SubtiWiki - User contributions [en]

YclM

2015-05-19T13:42:31Z

Fabian Commichau: /* This gene is a member of the following regulons */

* '''Description:''' aspartokinase III 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yclM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || aspartokinase III
|-
|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=BSU03790 yclM]
|-
|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=yclM yclM]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 4.783
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1362 bp, 454 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yczN]]'', ''[[yclN]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU03790 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU03790 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU03790 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yclM_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=yclM_430623_431987_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yclM_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU03790]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU03790

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU03790&redirect=T BSU03790]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12033]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + L-aspartate = ADP + 4-phospho-L-aspartate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:''' inhibited by the simultaneous presence of threonine and lysine {{PubMed|11471740}}

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU03790&redirect=T BSU03790]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P94417 P94417]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU03790]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.2.4 2.7.2.4]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''yclM'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yclM_430623_431987_-1 yclM] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 78 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>19946135 ,, </pubmed>
==Original publications==
<pubmed>11471740,,2152900, </pubmed>

[[Category:Protein-coding genes]]

Antibodies

2015-04-15T15:11:03Z

Fabian Commichau: /* Antibodies for Mycoplasma pneumoniae */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-FLAG: Supplier: Sigma-Aldrich. Dilution: 1:10.000
*anti-GFP: Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-Strep: Supplier: IBA, Göttingen. Dilution: 1:1.000
*anti-rabbit-IgG-AP secondary antibody: Supplier: Promega. Dilution: 1:100.000

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation: By a poor rabbit @ the SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[DarA]]: Generation: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: unpublished
*anti-[[GapA]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[GltC]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished
*anti-[[PrfA]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:10.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*anti-[[GlpD]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:X0.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/19028882 PubMed]
*anti-[[GlpK]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:X.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/19028882 PubMed]

Antibodies

2015-04-09T15:28:40Z

Fabian Commichau: /* Antibodies for Listeria monocytogenes */

Antibodies

2015-04-09T15:26:54Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-FLAG: Supplier: Sigma-Aldrich. Dilution: 1:10.000
*anti-GFP: Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-Strep: Supplier: IBA, Göttingen. Dilution: 1:1.000
*anti-rabbit-IgG-AP secondary antibody: Supplier: Promega. Dilution: 1:100.000

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation: By a poor rabbit @ the SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[DarA]]: Generation: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: unpublished
*anti-[[GapA]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[GltC]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:26:25Z

Fabian Commichau: /* Antibodies for Listeria monocytogenes */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-FLAG: Supplier: Sigma-Aldrich. Dilution: 1:10.000
*anti-GFP: Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-Strep: Supplier: IBA, Göttingen. Dilution: 1:1.000
*anti-rabbit-IgG-AP secondary antibody: Supplier: Promega. Dilution: 1:100.000

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[DarA]]: Generation: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: unpublished
*anti-[[GapA]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[GltC]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:26:06Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-FLAG: Supplier: Sigma-Aldrich. Dilution: 1:10.000
*anti-GFP: Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-Strep: Supplier: IBA, Göttingen. Dilution: 1:1.000
*anti-rabbit-IgG-AP secondary antibody: Supplier: Promega. Dilution: 1:100.000

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[DarA]]: Generation: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: unpublished
*anti-[[GapA]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[GltC]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:25:43Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-FLAG: Supplier: Sigma-Aldrich. Dilution: 1:10.000
*anti-GFP: Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-Strep: Supplier: IBA, Göttingen. Dilution: 1:1.000
*anti-rabbit-IgG-AP secondary antibody: Supplier: Promega. Dilution: 1:100.000

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: unpublished
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:25:29Z

Fabian Commichau: /* General Antibodies */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-FLAG: Supplier: Sigma-Aldrich. Dilution: 1:10.000
*anti-GFP: Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-Strep: Supplier: IBA, Göttingen. Dilution: 1:1.000
*anti-rabbit-IgG-AP secondary antibody: Supplier: Promega. Dilution: 1:100.000

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference:
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: unpublished
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:19:18Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-FLAG: Supplier: Sigma-Aldrich. Dilution: 1:10.000
*anti-GFP: Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-Strep:
*anti-rabbit-IgG-AP secondary antibody: Supplier: Promega. Dilution: 1:100.000

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference:
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: unpublished
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/12634343 PubMed]
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:18:08Z

Fabian Commichau: /* General Antibodies */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-FLAG: Supplier: Sigma-Aldrich. Dilution: 1:10.000
*anti-GFP: Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-Strep:
*anti-rabbit-IgG-AP secondary antibody: Supplier: Promega. Dilution: 1:100.000

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference:
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: unpublished
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference:
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:10:13Z

Fabian Commichau: /* General Antibodies */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-FLAG: Supplier: Sigma-Aldrich. Dilution: 1:10.000
*anti-GFP: Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-Strep:
*anti-rabbit-IgG-AP-secondary antibody: Supplier: Promega. Dilution: 1:10.000

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference:
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: unpublished
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference:
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:05:04Z

Fabian Commichau: /* General Antibodies */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma-Aldrich. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference:
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: unpublished
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference:
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:03:35Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference:
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference: unpublished
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference:
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:03:17Z

Fabian Commichau: /* Antibodies for Listeria monocytogenes */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference:
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference:
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference:
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000. Reference: unpublished

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:03:00Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference:
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000. Reference:
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference:
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:02:23Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000. Reference: [http://www.ncbi.nlm.nih.gov/pubmed/17608797 PubMed]

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:01:27Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000 [http://www.ncbi.nlm.nih.gov/sites/entrez/20630473 PubMed]
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T15:00:24Z

Fabian Commichau: /* General Antibodies */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T14:59:16Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[His]]:
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000
*anti-[[GltC]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T14:58:05Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[His]]:
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[GapA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:30.000
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T14:57:12Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[His]]:
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[GapA]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:30.000
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T14:56:59Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[His]]:
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[CggR]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[GapA]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000

==Antibodies for ''Listeria monocytogenes''==
*anti-[[CdaA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:5.000

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T14:55:55Z

Fabian Commichau: /* Antibodies for Listeria monocytogenes */

Antibodies

2015-04-09T14:54:46Z

Fabian Commichau: /* General Antibodies */

Antibodies

2015-04-09T14:54:37Z

Fabian Commichau: /* Antibodies for Bacillus subtilis */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GapA]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[His]]:
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
*anti-[[DarA]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution 1:10,000
*anti-[[GapA]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000

==Antibodies for ''Listeria monocytogenes''==
* [[xxx]]: nnnnnnnnnnnnn

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

Antibodies

2015-04-09T14:53:47Z

Fabian Commichau: /* General Antibodies */

Here you can find a list of available antibodies:

==General Antibodies==
*anti-[[FLAG]]: Generation/Supplier: Sigma. Dilution: 1:10.000
*anti-[[GapA]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[GFP]]: Generation/Supplier: MBL, Medical & Biological Laboratories. Dilution: 1:10.000
*anti-[[His]]:
*anti-[[RocG]]: Generation/Supplier: SeqLab Sequencing Laboratories. Dilution: 1:15.000
*anti-[[Strep]]:

==Antibodies for ''Bacillus subtilis''==
* anti-[[DarA]]: Dilution 1:10,000

==Antibodies for ''Listeria monocytogenes''==
* [[xxx]]: nnnnnnnnnnnnn

==Antibodies for ''Mycoplasma pneumoniae''==
*[[xxx]]: ennnnnnnnnn

SPINE

2015-03-09T09:18:12Z

Fabian Commichau: /* Studies that made use of SPINE: */

'''SPINE is a method to detect ''in vivo'' protein-protein interactions''' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]

==[http://www.iba-lifesciences.com/IBA-Applications-Protein-interaction-SPINE-Technology.html '''See the principle''' ]==

=='''A detailed protocol to detect the interaction between [[RocG]] and [[GltC]]:''' ==

1 litre of a ''B. subtilis'' culture was grown to an OD600 of approx. 1.0 and incubated with 0.6% formaldehyde ( 4% stock solution in PBS, pH 6.5!) for 20 minutes @ 37°C on a shaker.
The cells were harvested and washed once in 1 X PBS pH 6.5.
The pellets can then be stored @ -20 °C.
The [[GltC]] protein was expressed carrying a Strep-tag and [[RocG]] expression was induced by arginine ([http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]). Expression of the Strep-tagged GltC protein allows to test the functionality of the protein.
Crude extracts (10-15 ml) were prepared by using a French Press.
After a centrifugation step for 1 h @ 27.000 g the clarified crude extracts were loaded onto a Streptactin sepharose column (0.5-1 ml matrix) to isolate the cross-linked protein complexes (the detailed procedure for protein purification is described in the IBA manual, http://www.iba-go.com/).
After the purification of the protein complexes the crosslinks can be resolved by boiling the samples in Laemmli buffer for 10-15 minutes @ 95 °C ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]).
A 12.5% SDS gel was loaded with the samples and the proteins were then visualized by silver-staining. The interaction partner/s were identified by mass spectroscopy and Western blotting.

Preparation of the formaldehyde stock solution (max. 4% in 1 X PBS pH 6.5):
We use ''para''-formaldehyde (a white powder; http://en.wikipedia.org/wiki/Paraformaldehyde). ''para''-formaldehyde dissolves within approx. 20-30 minutes in 1 X PBS for @ 65 to 70 °C.

The sepharose matrix was purchased from the IBA company, Göttingen (http://www.iba-go.com/).

=='''Relevant plasmids:'''==

for use in ''B. subtilis'' (multicopy plasmids): [[pGP380]], [[pGP382]]

for use in ''B. subtilis'' (chromosomal integration under the control of the native promoter): [[pGP1389]]

for use in ''E. coli'': [[pGP172]], [[pGP574]]

=='''Biotin-containing proteins that are purified with the Strep-Tactin column'''==
[[PycA]], [[AccB]]

=='''The reference for the method:'''==
<pubmed> 17994626 </pubmed>

=='''SPINE for membrane proteins:'''==
<pubmed> 21472855 24300168 </pubmed>

=='''Studies that made use of SPINE:'''==
<pubmed> 17608797 19193632 20572937 20933603 21622759 21803996 21992469 22001508 22517742 23192352 22512862 24325460 24375102 24666271 25711804 </pubmed>

=='''The use of SPINE in other microbes:'''==
<pubmed> 21123179 </pubmed>

NagB

2015-01-08T10:07:42Z

Fabian Commichau: /* References */

* '''Description:''' glucosamine-6-phosphate deaminase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''nagB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glucosamine-6-phosphate deaminase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || N-acetylglucosamine utilization
|-
|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=BSU35020 nagB]
|-
|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=nagB nagB]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 5.717
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 726 bp, 242 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nagA]]'', ''[[nagR]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35020 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35020 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35020 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:nagB_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=nagBA_3596543_3597271_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:nagB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35020]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall degradation/ turnover]]}},
{{SubtiWiki category|[[utilization of specific carbon sources]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35020

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35020&redirect=T BSU35020]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12631]

=== Additional information===
* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed|21821766}}

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glucosamine 6-phosphate + H2O = D-fructose 6-phosphate + NH3 (according to Swiss-Prot)

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

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

=== 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=BSU35020&redirect=T BSU35020]

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2BKX 2BKX]{{PubMed|15755726}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O35000 O35000]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35020]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[nagA]]-[[nagB]]-[[nagR]]'' {{PubMed|21602348}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=nagBA_3596543_3597271_1 nagB] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|23667565}}

* '''Regulation:'''
** induced in the presence of N-acetylglucosamine ([[NagR]]) {{PubMed|24673833,21602348}}

* '''Regulatory mechanism:'''
** [[NagR]]: transcription repression {{PubMed|24673833,21602348}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>6174502,15755726 21821766 21602348 23667565 24673833,23876412 25564531 </pubmed>

[[Category:Protein-coding genes]]

NagA

2015-01-08T10:07:25Z

Fabian Commichau: /* References */

* '''Description:''' N-acetylglucosamine-6-phosphate deacetylase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''nagA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || N-acetylglucosamine-6-phosphate deacetylase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || N-acetylglucosamine utilization
|-
|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=BSU35010 nagA]
|-
|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=nagA nagA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 5.276
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1188 bp, 396 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[hprK]]'', ''[[nagB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35010 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35010 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35010 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:nagA_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=nagA_3595356_3596546_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:nagA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35010]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall degradation/ turnover]]}},
{{SubtiWiki category|[[utilization of specific carbon sources]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35010

===Phenotypes of a mutant ===
* no growth on N-acetylglucosamine {{PubMed|23667565}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35010&redirect=T BSU35010]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12630]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' N-acetyl-D-glucosamine 6-phosphate + H2O = D-glucosamine 6-phosphate + acetate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' K(M): 1.4 mM {{PubMed|14343123}}

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

* '''Modification:'''

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35010&redirect=T BSU35010]

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2VHL 2VHL] {{PubMed|14557261}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34450 O34450]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35010]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.1.25 3.5.1.25]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[nagA]]-[[nagB]]-[[nagR]]'' {{PubMed|21602348}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=nagA_3595356_3596546_1 nagA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|23667565}}

* '''Regulation:'''
** induced in the presence of N-acetylglucosamine ([[NagR]]) {{PubMed|24673833,21602348,14343123}}
** repressed by glucose (2.9-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:'''
** [[NagR]]: transcription repression {{PubMed|24673833,21602348}}
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 281 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>10627040, 14343123,12850135 6174502, 14557261 23667565 21602348 24673833,23876412 25564531 </pubmed>

[[Category:Protein-coding genes]]

NagR

2015-01-08T10:06:51Z

Fabian Commichau: /* References */

* '''Description:''' transcriptional regulator ([[GntR family]]) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''nagR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvoA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator ([[GntR family]])
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || probably regulator of the putative ''[[nagA]]-[[nagB]]-[[yvoA]]'' operon
|-
|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=BSU35030 nagR]
|-
|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=nagR nagR]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 6.768
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 729 bp, 243 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nagB]]'', ''[[yvnB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35030 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35030 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35030 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yvoA_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=yvoA_3597289_3598020_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:nagR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35030]]
|-
|}

__TOC__
 
 
 
 

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

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[NagR regulon]]}}
=The [[NagR regulon]]:=
* ''[[nagA]]-[[nagB]]-[[nagR]]'', ''[[nagP]]''

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35030

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35030&redirect=T BSU35030]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14124]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription repression of ''[[nagP]]'' and of the putative ''[[nagA]]-[[nagB]]-[[nagR]]'' operon in the absence of N-acetylglycosamine {{PubMed|24673833,20047956,21602348}}, weak repression of ''[[yflG]]'' {{PubMed|16207374}}

* '''Protein family:''' [[GntR family]] of transcription factors

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

=== Extended information on the protein ===

* '''Kinetic information:''' K(D) for N-acetylglucosamine-6-phosphate: 1 mM {{PubMed|20047956}}

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

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** N-acetylglucosamine-6-phosphate acts as the molecular inducer {{PubMed|20047956}}
** glucosamine-6-phosphate acts as the molecular inducer{{PubMed|21602348}}

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35030&redirect=T BSU35030]

* '''Structure:''' [http://www.rcsb.org/pdb/search/structidSearch.do?structureId=2WV0 2WVO] {{PubMed|20047956}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34817 O34817]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35030]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[nagA]]-[[nagB]]-[[nagR]]'' {{PubMed|21602348}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvoA_3597289_3598020_1 nagR] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|23667565}}

* '''Regulation:'''
** induced in the presence of N-acetylglucosamine ([[NagR]]) {{PubMed|24673833,21602348}}

* '''Regulatory mechanism:'''
** [[NagR]]: transcription repression {{PubMed|24673833,21602348}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>19342794,20047956 16207374 21602348 23667565 24673833 25564531 </pubmed>

[[Category:Protein-coding genes]]

CitA

2014-12-08T14:46:52Z

Fabian Commichau: /* Biological materials */

* '''Description:''' minor citrate synthase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || minor citrate synthase
|-
|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=BSU09440 citA]
|-
|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=citA citA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.778
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1098 bp, 366 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citR]], [[yhdF]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09440 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09440 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09440 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:citA_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=citA_1021057_1022157_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09440]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09440

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09440&redirect=T BSU09440]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10854]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

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

* '''Paralogous protein(s):''' [[MmgD]], [[CitZ]]

=== 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=BSU09440&redirect=T BSU09440]

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/2c6x 2C6X]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39119 P39119]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09440]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citA]]-[[yhdF]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citA_1021057_1022157_1 citA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045898}}

* '''Regulation:'''

* '''Regulatory mechanism:''' [[CitR]]: transcription repression {{PubMed|8045899}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP676 (erm), available in the [[Stülke]] lab
** GP1282 (''[[citA]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP1753 (''[[citR]] [[citA]]''::''aphA3''), the kanamycin resistance cassette can be cut out by introducing the ''cre''-rekombinase into the chromosom of ''B. subtilis'', available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP2516 (N-terminal Strep-tag, purification from ''E. coli'', in [[pGP172]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:'''
** GP1287 (''spc'', based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>8045899,8045898, 22383849</pubmed>

[[Category:Protein-coding genes]]

CitZ

2014-12-08T14:46:19Z

Fabian Commichau: /* Biological materials */

* '''Description:''' citrate synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|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=BSU29140 citZ]
|-
|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=CitZ CitZ]
|-
|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=citZ citZ]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[ytwI]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29140 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29140 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29140 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:citZ_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=citZ_2981151_2982269_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citZ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29140]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
* glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29140&redirect=T BSU29140]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

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

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:'''
** Michaelis-Menten (Random Sequential Reaction Mechanism) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** specific activity: 0.141 µmol min-1 (mg protein)-1 {{PubMed|24571712}}

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

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:'''
** Inhibited by acetyl-CoA, 2-oxoglutarate and NADH [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
** Inhibited by citrate and CoA (competitively against acetyl-CoA and non-competitively against oxaloacetate) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by ATP competitively in ''B. subtilis'' strain 168 and HS 1A17 [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
*** In ''B. subtilis'' strain HS 2A2, ATP inhibits a non-competitive fashion [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Activated by AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}

* '''[[Localization]]:'''
** cytoplasm (homogeneously distributed throughout the cell) {{PubMed|24825009}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29140&redirect=T BSU29140]

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]
** [http://www.rcsb.org/pdb/101/motm.do?momID=93 A discussion of citrate synthase structure]
* '''UniProt:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===
* extensive information on the structure and enzymatic properties of CitZ can be found at [http://www.proteopedia.org/wiki/index.php/Citrate_synthase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citZ_2981151_2982269_-1 citZ] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** repression by glucose (6.7-fold) ([[CcpA]]) {{PubMed|12100558,12850135}}
** repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** reduced expression at excess citrate concentrations or iron depletion ([[CitB]]) {{PubMed|23354745}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** [[CitB]]: mRNA destabilization upon citrate accumulation or iron limitation {{PubMed|23354745}}

* '''Additional information:'''
** The mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed|20525796}}
** number of protein molecules per cell (minimal medium with glucose and ammonium): 8373 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 20578 {{PubMed|24696501}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 22342 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 10224 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 18693 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:'''
** GP678 (erm), GP797 (spec) available in [[Jörg Stülke]]'s lab
** 1A999 (''citZ''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]
** GP790 (''[[citZ]]-[[icd]]-[[mdh]]''::''kan''), available in [[Jörg Stülke]]'s lab
** GP797 (''citZ''::''spec''), allows expression of ''[[icd]]'' and ''[[mdh]]'', available in [[Jörg Stülke]]'s lab
** GP1281 (''citZ''::''erm''), allows expression of ''[[icd]]'' and ''[[mdh]]'', available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
** pGP1776 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)
** pGP1761 (expression with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab
** pGP2515 (N-terminal Strep-tag, purification from ''E. coli'', 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:''' available in [[Linc Sonenshein]]'s lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

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

=Your additional remarks=

=References=
==Reviews==
<pubmed>3013232 </pubmed>
==Original publications==
<pubmed>10348849,8045899,22900538,10656796,12850135 17218307 12100558 9642180 8045898 8655569 4211224 4980242 20525796 24825009 20933603 23354745 24571712</pubmed>

[[Category:Protein-coding genes]]

MgsA

2014-12-08T14:45:06Z

Fabian Commichau: /* Biological materials */

YvcL

2014-12-08T14:41:10Z

Fabian Commichau: /* Biological materials */

RpsJ

2014-12-08T14:36:46Z

Fabian Commichau: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rpsJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tetA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes {{PubMed|23002217,12682299}}
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[ribosomal protein]] S10 (BS13)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[translation]]
|-
|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=BSU01150 rpsJ]
|-
|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=RpsJ RpsJ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 10.207
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 306 bp, 102 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybaC]]'', ''[[rplC]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01150 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01150 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01150 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:rpsJ_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=rpsJ_135364_135672_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:rpsJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01150]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01150

===Phenotypes of a mutant ===

essential {{PubMed|23002217,12682299}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01150&redirect=T BSU01150]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19008]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' [[ribosomal protein]] S10P 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]]:'''
** located near the aminoacyl-tRNA site of the 30S ribosomal subunit {{PubMed|23759864}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01150&redirect=T BSU01150]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P21471 P21471]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01150]

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

=== Additional information===

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rpsJ_135364_135672_1 rpsJ] {{PubMed|22383849}}

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

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

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 8159 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 13952 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''
** pGP605 (in [[pAC6]]), available in [[Stülke]] lab
** pGP2201 (in [[pAC7]]), available in [[Stülke]] lab
** pGP2439 (in [[pAC7]]), available in [[Stülke]] lab
** pGP2472 (in [[pAC5]]), available in [[Stülke]] lab
** pGP2473 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15621428 </pubmed>
==Original publications==
<pubmed> 19653700, 9371452 11948165 8635744 23759864 23002217< /pubmed>
[[Category:Protein-coding genes]]

YpjD

2014-12-08T14:35:56Z

Fabian Commichau: /* Biological materials */

* '''Description:''' putative pyrophosphatase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ypjD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''jojD ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || putative pyrophosphatase
|-
|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=BSU22500 ypjD]
|-
|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=ypjD ypjD]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 4.952
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 333 bp, 111 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dapB]]'', ''[[ypjC]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU22500 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU22500 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU22500 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ypjD_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=ypjD_2360155_2360490_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ypjD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU22500]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU22500

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU22500&redirect=T BSU22500]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11210]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' 6-phosphogluconate dehydrogenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU22500&redirect=T BSU22500]

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

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42979 P42979]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU22500]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ypjD]]-[[dapB]]-[[mgsA]]-[[bshB1]]-[[bshA]]-[[cca]]-[[birA]]'' {{PubMed|20308541}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ypjD_2360155_2360490_-1 ypjD] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|23894131}}

* '''Regulation:'''
** induced by diamide stess (thiol depletion) ([[Spx]]) {{PubMed|23894131}}

* '''Regulatory mechanism:'''
** [[Spx]]: transcription activation {{PubMed|23894131}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''
** pGP2437 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Operon and expression==
<pubmed> 20308541 23894131</pubmed>
[[Category:Protein-coding genes]]

RpsJ

2014-12-08T14:34:38Z

Fabian Commichau: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rpsJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tetA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes {{PubMed|23002217,12682299}}
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[ribosomal protein]] S10 (BS13)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[translation]]
|-
|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=BSU01150 rpsJ]
|-
|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=RpsJ RpsJ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 10.207
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 306 bp, 102 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybaC]]'', ''[[rplC]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01150 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01150 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01150 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:rpsJ_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=rpsJ_135364_135672_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:rpsJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01150]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01150

===Phenotypes of a mutant ===

essential {{PubMed|23002217,12682299}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01150&redirect=T BSU01150]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19008]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' [[ribosomal protein]] S10P 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]]:'''
** located near the aminoacyl-tRNA site of the 30S ribosomal subunit {{PubMed|23759864}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01150&redirect=T BSU01150]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P21471 P21471]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01150]

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

=== Additional information===

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rpsJ_135364_135672_1 rpsJ] {{PubMed|22383849}}

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

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

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 8159 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 13952 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''
** pGP605 (in [[pAC6]]), available in [[Stülke]] lab
** pGP2201 (in [[pAC7]]), available in [[Stülke]] lab
** pGP2439 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15621428 </pubmed>
==Original publications==
<pubmed> 19653700, 9371452 11948165 8635744 23759864 23002217< /pubmed>
[[Category:Protein-coding genes]]

PtsH

2014-12-08T14:27:03Z

Fabian Commichau: /* Biological materials */

* '''Description:''' HPr, General component of the sugar phosphotransferase system ([[PTS]]). 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ptsH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || histidine-containing phosphocarrier protein HPr of the [[PTS]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[PTS]]-dependent sugar transport and carbon catabolite repression
|-
|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=BSU13900 ptsH]
|-
|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=PtsH PtsH]
|-
|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=ptsH PtsH]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 9,1 kDa, 4.58
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 264 bp, 88 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptsG]]'', ''[[ptsI]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13900 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13900 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13900 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ptsH_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=ptsH_1459384_1459650_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ptsH_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13900]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[phosphotransferase systems]]}},
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[phosphoproteins]]}},
[[most abundant proteins]]

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[GlcT regulon]]}},
{{SubtiWiki regulon|[[stringent response]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU13900

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13900&redirect=T BSU13900]

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

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10200]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Protein HPr N(pi)-phospho-L-histidine + protein EIIA = protein HPr + protein EIIA N(tau)-phospho-L-histidine (according to Swiss-Prot) Protein HPr N(pi)-phospho-L-histidine + protein EIIA = protein [[PtsH|HPr]] + protein EIIA N(tau)-phospho-L-histidine

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:''' HPr Domain (2–88)

* '''Modification:'''
** transient phosphorylation by [[PtsI |Enzyme I]] of the PTS on His-15
** regulatory phosphorylation on Ser-46 by [[HprK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2507315 PubMed]
** an extensive study on ''in vivo'' HPr phosphorylation can be found in Singh et al. (2008) [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]
** weak phosphorylation on Ser-12 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
** ''in vitro'' phosphorylated by [[PrkC]] on Ser-12 {{PubMed|20389117}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[HprK]]-[[PtsH|HPr]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12009882 PubMed]
** [[PtsI|Enzyme I]]-[[PtsH|HPr]]
** [[PtsH|HPr]]-[[PtsG]] {{PubMed|8418852}}, [[PtsH]]-[[MtlF]] {{PubMed|20444094}}, [[ManP]]-[[PtsH|HPr]], [[GmuA]]-[[PtsH|HPr]]
** [[GamP]]-[[PtsH|HPr]], [[BglP]]-[[PtsH|HPr]], [[LicA]]-[[PtsH|HPr]], [[LevD]]-[[PtsH|HPr]]
** [[FruA]]-[[PtsH|HPr]], [[YpqE]]-[[PtsH|HPr]]
** [[PtsH|HPr]]-[[LicT]], [[PtsH|HPr]]-[[SacY]], [[PtsH|HPr]]-[[SacT]], [[PtsH|HPr]]-[[GlcT]]
** [[PtsH|HPr]]-[[MtlR]] {{PubMed|20444094}}, [[PtsH|HPr]]-[[LicR]], [[PtsH|HPr]]-[[LevR]],[[PtsH|HPr]]-[[ManR]]
** [[PtsH|HPr]]-[[GlpK]]
** [[GapA]]-[[PtsH|HPr]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
** [[PtsH|HPr(Ser-46)-P]]-[[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12432959 PubMed]
** [[PtsH|HPr]]-[[RbsR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16519689 PubMed]
** [[PtsH|HPr(His)-P]]-[[RhgR]] {{PubMed|19651770}}

* '''[[Localization]]:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13900&redirect=T BSU13900]

* '''Structure:'''
** [http://www.rcsb.org/pdb/explore.do?structureId=1KKM 1KKM] (complex of ''L. casei'' [[HprK]] with ''B. subtilis'' HPr-Ser-P)
** [http://www.rcsb.org/pdb/explore.do?structureId=1KKL 1KKL] (complex of ''Lactobacillus casei'' [[HprK]] with ''B. subtilis'' HPr)
** [http://www.rcsb.org/pdb/explore.do?structureId=2HID 2HID] (NMR)
** [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3OQM 3OQM] (complex of ''B. subtilis'' CcpA with P-Ser-[[PtsH |HPr]] and the ''[[ackA]]'' operator site)
** [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3OQN 3OQN] (complex of ''B. subtilis'' CcpA with P-Ser-[[PtsH |HPr]] and the ''[[gntR]]'' operator site)
** [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3OQO 3OQO] (complex of ''B. subtilis'' CcpA with P-Ser-[[PtsH |HPr]] and a optimal synthetic operator site)
* '''UniProt:''' [http://www.uniprot.org/uniprot/P08877 P08877]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13900]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.11.- 2.7.11.-]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[ptsG]]-[[ptsH]]-[[ptsI]]'' {{PubMed|11902727}}
**''[[ptsH]]-[[ptsI]]'' {{PubMed|11902727}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ptsH_1459384_1459650_1 ptsH] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''
** ''[[ptsG]]'': [[SigA]] {{PubMed|11902727}}
** ''[[ptsH]]'': [[SigA]] {{PubMed|11902727}}

* '''Regulation:'''
** expression activated by glucose (2 fold) ([[GlcT]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** the ''[[ptsH]]'' promoter is constitutive {{PubMed|11902727}}
** subject to negative stringent control upon amino acid limitation (due to control of'' [[ptsG]]'' transcription initiation) {{PubMed|20081037}}

* '''Regulatory mechanism:'''
** ''[[ptsG]]'': transcriptional antitermination via the [[GlcT]]-dependent [[RNA switch]] {{PubMed|9765562}}

* '''Additional information:'''
** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
** number of protein molecules per cell (minimal medium with glucose and ammonium): 352 {{PubMed|24696501}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 7193 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 914 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 5795 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:''' available in [[Jörg Stülke]]'s lab:
** MZ303 (cat)
** GP507 ptsH1 (S46A)
** GP506 (ptsH-H15A)
** GP777 (replacement of ''[[glcT]]'' and the ''[[ptsG]]-[[ptsH]]-[[ptsI]]'' operon by a spc cassette), {{PubMed|22722928}}

* '''Expression vector:'''
** pGP438 (with N-terminal Strep-tag, in [[pGP172]]), available in [[Jörg Stülke]]'s lab
** pAG2 (His-tag) {{PubMed|9237995}}, available in [[Anne Galinier]] lab
** pGP371(expression / purification of HPr-S46A, with His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab
** pGP1415 (HPr, expression in ''B. subtilis'', from [[pBQ200]]), available in [[Jörg Stülke]]'s lab
** pGP961 (HPr, expression in ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], available in [[Jörg Stülke]]'s lab
** pGP1416 (HPr-H15A, expression in ''B. subtilis'', from [[pBQ200]]), available in [[Jörg Stülke]]'s lab
** pGP2431 (N-terminal Strep-tag, expression and purification from ''B. subtilis'', in [[pGP380]]), for [[SPINE]], available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''CFP fusion:''' B. subtilis GP1267 ptsH-cfp ermC- without terminator, available in [[Jörg Stülke]]'s lab

* '''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=

[[Josef Deutscher]], Paris-Grignon, France

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

[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]

[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]

[[Boris Görke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]

[[Anne Galinier]], University of Marseille, France

=Your additional remarks=

=References=
<pubmed>16519689,,12850135 17218307 16519689 17142398 12359875 1577686 9162046 11929549 9336834 7803390, 7623661, 2846556, 8169206, 9973552, 15126459, 10048041, 12169607, 9622354, 10217795, 17693724, 18757537 , 9202047 , 7592487, 15369672 , 14527945, 2507315 8580838 19651770 8418852 1303754 1549615 20081037 20389117 20444094 22001508 22722928 23551403 15378759</pubmed>

[[Category:Protein-coding genes]]

PtsH

2014-12-08T14:26:11Z

Fabian Commichau: /* Biological materials */

* '''Description:''' HPr, General component of the sugar phosphotransferase system ([[PTS]]). 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ptsH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || histidine-containing phosphocarrier protein HPr of the [[PTS]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[PTS]]-dependent sugar transport and carbon catabolite repression
|-
|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=BSU13900 ptsH]
|-
|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=PtsH PtsH]
|-
|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=ptsH PtsH]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 9,1 kDa, 4.58
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 264 bp, 88 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptsG]]'', ''[[ptsI]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13900 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13900 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13900 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ptsH_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=ptsH_1459384_1459650_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ptsH_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13900]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[phosphotransferase systems]]}},
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[phosphoproteins]]}},
[[most abundant proteins]]

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[GlcT regulon]]}},
{{SubtiWiki regulon|[[stringent response]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU13900

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13900&redirect=T BSU13900]

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

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10200]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Protein HPr N(pi)-phospho-L-histidine + protein EIIA = protein HPr + protein EIIA N(tau)-phospho-L-histidine (according to Swiss-Prot) Protein HPr N(pi)-phospho-L-histidine + protein EIIA = protein [[PtsH|HPr]] + protein EIIA N(tau)-phospho-L-histidine

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:''' HPr Domain (2–88)

* '''Modification:'''
** transient phosphorylation by [[PtsI |Enzyme I]] of the PTS on His-15
** regulatory phosphorylation on Ser-46 by [[HprK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2507315 PubMed]
** an extensive study on ''in vivo'' HPr phosphorylation can be found in Singh et al. (2008) [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]
** weak phosphorylation on Ser-12 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
** ''in vitro'' phosphorylated by [[PrkC]] on Ser-12 {{PubMed|20389117}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[HprK]]-[[PtsH|HPr]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12009882 PubMed]
** [[PtsI|Enzyme I]]-[[PtsH|HPr]]
** [[PtsH|HPr]]-[[PtsG]] {{PubMed|8418852}}, [[PtsH]]-[[MtlF]] {{PubMed|20444094}}, [[ManP]]-[[PtsH|HPr]], [[GmuA]]-[[PtsH|HPr]]
** [[GamP]]-[[PtsH|HPr]], [[BglP]]-[[PtsH|HPr]], [[LicA]]-[[PtsH|HPr]], [[LevD]]-[[PtsH|HPr]]
** [[FruA]]-[[PtsH|HPr]], [[YpqE]]-[[PtsH|HPr]]
** [[PtsH|HPr]]-[[LicT]], [[PtsH|HPr]]-[[SacY]], [[PtsH|HPr]]-[[SacT]], [[PtsH|HPr]]-[[GlcT]]
** [[PtsH|HPr]]-[[MtlR]] {{PubMed|20444094}}, [[PtsH|HPr]]-[[LicR]], [[PtsH|HPr]]-[[LevR]],[[PtsH|HPr]]-[[ManR]]
** [[PtsH|HPr]]-[[GlpK]]
** [[GapA]]-[[PtsH|HPr]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
** [[PtsH|HPr(Ser-46)-P]]-[[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12432959 PubMed]
** [[PtsH|HPr]]-[[RbsR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16519689 PubMed]
** [[PtsH|HPr(His)-P]]-[[RhgR]] {{PubMed|19651770}}

* '''[[Localization]]:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13900&redirect=T BSU13900]

* '''Structure:'''
** [http://www.rcsb.org/pdb/explore.do?structureId=1KKM 1KKM] (complex of ''L. casei'' [[HprK]] with ''B. subtilis'' HPr-Ser-P)
** [http://www.rcsb.org/pdb/explore.do?structureId=1KKL 1KKL] (complex of ''Lactobacillus casei'' [[HprK]] with ''B. subtilis'' HPr)
** [http://www.rcsb.org/pdb/explore.do?structureId=2HID 2HID] (NMR)
** [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3OQM 3OQM] (complex of ''B. subtilis'' CcpA with P-Ser-[[PtsH |HPr]] and the ''[[ackA]]'' operator site)
** [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3OQN 3OQN] (complex of ''B. subtilis'' CcpA with P-Ser-[[PtsH |HPr]] and the ''[[gntR]]'' operator site)
** [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3OQO 3OQO] (complex of ''B. subtilis'' CcpA with P-Ser-[[PtsH |HPr]] and a optimal synthetic operator site)
* '''UniProt:''' [http://www.uniprot.org/uniprot/P08877 P08877]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13900]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.11.- 2.7.11.-]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[ptsG]]-[[ptsH]]-[[ptsI]]'' {{PubMed|11902727}}
**''[[ptsH]]-[[ptsI]]'' {{PubMed|11902727}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ptsH_1459384_1459650_1 ptsH] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''
** ''[[ptsG]]'': [[SigA]] {{PubMed|11902727}}
** ''[[ptsH]]'': [[SigA]] {{PubMed|11902727}}

* '''Regulation:'''
** expression activated by glucose (2 fold) ([[GlcT]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** the ''[[ptsH]]'' promoter is constitutive {{PubMed|11902727}}
** subject to negative stringent control upon amino acid limitation (due to control of'' [[ptsG]]'' transcription initiation) {{PubMed|20081037}}

* '''Regulatory mechanism:'''
** ''[[ptsG]]'': transcriptional antitermination via the [[GlcT]]-dependent [[RNA switch]] {{PubMed|9765562}}

* '''Additional information:'''
** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
** number of protein molecules per cell (minimal medium with glucose and ammonium): 352 {{PubMed|24696501}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 7193 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 914 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 5795 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:''' available in [[Jörg Stülke]]'s lab:
** MZ303 (cat)
** GP507 ptsH1 (S46A)
** GP506 (ptsH-H15A)
** GP777 (replacement of ''[[glcT]]'' and the ''[[ptsG]]-[[ptsH]]-[[ptsI]]'' operon by a spc cassette), {{PubMed|22722928}}

* '''Expression vector:'''
** pGP438 (with N-terminal Strep-tag, in [[pGP172]]), available in [[Jörg Stülke]]'s lab
** pAG2 (His-tag) {{PubMed|9237995}}, available in [[Anne Galinier]] lab
** pGP371(expression / purification of HPr-S46A, with His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab
** pGP1415 (HPr, expression in ''B. subtilis'', from [[pBQ200]]), available in [[Jörg Stülke]]'s lab
** pGP961 (HPr, expression in ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], available in [[Jörg Stülke]]'s lab
** pGP1416 (HPr-H15A, expression in ''B. subtilis'', from [[pBQ200]]), available in [[Jörg Stülke]]'s lab
** pGP2431 (N-terminal Strep-tag, purification from ''B. subtilis'', in [[pGP380]]), for [[SPINE]], available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''CFP fusion:''' B. subtilis GP1267 ptsH-cfp ermC- without terminator, available in [[Jörg Stülke]]'s lab

* '''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=

[[Josef Deutscher]], Paris-Grignon, France

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

[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]

[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]

[[Boris Görke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]

[[Anne Galinier]], University of Marseille, France

=Your additional remarks=

=References=
<pubmed>16519689,,12850135 17218307 16519689 17142398 12359875 1577686 9162046 11929549 9336834 7803390, 7623661, 2846556, 8169206, 9973552, 15126459, 10048041, 12169607, 9622354, 10217795, 17693724, 18757537 , 9202047 , 7592487, 15369672 , 14527945, 2507315 8580838 19651770 8418852 1303754 1549615 20081037 20389117 20444094 22001508 22722928 23551403 15378759</pubmed>

[[Category:Protein-coding genes]]

YvcL

2014-12-08T14:21:09Z

Fabian Commichau: /* Biological materials */

* '''Description:''' WhiA family protein, involved in Z ring assembly, putative transcription factor 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yvcL''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[cell division]] protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of Z ring asembly
|-
|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=BSU34750 yvcL]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 9.479
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 948 bp, 316 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[crh]]'', ''[[yvcK]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34750 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34750 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34750 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yvcL_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=whiA_3569573_3570523_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yvcL_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34750]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell division]]}},
{{SubtiWiki category|[[transcription factors and their control]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34750

===Phenotypes of a mutant ===
* a ''[[yvcL]] [[zapA]]'' double mutant grows poorly, and the cells are filamentous (due to a defect in Z ring assembly) {{PubMed|24097947}}
* a ''[[yvcL]] [[ezrA]]'' double mutant grows poorly, and the cells are filamentous {{PubMed|24097947}}
* a ''[[yvcL]] [[minC]]-[[minD]]'' mutant grows poorly, and the cells are filamentous {{PubMed|24097947}}
* a ''[[yvcL]] [[noc]]'' double mutant grows poorly, and the cells are filamentous {{PubMed|24097947}}
* the defects of the ''[[yvcL]] [[zapA]]'' double mutant can be suppressed by inactivation of either ''[[gtaB]]'', ''[[pgcA]]'', or ''[[ugtP]]'' {{PubMed|24097947}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34750&redirect=T BSU34750]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12402]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' WhiA family [http://www.ncbi.nlm.nih.gov/pubmed/10986251 PubMed]

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:''' suggested HTH domain at the N terminus [http://www.ncbi.nlm.nih.gov/sites/entrez/19836336 PubMed]

* '''Modification:'''

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

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

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

* '''[[Localization]]:'''
** localizes to the nucleoid {{PubMed|24097947}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34750&redirect=T BSU34750]

* '''Structure:'''
** [http://www.rcsb.org/pdb/explore.do?structureId=3HYI 3HYI] (Crystal structure of full-length DUF199/WhiA from ''Thermotoga maritima'')
** [http://www.rcsb.org/pdb/explore.do?structureId=3HYJ 3HYJ] (Crystal structure of the N-terminal LAGLIDADG domain of DUF199/WhiA)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O06975 O06975]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yvcI]]-[[yvcJ]]-[[yvcK]]-[[yvcL]]-[[crh]]-[[yvcN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=whiA_3569573_3570523_-1 yvcL] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]

* '''Regulation:'''
** constitutive expression at both protein and RNA levels {{PubMed|24097947,22383849}}
** very weak stimuation of expression by citrate and succinate [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP231 (''amyE::P[[rpsJ]]-lacZ, yvcL::cat'') available in [[ Jörg Stülke]]'s lab; plasmid pGP1468 was used to disrupt the gene.

* '''Expression vector:'''
** pGP1469 for expression in ''B. subtilis'' (in [[pGP382]], with C-terminal STREP-TAG), available in [[ Jörg Stülke]]'s lab
** pGP2429 (N-terminal Strep-Tag, purification from ''E. coli'' and/or ''B. subtilis'', in pDG148), for [[SPINE]], available in [[Jörg Stülke]]'s lab
** pGP2430 (C-terminal Strep-Tag, purification from ''E. coli'' and/or ''B. subtilis'', in pDG148), 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 and [[Boris Görke]]'s labs

* '''Antibody:''' available in [[Leendert Hamoen]]'s lab {{PubMed|24097947}}

=Labs working on this gene/protein=

=Your additional remarks=
WhiA orthologues are present in all Gram-positive bacteria and best characterized by the WhiA sporulation control factor in ''Streptomyces coelicolor''. They are thought to act as genetic regulators that have evolved from LAGLIDADG homing endonucleases (LHE).

=References=

<pubmed>9237995 16272399 10986251 19836336 17603302, 24097947 </pubmed>

[[Category:Protein-coding genes]]

YvcL

2014-12-08T14:20:32Z

Fabian Commichau: /* Biological materials */

* '''Description:''' WhiA family protein, involved in Z ring assembly, putative transcription factor 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yvcL''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[cell division]] protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of Z ring asembly
|-
|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=BSU34750 yvcL]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 9.479
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 948 bp, 316 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[crh]]'', ''[[yvcK]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34750 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34750 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34750 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yvcL_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=whiA_3569573_3570523_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yvcL_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34750]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell division]]}},
{{SubtiWiki category|[[transcription factors and their control]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34750

===Phenotypes of a mutant ===
* a ''[[yvcL]] [[zapA]]'' double mutant grows poorly, and the cells are filamentous (due to a defect in Z ring assembly) {{PubMed|24097947}}
* a ''[[yvcL]] [[ezrA]]'' double mutant grows poorly, and the cells are filamentous {{PubMed|24097947}}
* a ''[[yvcL]] [[minC]]-[[minD]]'' mutant grows poorly, and the cells are filamentous {{PubMed|24097947}}
* a ''[[yvcL]] [[noc]]'' double mutant grows poorly, and the cells are filamentous {{PubMed|24097947}}
* the defects of the ''[[yvcL]] [[zapA]]'' double mutant can be suppressed by inactivation of either ''[[gtaB]]'', ''[[pgcA]]'', or ''[[ugtP]]'' {{PubMed|24097947}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34750&redirect=T BSU34750]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12402]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' WhiA family [http://www.ncbi.nlm.nih.gov/pubmed/10986251 PubMed]

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:''' suggested HTH domain at the N terminus [http://www.ncbi.nlm.nih.gov/sites/entrez/19836336 PubMed]

* '''Modification:'''

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

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

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

* '''[[Localization]]:'''
** localizes to the nucleoid {{PubMed|24097947}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU34750&redirect=T BSU34750]

* '''Structure:'''
** [http://www.rcsb.org/pdb/explore.do?structureId=3HYI 3HYI] (Crystal structure of full-length DUF199/WhiA from ''Thermotoga maritima'')
** [http://www.rcsb.org/pdb/explore.do?structureId=3HYJ 3HYJ] (Crystal structure of the N-terminal LAGLIDADG domain of DUF199/WhiA)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O06975 O06975]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yvcI]]-[[yvcJ]]-[[yvcK]]-[[yvcL]]-[[crh]]-[[yvcN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=whiA_3569573_3570523_-1 yvcL] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]

* '''Regulation:'''
** constitutive expression at both protein and RNA levels {{PubMed|24097947,22383849}}
** very weak stimuation of expression by citrate and succinate [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP231 (''amyE::P[[rpsJ]]-lacZ, yvcL::cat'') available in [[ Jörg Stülke]]'s lab; plasmid pGP1468 was used to disrupt the gene.

* '''Expression vector:'''
** pGP1469 for expression in ''B. subtilis'' (in [[pGP382]], with C-terminal STREP-TAG), available in [[ Jörg Stülke]]'s lab
** pGP2429 (N-terminal Strep-tag, purification from ''E. coli'' and/or ''B. subtilis'', in pDG148), 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 and [[Boris Görke]]'s labs

* '''Antibody:''' available in [[Leendert Hamoen]]'s lab {{PubMed|24097947}}

=Labs working on this gene/protein=

=Your additional remarks=
WhiA orthologues are present in all Gram-positive bacteria and best characterized by the WhiA sporulation control factor in ''Streptomyces coelicolor''. They are thought to act as genetic regulators that have evolved from LAGLIDADG homing endonucleases (LHE).

=References=

<pubmed>9237995 16272399 10986251 19836336 17603302, 24097947 </pubmed>

[[Category:Protein-coding genes]]

CitR

2014-12-08T14:09:10Z

Fabian Commichau: /* Biological materials */

CitA

2014-12-08T14:08:26Z

Fabian Commichau: /* Biological materials */

* '''Description:''' minor citrate synthase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || minor citrate synthase
|-
|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=BSU09440 citA]
|-
|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=citA citA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.778
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1098 bp, 366 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citR]], [[yhdF]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09440 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09440 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09440 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:citA_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=citA_1021057_1022157_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09440]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09440

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09440&redirect=T BSU09440]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10854]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

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

* '''Paralogous protein(s):''' [[MmgD]], [[CitZ]]

=== 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=BSU09440&redirect=T BSU09440]

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/2c6x 2C6X]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39119 P39119]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09440]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citA]]-[[yhdF]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citA_1021057_1022157_1 citA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045898}}

* '''Regulation:'''

* '''Regulatory mechanism:''' [[CitR]]: transcription repression {{PubMed|8045899}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP676 (erm), available in the [[Stülke]] lab
** GP1282 (''[[citA]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP1753 (''[[citR]] [[citA]]''::''aphA3''), the kanamycin resistance cassette can be cut out by introducing the ''cre''-rekombinase into the chromosom of ''B. subtilis'', available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:'''
** GP1287 (''spc'', based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>8045899,8045898, 22383849</pubmed>

[[Category:Protein-coding genes]]

CitA

2014-12-08T14:06:00Z

Fabian Commichau: /* Biological materials */

* '''Description:''' minor citrate synthase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || minor citrate synthase
|-
|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=BSU09440 citA]
|-
|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=citA citA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.778
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1098 bp, 366 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citR]], [[yhdF]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09440 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09440 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09440 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:citA_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=citA_1021057_1022157_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09440]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09440

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09440&redirect=T BSU09440]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10854]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

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

* '''Paralogous protein(s):''' [[MmgD]], [[CitZ]]

=== 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=BSU09440&redirect=T BSU09440]

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/2c6x 2C6X]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39119 P39119]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09440]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citA]]-[[yhdF]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citA_1021057_1022157_1 citA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045898}}

* '''Regulation:'''

* '''Regulatory mechanism:''' [[CitR]]: transcription repression {{PubMed|8045899}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP676 (erm), available in the [[Stülke]] lab
** GP1282 (''[[citA]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP1753 (''[[citR]] [[citA]]''::''aphA3''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:'''
** GP1287 (''spc'', based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>8045899,8045898, 22383849</pubmed>

[[Category:Protein-coding genes]]

CitA

2014-12-08T14:05:03Z

Fabian Commichau: /* Biological materials */

* '''Description:''' minor citrate synthase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || minor citrate synthase
|-
|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=BSU09440 citA]
|-
|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=citA citA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.778
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1098 bp, 366 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citR]], [[yhdF]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09440 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09440 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09440 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:citA_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=citA_1021057_1022157_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09440]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09440

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09440&redirect=T BSU09440]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10854]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

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

* '''Paralogous protein(s):''' [[MmgD]], [[CitZ]]

=== 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=BSU09440&redirect=T BSU09440]

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/2c6x 2C6X]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39119 P39119]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09440]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citA]]-[[yhdF]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citA_1021057_1022157_1 citA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045898}}

* '''Regulation:'''

* '''Regulatory mechanism:''' [[CitR]]: transcription repression {{PubMed|8045899}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP676 (erm), available in the [[Stülke]] lab
** GP1282 (''[[citA]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP1753 (''[[citR'']] ''citA''::''aphA3''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:'''
** GP1287 (''spc'', based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>8045899,8045898, 22383849</pubmed>

[[Category:Protein-coding genes]]

CitA

2014-12-08T14:04:38Z

Fabian Commichau: /* Biological materials */

* '''Description:''' minor citrate synthase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || minor citrate synthase
|-
|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=BSU09440 citA]
|-
|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=citA citA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.778
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1098 bp, 366 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citR]], [[yhdF]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09440 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09440 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09440 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:citA_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=citA_1021057_1022157_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09440]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09440

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09440&redirect=T BSU09440]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10854]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

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

* '''Paralogous protein(s):''' [[MmgD]], [[CitZ]]

=== 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=BSU09440&redirect=T BSU09440]

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/2c6x 2C6X]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39119 P39119]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09440]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citA]]-[[yhdF]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citA_1021057_1022157_1 citA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045898}}

* '''Regulation:'''

* '''Regulatory mechanism:''' [[CitR]]: transcription repression {{PubMed|8045899}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP676 (erm), available in the [[Stülke]] lab
** GP1282 (''[[citA]]''::''cat''), available in [[Jörg Stülke]]'s lab
** GP1753 (''citR'' ''citA''::''aphA3''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:'''
** GP1287 (''spc'', based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>8045899,8045898, 22383849</pubmed>

[[Category:Protein-coding genes]]

CitA

2014-12-08T14:02:57Z

Fabian Commichau: /* Biological materials */

* '''Description:''' minor citrate synthase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || minor citrate synthase
|-
|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=BSU09440 citA]
|-
|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=citA citA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.778
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1098 bp, 366 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citR]], [[yhdF]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09440 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09440 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09440 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:citA_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=citA_1021057_1022157_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09440]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09440

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09440&redirect=T BSU09440]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10854]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

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

* '''Paralogous protein(s):''' [[MmgD]], [[CitZ]]

=== 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=BSU09440&redirect=T BSU09440]

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/2c6x 2C6X]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39119 P39119]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09440]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citA]]-[[yhdF]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citA_1021057_1022157_1 citA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045898}}

* '''Regulation:'''

* '''Regulatory mechanism:''' [[CitR]]: transcription repression {{PubMed|8045899}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP676 (erm), available in the [[Stülke]] lab
** GP1282 (''[[citA]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:'''
** GP1287 (''spc'', based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>8045899,8045898, 22383849</pubmed>

[[Category:Protein-coding genes]]

CitR

2014-12-08T13:58:23Z

Fabian Commichau: /* Biological materials */

* '''Description:''' transcriptional repressor of ''[[citA]]'' 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor ([[LysR family]])
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of the minor citrate synthase
|-
|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=BSU09430 citR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=citR citR]'''
|-
|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=CitR CitR]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 8.67
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 924 bp, 308 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lytE]]'', ''[[citA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09430 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09430 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09430 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:citR_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=citR_1020073_1020948_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09430]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription factors and their control]]}}

= This gene is a member of the following [[regulons]] =
=The [[CitR regulon]]:=
* ''[[citA]]''

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09430

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09430&redirect=T BSU09430]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10853]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' [[LysR family]]

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09430&redirect=T BSU09430]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39127 P39127]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09430]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''citR'' {{PubMed|8045898}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citR_1020073_1020948_-1 citR] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1283 (''[[citA]]''::''aphA3''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>8045898,8045899,, </pubmed>

[[Category:Protein-coding genes]]

CitA

2014-12-08T13:57:37Z

Fabian Commichau: /* Biological materials */

* '''Description:''' minor citrate synthase 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || minor citrate synthase
|-
|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=BSU09440 citA]
|-
|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=citA citA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.778
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1098 bp, 366 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citR]], [[yhdF]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09440 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09440 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09440 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:citA_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=citA_1021057_1022157_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09440]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09440

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09440&redirect=T BSU09440]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10854]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

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

* '''Paralogous protein(s):''' [[MmgD]], [[CitZ]]

=== 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=BSU09440&redirect=T BSU09440]

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/2c6x 2C6X]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39119 P39119]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09440]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citA]]-[[yhdF]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citA_1021057_1022157_1 citA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045898}}

* '''Regulation:'''

* '''Regulatory mechanism:''' [[CitR]]: transcription repression {{PubMed|8045899}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP676 (erm), available in the [[Stülke]] lab
** GP1282 (''[[citA]]''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>8045899,8045898, 22383849</pubmed>

[[Category:Protein-coding genes]]

CitZ

2014-12-08T13:55:37Z

Fabian Commichau: /* Biological materials */

* '''Description:''' citrate synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|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=BSU29140 citZ]
|-
|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=CitZ CitZ]
|-
|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=citZ citZ]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[ytwI]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29140 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29140 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29140 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:citZ_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=citZ_2981151_2982269_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citZ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29140]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
* glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29140&redirect=T BSU29140]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

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

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:'''
** Michaelis-Menten (Random Sequential Reaction Mechanism) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** specific activity: 0.141 µmol min-1 (mg protein)-1 {{PubMed|24571712}}

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

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:'''
** Inhibited by acetyl-CoA, 2-oxoglutarate and NADH [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
** Inhibited by citrate and CoA (competitively against acetyl-CoA and non-competitively against oxaloacetate) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by ATP competitively in ''B. subtilis'' strain 168 and HS 1A17 [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
*** In ''B. subtilis'' strain HS 2A2, ATP inhibits a non-competitive fashion [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Activated by AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}

* '''[[Localization]]:'''
** cytoplasm (homogeneously distributed throughout the cell) {{PubMed|24825009}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29140&redirect=T BSU29140]

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]
** [http://www.rcsb.org/pdb/101/motm.do?momID=93 A discussion of citrate synthase structure]
* '''UniProt:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===
* extensive information on the structure and enzymatic properties of CitZ can be found at [http://www.proteopedia.org/wiki/index.php/Citrate_synthase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citZ_2981151_2982269_-1 citZ] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** repression by glucose (6.7-fold) ([[CcpA]]) {{PubMed|12100558,12850135}}
** repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** reduced expression at excess citrate concentrations or iron depletion ([[CitB]]) {{PubMed|23354745}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** [[CitB]]: mRNA destabilization upon citrate accumulation or iron limitation {{PubMed|23354745}}

* '''Additional information:'''
** The mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed|20525796}}
** number of protein molecules per cell (minimal medium with glucose and ammonium): 8373 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 20578 {{PubMed|24696501}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 22342 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 10224 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 18693 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:'''
** GP678 (erm), GP797 (spec) available in [[Jörg Stülke]]'s lab
** 1A999 (''citZ''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]
** GP790 (''[[citZ]]-[[icd]]-[[mdh]]''::''kan''), available in [[Jörg Stülke]]'s lab
** GP797 (''citZ''::''spec''), allows expression of ''[[icd]]'' and ''[[mdh]]'', available in [[Jörg Stülke]]'s lab
** GP1281 (''citZ''::''erm''), allows expression of ''[[icd]]'' and ''[[mdh]]'', available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
** pGP1776 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)
** pGP1761 (expression with N-terminal His-tag from ''E. coli'', 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

* '''Antibody:''' available in [[Linc Sonenshein]]'s lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

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

=Your additional remarks=

=References=
==Reviews==
<pubmed>3013232 </pubmed>
==Original publications==
<pubmed>10348849,8045899,22900538,10656796,12850135 17218307 12100558 9642180 8045898 8655569 4211224 4980242 20525796 24825009 20933603 23354745 24571712</pubmed>

[[Category:Protein-coding genes]]