfI ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || heme-binding protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of heme
|-
|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=BSU37670 hemQ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=HemQ HemQ]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 4.972
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pta]]'', ''[[bacG]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU37670 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU37670 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU37670 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywfI_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=ywfI_3866596_3867360_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:hemQ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU37670]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37670

===Phenotypes of a mutant ===
defect in heme biosynthesis

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU37670&redirect=T BSU37670]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10633]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0447 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-41 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU37670&redirect=T BSU37670]

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1T0T 1T0T] (''Geobacillus stearothermophilus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39645 P39645]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37670]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''hemQ'' {{PubMed|9353933}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywfI_3866596_3867360_1 hemQ] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 358 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 1041 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
**pGP2643: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab
**pGP2644: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, 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

* '''FLAG-tag vector:'''
** pGP2658 ''hemQ-3xFLAG ermC'' (based on [[pBQ200]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17218307, 9353933 20543190 </pubmed>

[[Category:Protein-coding genes]]

HemQ

2015-04-01T11:38:17Z

Jgundlach: /* Biological materials */

* '''Description:''' heme-binding protein, essential for heme biosynthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hemQ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-87r, ywfI ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || heme-binding protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of heme
|-
|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=BSU37670 hemQ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=HemQ HemQ]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 4.972
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pta]]'', ''[[bacG]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU37670 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU37670 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU37670 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywfI_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=ywfI_3866596_3867360_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:hemQ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU37670]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37670

===Phenotypes of a mutant ===
defect in heme biosynthesis

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU37670&redirect=T BSU37670]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10633]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0447 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-41 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU37670&redirect=T BSU37670]

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1T0T 1T0T] (''Geobacillus stearothermophilus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39645 P39645]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37670]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''hemQ'' {{PubMed|9353933}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywfI_3866596_3867360_1 hemQ] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 358 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 1041 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
**pGP2643: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab
**pGP2644: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, 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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17218307, 9353933 20543190 </pubmed>

[[Category:Protein-coding genes]]

HemQ

2015-04-01T11:37:23Z

Jgundlach: /* Biological materials */

* '''Description:''' heme-binding protein, essential for heme biosynthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hemQ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-87r, ywfI ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || heme-binding protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of heme
|-
|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=BSU37670 hemQ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=HemQ HemQ]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 4.972
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pta]]'', ''[[bacG]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU37670 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU37670 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU37670 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywfI_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=ywfI_3866596_3867360_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:hemQ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU37670]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37670

===Phenotypes of a mutant ===
defect in heme biosynthesis

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU37670&redirect=T BSU37670]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10633]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0447 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-41 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU37670&redirect=T BSU37670]

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1T0T 1T0T] (''Geobacillus stearothermophilus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39645 P39645]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37670]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''hemQ'' {{PubMed|9353933}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywfI_3866596_3867360_1 hemQ] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 358 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 1041 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
**pGP2643: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab
**pGP2644: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, 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>17218307, 9353933 20543190 </pubmed>

[[Category:Protein-coding genes]]

HemQ

2015-04-01T11:36:43Z

Jgundlach: /* Biological materials */

* '''Description:''' heme-binding protein, essential for heme biosynthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hemQ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-87r, ywfI ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || heme-binding protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of heme
|-
|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=BSU37670 hemQ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=HemQ HemQ]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 4.972
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pta]]'', ''[[bacG]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU37670 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU37670 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU37670 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywfI_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=ywfI_3866596_3867360_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:hemQ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU37670]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37670

===Phenotypes of a mutant ===
defect in heme biosynthesis

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU37670&redirect=T BSU37670]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10633]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0447 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-41 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU37670&redirect=T BSU37670]

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1T0T 1T0T] (''Geobacillus stearothermophilus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39645 P39645]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37670]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''hemQ'' {{PubMed|9353933}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywfI_3866596_3867360_1 hemQ] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 358 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 1041 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
**pGP2644: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, 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>17218307, 9353933 20543190 </pubmed>

[[Category:Protein-coding genes]]

YaaR

2015-04-01T11:31:08Z

Jgundlach: /* Biological materials */

HolB

2015-04-01T11:30:28Z

Jgundlach: /* Biological materials */

Tmk

2015-04-01T11:28:57Z

Jgundlach: /* Biological materials */

YaaR

2015-04-01T11:24:30Z

Jgundlach: /* Biological materials */

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yaaR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00300 yaaR]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 9.715
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 438 bp, 146 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[darA]]'', ''[[holB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00300 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00300 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00300 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yaaR_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=yaaR_40213_40653_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yaaR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00300]]
|-
|}

__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:''' BSU00300

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00300&redirect=T BSU00300]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10094]

=== 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:'''

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00300&redirect=T BSU00300]

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=2qup 2QUP] (from ''Bacillus halodurans'', 40% identity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37539 P37539]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00300]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[darA]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaR_40213_40653_1 yaaR] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1713 (''[[yaaQ]]-[[yaaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
** BKE00300 (''[[yaaR]]''::''erm'', available in the BGSC and in [[Jörg Stülke]]'s lab)

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 22383849</pubmed>
[[Category:Protein-coding genes]]

HolB

2015-04-01T11:24:06Z

Jgundlach: /* Biological materials */

* '''Description:''' DNA polymerase III (delta' subunit), part of the clamp-loader complex and the [[replisome]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''holB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaS ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase III (delta' subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]]
|-
|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=BSU00310 holB]
|-
|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=HolB HolB]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 6.334
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 987 bp, 329 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaR]]'', ''[[yaaT]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00310 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00310 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00310 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:holB_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=holB_40665_41654_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:holB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00310]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00310

===Phenotypes of a mutant ===

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00310&redirect=T BSU00310]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10095]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)
** required for bacteriophage SPP1 replication {{PubMed|23268446}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[DnaX]](3)-[[HolA]]-[[HolB]], the clamp-loader complex {{PubMed|23525462}}
** part of the [[replisome]]: [[PolC]]-[[HolA]]-[[HolB]]-[[DnaX]]-[[DnaN]]-[[DnaG]]-[[DnaC]]-[[DnaI]]-[[DnaD]]-[[SsbA]]-[[DnaE]]-[[PriA]]-[[DnaB]] {{PubMed|20122408}}

* '''[[Localization]]:'''
** forms foci {{PubMed|21958350}}
** cytoplasm (homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00310&redirect=T BSU00310]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37540 P37540]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00310]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.7 2.7.7.7]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[darA]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=holB_40665_41654_1 holB] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>23268446,21958350 16479537 20122408 23525462 22383849</pubmed>

[[Category:Protein-coding genes]]

Tmk

2015-04-01T11:23:41Z

Jgundlach: /* Biological materials */

* '''Description:''' thymidylate kinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tmk''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaP ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || thymidylate kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TTP 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=BSU00280 tmk]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tmk tmk]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 4.866
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaO]]'', ''[[darA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00280 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00280 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00280 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:tmk_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=tmk_39159_39797_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tmk_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00280]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[biosynthesis/ acquisition of nucleotides]]}},
{{SubtiWiki category|[[essential genes]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00280

===Phenotypes of a mutant ===

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00280&redirect=T BSU00280]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10092]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + dTMP = ADP + dTDP (according to Swiss-Prot)

* '''Protein family:''' thymidylate kinase 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 ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00280&redirect=T BSU00280]

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2CCK 2CCK] (from ''Staphylococcus aureus'', 53% identity, 74% similarity) {{PubMed|16522804}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37537 P37537]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00280]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.4.9 2.7.4.9]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tmk_39159_39797_1 tmk] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 16522804</pubmed>
[[Category:Protein-coding genes]]

Paper

2014-12-01T07:43:39Z

Jgundlach: /* Christina Hach */

* strongly repressed in response to glucose starvation in M9 medium {{PubMed|23033921}}: [[hupA]] [[cycC]]

==not yet in SubtiWiki==
<pubmed> 24223955 24386445 24390483 24682323 25039821 25118291 25115591 </pubmed>

==POTM==
<pubmed> 25403286, 25402772 </pubmed>

== Laura Griese==
<pubmed> 25074408 23182676 23475962 </pubmed>

== Jan Gundlach==
<pubmed> 25215494 15968460 9787636 </pubmed>

== Christina Hach ==
<pubmed> 11847102 23812326 25433025 </pubmed>

== für Master-Seminar ==
<pubmed> 25317564 </pubmed>

PGP1370

2014-11-24T14:03:30Z

Jgundlach: Created page with "'''Application:''' The vector was constructed in the Stülke lab and it is suitable for fusion of C-terminal 3xFLAG-tag to the protein of interest in ''B. subtilis''. The pla..."

'''Application:'''

The vector was constructed in the Stülke lab and it is suitable for fusion of C-terminal 3xFLAG-tag to the protein of interest in ''B. subtilis''. The plasmid confers resistance to ampicillin and erythromycin in ''E. coli'' and ''B. subtilis'', respectively. [[pGP1370]] is based on the vector pBQ200. A Shine-Dalgarno sequence has to be fused to the open reading frame during PCR.

Sequencing primers:
*'''M13_puc_for:''' 5‘-GTAAAACGACGGCCAGTG-3‘
*'''M13_puc_rev:''' 5‘-GGAAACAGCTATGACCATG-3‘
*'''FX125 (rev; primes -85bp of MCS):''' 5‘-GGCTCGTATGTTGTGTGG-3‘
*'''JN54 (fwd; primes +63bp of MCS):''' 5‘-GTGAAAAATGAGCCGAAAGCAG-3‘

Paper

2014-11-18T13:41:15Z

Jgundlach:

* strongly repressed in response to glucose starvation in M9 medium {{PubMed|23033921}}: [[hupA]] [[cycC]]

==not yet in SubtiWiki==
<pubmed> 24317403 24223955 24386445 24390483 24682323 25039821 25118291 25115591 </pubmed>

===sonst (nur Excel-Liste)===

==POTM==
<pubmed> </pubmed>

== Nils Jäger==
<pubmed> 24349456 23671116 23192352</pubmed>

== Jan Gundlach==
<pubmed> 25215494 15968460 9787636 </pubmed>

== Christina Hach ==
<pubmed> 11847102 23812326 </pubmed>

== für Master-Seminar ==
<pubmed> 25317564 </pubmed>

FtsW

2014-09-19T08:22:25Z

Jgundlach:

DivIC

2014-09-19T08:21:48Z

Jgundlach:

* '''Description:''' cell-division initiation protein (septum formation), component of septosome (with [[DivIB]]) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''divIC''
|-
|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''' || cell-division protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || septum formation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00620 divIC]
|-
|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=DivIC DivIC]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 9.968
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yabQ]]'', ''[[yabR]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00620 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:divIC_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=divIC_69168_69545_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:divIC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00620]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00620

===Phenotypes of a mutant ===

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00620&redirect=T BSU00620]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yabMNOPQ-divIC-yabR.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10125]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' stabilizes [[FtsL]] against [[RasP]] cleavage {{PubMed|20644139}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[DivIC]]-[[FtsL]] {{PubMed|10844672}}
** [[PbpB]]-[[DivIB]]-([[FtsL]]-[[DivIC]])2 {{PubMed|20870765}}, as part of the [[divisome]]

* '''[[Localization]]:''' membrane bound [http://www.ncbi.nlm.nih.gov/sites/entrez/9426141 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00620&redirect=T BSU00620]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37471 P37471]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00620]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[yabM]]-[[yabN]]-[[yabO]]-[[yabP]]-[[yabQ]]-[[divIC]]-[[yabR]]'' {{PubMed|11283287}}
** ''[[yabP]]-[[yabQ]]-[[divIC]]-[[yabR]]'' {{PubMed|11283287}}
** ''[[divIC]]-[[yabR]]'' {{PubMed|11283287}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=divIC_69168_69545_1 divIC] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[yabM]]'': unknown
** ''[[yabP]]'': [[SigE]] {{PubMed|11283287}}
** ''[[divIC]]'': [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18179421 PubMed], [[SigX]] {{PubMed|12207695}}, [[SigW]] {{PubMed|12207695}}

* '''Regulation:''' expressed during sporulation ([[SigE]]) {{PubMed|11283287}} and under stress conditions

* '''Regulatory mechanism:'''

* '''Additional information:''' there are about 50,000 molecules of DivIC per cell [http://www.ncbi.nlm.nih.gov/sites/entrez/9426141 PubMed]

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:'''
** GP2006 ''divIC-3xFLAG ermC'' (based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18179421,16936019,10217758,9720875,8113187,10323866,9426141,10852898,10844672,11283287 , 11994149, 20644139</pubmed>
'''Additional publications:''' {{PubMed|20870765}}
[[Category:Protein-coding genes]]

DivIB

2014-09-19T08:20:51Z

Jgundlach:

FtsL

2014-09-19T08:19:33Z

Jgundlach:

PbpB

2014-08-15T15:54:34Z

Jgundlach:

* '''Description:''' class B [[penicillin-binding protein]] 2B, Pbp2B 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pbpB''
|-
|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''' || [[penicillin-binding protein]] 2B
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || septation, [[cell division]]
|-
|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=BSU15160 pbpB]
|-
|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=PbpB PbpB]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 79 kDa, 9.234
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2148 bp, 716 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ftsL]]'', ''[[spoVD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15160 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15160 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15160 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:pbpB_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=pbpB_1581947_1584097_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:pbpB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU15160]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU15160

===Phenotypes of a mutant ===

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15160&redirect=T BSU15160]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yllB-ylxA-ftsL-pbpB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10221]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** folding requires [[PrsA]] {{PubMed|20487272}}
** [[PbpB]]-[[DivIB]]-([[FtsL]]-[[DivIC]])2 {{PubMed|20870765}}, as part of the [[divisome]]
** [[WalK]]-[[PbpB]] {{PubMed|21219466}}

* '''[[Localization]]:'''
** cell membrane {{PubMed|23869552,20870765}}
** division sites {{PubMed|23895585}}
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
** localizes to the sporulation septum during sporulation [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15160&redirect=T BSU15160]

* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=1rp5 1RP5] (PBP 2x from ''Streptococcus pneumoniae'', 32% identity) {{PubMed|14734544}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q07868 Q07868]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU15160]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[mraZ]]-[[mraW]]-[[ftsL]]-[[pbpB]]'' {{PubMed|8636036,8244929}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pbpB_1581947_1584097_1 pbpB] {{PubMed|22383849}}

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

* '''Regulation:'''
** constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:'''
** GP2003 ''pbpB-3xFLAG spec'' (based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

[[Jeff Errington]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/jeff.errington homepage]

=Your additional remarks=

=References=
<pubmed>8636036,14731276,8244929,20487272,10652091, 19429628, 18957862 21219466 20870765 14734544 23895585 24655324 </pubmed>

[[Category:Protein-coding genes]]

MurG

2014-08-15T15:53:38Z

Jgundlach:

* '''Description:''' UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''murG''
|-
|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''' || UDP-N-acetylglucosamine-
N-acetylmuramyl-(pentapeptide)pyrophosphoryl- 
undecaprenol N-acetylglucosamine transferase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || peptidoglycan precursor 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=BSU15220 murG]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=murG murG]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 9.568
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1089 bp, 363 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoVE]]'', ''[[murB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15220 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15220 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15220 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:murG_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=murG_1591540_1592631_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:murG_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU15220]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU15220

===Phenotypes of a mutant ===

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15220&redirect=T BSU15220]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10227]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** converts lipid I to lipid II by attaching GlcNAc to the bactoprenol carrier-conjugated UDP-N-acetylmuramic acid (UDP-MurNAc) pentapeptide molecule
** UDP-N-acetylglucosamine + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = UDP + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:'''

* '''Modification:'''

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

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

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

* '''[[Localization]]:'''
** peripheral membrane protein {{PubMed|24706874}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15220&redirect=T BSU15220]

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1F0K 1F0K] (from ''Escherichia coli'', 30% identity, 52% similarity) {{PubMed|10892798}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37585 P37585]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU15220]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.4.1.227 2.4.1.227]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[murE]]-[[mraY]]-[[murD]]-[[spoVE]]-[[murG]]-[[murB]]-[[divIB]]-[[ylxW]]-[[ylxX]]-[[sbp]]'' {{PubMed|1391053}}
** ''[[spoVE]]-[[murG]]-[[murB]]-[[divIB]]-[[ylxW]]-[[ylxX]]-[[sbp]]'' {{PubMed|1391053}}
** ''[[murG]]-[[murB]]-[[divIB]]-[[ylxW]]-[[ylxX]]-[[sbp]]'' {{PubMed|18179421}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=murG_1591540_1592631_1 murG] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''
** ''[[spoVE]]'': [[SigE]] {{PubMed|8320223}}
** within ''[[murG]]'': [[SigM]] {{PubMed|18179421}}

* '''Regulation:'''
** expressed during vegatative growth, then switched off, and again expressed during sporulation in the mother cell ([[SigE]]) {{PubMed|1391053}}

* '''Regulatory mechanism:'''
** [[SpoIIID]]: transcription repression {{PubMed|15383836}}

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 82 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 627 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:'''
** GP2002 ''murG-3xFLAG ermC'' (based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 22092867,18063720,18081839, 1391053 8320223 15383836 18179421 10790316 24706874 </pubmed>

[[Category:Protein-coding genes]]

MraY

2014-08-15T15:53:01Z

Jgundlach:

* '''Description:''' phospho-N-acetylmuramoyl-pentapeptide-transferase (meso-2,6-diaminopimelate), catalyzes the first commited membrane-bound step of bacterial peptidoglycan synthesis leading to the formation of lipid I 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mraY''
|-
|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''' || phospho-N-acetylmuramoyl-pentapeptide-transferase (meso-2,6-diaminopimelate)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || peptidoglycan precursor 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=BSU15190 mraY]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=mraY mraY]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 8.966
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 972 bp, 324 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murE]]'', ''[[murD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15190 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15190 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15190 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:mraY_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=mraY_1587926_1588900_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mraY_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU15190]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU15190

===Phenotypes of a mutant ===

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15190&redirect=T BSU15190]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10224]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' UDP-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala) + undecaprenyl phosphate = UMP + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15190&redirect=T BSU15190]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q03521 Q03521]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU15190]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.8.13 2.7.8.13]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[murE]]-[[mraY]]-[[murD]]-[[spoVE]]-[[murG]]-[[murB]]-[[divIB]]-[[ylxW]]-[[ylxX]]-[[sbp]]'' {{PubMed|1391053}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mraY_1587926_1588900_1 mraY] {{PubMed|22383849}}

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

* '''Regulation:'''
** expressed during vegatative growth {{PubMed|1391053}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:'''
** GP2001 ''mraY-3xFLAG ermC'' (based on [[pGP1087]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>15131133,8436954,18791230,18081839,7734839, 21937437, 18672909,20537545 10790316 1391053 24895118 </pubmed>

[[Category:Protein-coding genes]]

DarA

2014-08-14T14:19:00Z

Jgundlach:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yaaQ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' ||
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00290 yaaQ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 6.088
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 327 bp, 109 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tmk]]'', ''[[yaaR]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00290 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yaaQ_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=yaaQ_39871_40200_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yaaQ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00290]]
|-
|}

__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:''' BSU00290

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00290&redirect=T BSU00290]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10093]

=== 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:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** forms homo-trimers (see [http://www.pdb.org/pdb/explore/explore.do?structureId=3m05 3M05])

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00290&redirect=T BSU00290]

* '''Structure:'''
** [http://www.pdb.org/pdb/explore/explore.do?structureId=3m05 3M05] (the protein from ''Pediococcus pentosaceus'', 50% identity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37538 P37538]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00290]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yaaQ]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaQ_39871_40200_1 yaaQ] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 1030 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 922 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 894 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:'''
** GP1712 (''[[yaaQ]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP1713 (''[[yaaQ]]-[[yaaR]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
**pGP2601: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab

**pGP2603: expression of ''yaaQ''-Strep by [[pGP382]] in ''B. subtilis'' suitable for [[SPINE]], 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

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

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 22383849</pubmed>
[[Category:Protein-coding genes]]