SubtiWiki - User contributions [en]

YetJ

2014-07-11T07:52:21Z

Heilers: /* Database entries */

* '''Description:''' unknown 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yetJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pH-sensitive calcium leak across membranes
|-
|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=BSU07200 yetJ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 9.137
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 642 bp, 214 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yezD]]'', ''[[yetK]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07200 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07200 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07200 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yetJ_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=yetJ_787992_788636_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yetJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07200]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07200

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12866]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' BI1 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

* '''Structure:''' [http://pdbj.org/mine/summary/4pgu 4PGU]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31539 O31539]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07200]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yetJ_787992_788636_1 yetJ] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

<pubmed> 24904158

YetJ

2014-07-11T07:52:09Z

Heilers: /* Database entries */

YetJ

2014-07-11T07:51:48Z

Heilers: /* Database entries */

* '''Description:''' unknown 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yetJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pH-sensitive calcium leak across membranes
|-
|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=BSU07200 yetJ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 9.137
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 642 bp, 214 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yezD]]'', ''[[yetK]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07200 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07200 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07200 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yetJ_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=yetJ_787992_788636_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yetJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07200]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07200

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12866]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' BI1 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

* '''Structure:'''
[http://pdbj.org/mine/summary/4pgu 4PGU]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31539 O31539]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07200]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yetJ_787992_788636_1 yetJ] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

<pubmed> 24904158

YetJ

2014-07-11T07:49:38Z

Heilers: /* Database entries */

* '''Description:''' unknown 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yetJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pH-sensitive calcium leak across membranes
|-
|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=BSU07200 yetJ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 9.137
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 642 bp, 214 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yezD]]'', ''[[yetK]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07200 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07200 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07200 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yetJ_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=yetJ_787992_788636_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yetJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07200]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07200

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12866]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' BI1 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

* '''Structure:''' 4PGU

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31539 O31539]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07200]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yetJ_787992_788636_1 yetJ] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

<pubmed> 24904158

YetJ

2014-07-11T07:47:11Z

Heilers:

* '''Description:''' unknown 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yetJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pH-sensitive calcium leak across membranes
|-
|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=BSU07200 yetJ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 9.137
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 642 bp, 214 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yezD]]'', ''[[yetK]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07200 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07200 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07200 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yetJ_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=yetJ_787992_788636_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yetJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07200]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07200

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12866]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' BI1 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31539 O31539]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07200]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yetJ_787992_788636_1 yetJ] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

<pubmed> 24904158

YetJ

2014-07-11T07:46:12Z

Heilers: /* References */

* '''Description:''' unknown 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yetJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07200 yetJ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 9.137
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 642 bp, 214 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yezD]]'', ''[[yetK]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07200 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07200 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07200 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yetJ_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=yetJ_787992_788636_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yetJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07200]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07200

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12866]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' BI1 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31539 O31539]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07200]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yetJ_787992_788636_1 yetJ] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

<pubmed> 24904158

YetJ

2014-07-11T07:45:47Z

Heilers: /* References */

* '''Description:''' unknown 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yetJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07200 yetJ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 9.137
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 642 bp, 214 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yezD]]'', ''[[yetK]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07200 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07200 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07200 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yetJ_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=yetJ_787992_788636_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yetJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07200]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07200

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12866]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' BI1 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU07200&redirect=T BSU07200]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31539 O31539]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07200]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yetJ_787992_788636_1 yetJ] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 24904158

[[Category:Protein-coding genes]]

Rnc

2011-11-30T10:25:48Z

Heilers: /* References */

* '''Description:''' [[RNase]] III; required for the degradation of sense/antisense transcripts in Gram positive, low GC bacteria 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rnc''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rncS ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || endoribonuclease III
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor (''[[scr]]'')
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 8.076
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 747 bp, 249 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[acpA]]'', ''[[smc]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13466]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:rnc_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[Rnases]]}},
{{SubtiWiki category|[[translation]]}},
{{SubtiWiki category|[[protein secretion]]}},
{{SubtiWiki category|[[essential genes]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU15930

===Phenotypes of a mutant ===

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

''rnc'' is essential [http://www.ncbi.nlm.nih.gov/sites/entrez/11123676 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rnc-smc-ftsY.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11537]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Endonucleolytic cleavage to 5'-phosphomonoester (according to Swiss-Prot) cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor (''[[scr]]'')

* '''Protein 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 ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P51833 P51833]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU15930]

* '''E.C. number:''' 3.1.26.3

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[rnc]]-[[smc]]-[[ftsY]]'' {{PubMed|11021934}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11021934}}

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

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]

[[Ciaran Condon]], IBPC, Paris, France [http://www.ibpc.fr/UPR9073/condon/index_en.html Homepage]

=Your additional remarks=

=References=

<pubmed>9393702 11123676 7527387 9677377 17576666, 11021934 6409421 22123973</pubmed>

[[Category:Protein-coding genes]]

Rnc

2011-11-30T10:24:56Z

Heilers:

Rnc

2011-11-30T10:24:13Z

Heilers:

* '''Description:''' [[RNase]] III ; required for the degradation of sense/antisense transcripts in Gram positive, low GC bacteria

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rnc''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rncS ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || endoribonuclease III
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor (''[[scr]]'')
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 8.076
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 747 bp, 249 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[acpA]]'', ''[[smc]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13466]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:rnc_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[Rnases]]}},
{{SubtiWiki category|[[translation]]}},
{{SubtiWiki category|[[protein secretion]]}},
{{SubtiWiki category|[[essential genes]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU15930

===Phenotypes of a mutant ===

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

''rnc'' is essential [http://www.ncbi.nlm.nih.gov/sites/entrez/11123676 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rnc-smc-ftsY.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11537]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Endonucleolytic cleavage to 5'-phosphomonoester (according to Swiss-Prot) cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor (''[[scr]]'')

* '''Protein 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 ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P51833 P51833]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU15930]

* '''E.C. number:''' 3.1.26.3

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[rnc]]-[[smc]]-[[ftsY]]'' {{PubMed|11021934}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11021934}}

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

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]

[[Ciaran Condon]], IBPC, Paris, France [http://www.ibpc.fr/UPR9073/condon/index_en.html Homepage]

=Your additional remarks=

=References=

<pubmed>9393702 11123676 7527387 9677377 17576666, 11021934 6409421 </pubmed>

[[Category:Protein-coding genes]]

RNases

2011-10-14T10:06:54Z

Heilers: /* Reviews on RNases in Bacillus subtilis */

===RNases are involved in the processing and degradation of the different classes of mRNAs, tRNAs, rRNAs and [[small RNAs]]===
{{CategoryTree
|Parents=
* 3. [[Information processing]]
** 3.2. [[RNA synthesis and degradation]]
|Neighbours=
* 3.2.1. [[Transcription]]
* 3.2.2. [[RNA chaperones]]
* 3.2.3. [[DEAD-box RNA helicases]]
* 3.2.4. [[RNases]]
|Related=
[[RNA degradosome]]
|}}

__TOC__
 

==Exoribonucleases==
* [[rnjA|RNase J1]]: 5'-3' activity, does also have endonuclease activity

* [[rph|RNase PH]]: 3'-5' activity
* [[YhaM]]: 3'-5' activity
* [[rnr|RNase R]]: 3'-5' activity
* [[pnpA|polynucleotide phosphorylase]]: 3'-5' activity

* [[nrnA|nano-RNase A]]: degrades oligonucleotides
* [[nrnB|nano-RNase B]]: degrades oligonucleotides

==Endoribonucleases==
* [[rnjA|RNase J1]]: ssRNA endonuclease, does also have exonuclease activity
* [[rnjB|RNase J2]]: ssRNA endonuclease, may also have exonuclease activity

* [[rny|RNase Y]]: ssRNA endonuclease
* [[rnpA|RNase P]]: ssRNA endonuclease
* [[rnz|RNase Z]]: ssRNA endonuclease

* [[ndoA|RNase Endo A]]

* [[rnhB|RNase HII]]: cleaves RNA in RNA-DNA hybrids
* [[rnhC|RNase HIII]]: cleaves RNA in RNA-DNA hybrids

* [[yurI|RNase Bsn]]: extracellular RNase

* [[rnc|RNase III]]: dsRNA endonuclease
* [[mrnC|mini-III]]: dsRNA endonuclease
* [[rnmV|RNase M5]]: dsRNA endonuclease

==Labs working on RNases==
* [[David Bechhofer]]
* [[Ciaran Condon]]
* [[Harald Putzer]]
* [[Jörg Stülke]]

==Reviews on RNases in ''Bacillus subtilis''==
'''Additional reviews:''' {{PubMed|21957024}}
<pubmed> 19215774 12794188 12490701 20659169 21334965 19767421 21976285</pubmed>

=Back to [[categories]]=

T-box

2011-07-27T10:46:40Z

Heilers: /* Reviews on T-box regulation */

The T-box element is an [[RNA switch]] that controls genes involved in amino acid metabolism.

In the absence of an amino acid, the uncharged tRNA binds the T-box region in the leader region of the mRNA of the controlled gene/ operon and thereby prevents the formation of a transcription terminator. The result is gene expression of the target gene in the absence of the specific amino acid.

==Complete list of genes controlled by T-box elements==

* Induction by alanine limitation
** ''[[alaS]]''

* Induction by aspartate limitation
** ''[[hisS]]-[[aspS]]''

* Induction by cysteine limitation
** ''[[cysE]]-[[cysS]]-[[mrnC]]-[[yacO]]-[[yacP]]''

* Induction by glycine limitation
** ''[[glyA]], [[glyQ]]-[[glyS]]''

* Induction by histidine limitation
** ''[[hisS]]-[[aspS]]''

* Induction by isoleucine limitation
** ''[[ileS]]'', ''[[ilvB]]-[[ilvH]]-[[ilvC]]-[[leuA]]-[[leuA]]-[[leuC]]-[[leuD]]''

* Induction by leucine limitation
** ''[[leuS]]'', ''[[ilvB]]-[[ilvH]]-[[ilvC]]-[[leuA]]-[[leuA]]-[[leuC]]-[[leuD]]''

* Induction by phenyalanine limitation
** ''[[pheS]]-[[pheT]]''

* Induction by proline limitation
** ''[[proB]]-[[proA]]'', ''[[proI]]''

* Induction by serine limitation
** ''[[serS]]''

* Induction by threonine limitation
** ''[[thrS]], [[thrZ]]-[[ywhA]]''

* Induction by tryptophan limitation
** ''[[rtpA]]-[[ycbK]]'', ''[[trpS]]''

* Induction by tyrosine limitation
** ''[[tyrS]], [[tyrZ]]''

* Induction by valine limitation
** ''[[valS]]'', ''[[ilvB]]-[[ilvH]]-[[ilvC]]-[[leuA]]-[[leuA]]-[[leuC]]-[[leuD]]''

==Structure of a T-box ribowsitch==

<pubmed> 12547201</pubmed>

==Reviews on T-box regulation==

<pubmed> 19258532,7527891, 11917026 ,8348614,17381302 10546897 19932103 18625071 </pubmed>

=See also:=
* [[RNA switch]]

=Back to [[regulons]]=

CcpN regulon

2011-06-08T14:24:07Z

Heilers: /* Repression */

{{RegulonTable|
Regulator=[[CcpN]]
}}

= Genes in this regulon =

=== Repression ===
* ''[[gapB]]-[[speD]]''
* ''[[pckA]]''
* ''[[Sr1]]''

=== Unknown ===
* ''[[YhaM]]''

=Back to [[regulons]]=

YhaM

2011-06-08T14:23:12Z

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

* '''Description:''' [[RNase]], 3'-> 5' exoribonuclease 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhaM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] YhaM
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA degradation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.851
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 942 bp, 314 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sbcE]]'', ''[[yhaL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12833]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yhaM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09930

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12989]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 3'-5' exoribonuclease

* '''Protein family:''' OB DNA-binding domain (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07521 O07521]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09930]

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

=== Additional information===

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

* '''Operon:''' ''[[yhaO]]-[[sbcE]]-[[yhaM]]'' {{PubMed|16267290}}

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

* '''Regulation:'''
** induced by DNA damage ([[LexA]]) {{PubMed|16267290}}
** putatively regulated by [[CcpN]] {{PubMed|19732150}}

* '''Regulatory mechanism:'''
** [[LexA]]: transcription repression {{PubMed|16267290}}

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]

=Your additional remarks=

=References=

<pubmed> 19732150 12399495 19553197, 16267290, 16479537,17981983, 15805522 19880604 </pubmed>

[[Category:Protein-coding genes]]

YhaM

2011-06-08T14:22:38Z

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

* '''Description:''' [[RNase]], 3'-> 5' exoribonuclease 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhaM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] YhaM
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA degradation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.851
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 942 bp, 314 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sbcE]]'', ''[[yhaL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12833]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yhaM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09930

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12989]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 3'-5' exoribonuclease

* '''Protein family:''' OB DNA-binding domain (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07521 O07521]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09930]

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

=== Additional information===

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

* '''Operon:''' ''[[yhaO]]-[[sbcE]]-[[yhaM]]'' {{PubMed|16267290}}

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

* '''Regulation:'''
** induced by DNA damage ([[LexA]]) {{PubMed|16267290}}
** putatively regulated by [[CcpN]] {{PubMed|19732150}}

* '''Regulatory mechanism:'''
** [[LexA]]: transcription repression {{PubMed|16267290}}

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]

=Your additional remarks=

=References=

<pubmed> 19732150 12399495 19553197, 16267290, 16479537,17981983, 15805522 19880604 </pubmed>

[[Category:Protein-coding genes]]

YhaM

2011-06-08T14:21:51Z

Heilers: /* References */

* '''Description:''' [[RNase]], 3'-> 5' exoribonuclease 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhaM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] YhaM
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA degradation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.851
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 942 bp, 314 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sbcE]]'', ''[[yhaL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12833]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yhaM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09930

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12989]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 3'-5' exoribonuclease

* '''Protein family:''' OB DNA-binding domain (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07521 O07521]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09930]

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

=== Additional information===

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

* '''Operon:''' ''[[yhaO]]-[[sbcE]]-[[yhaM]]'' {{PubMed|16267290}}

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

* '''Regulation:'''
** induced by DNA damage ([[LexA]]) {{PubMed|16267290}}
** putatively regulated by [[CcpN]] {{PubMed|19732150}}

* '''Regulatory mechanism:'''
** [[LexA]]: transcription repression {{PubMed|16267290}}

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]

=Your additional remarks=

=References=

<pubmed> 19732150 12399495 19553197, 16267290, 16479537,17981983, 15805522 19880604 </pubmed>

[[Category:Protein-coding genes]]

YhaM

2011-06-08T14:21:16Z

Heilers: /* Expression and regulation */

* '''Description:''' [[RNase]], 3'-> 5' exoribonuclease 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhaM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] YhaM
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA degradation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.851
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 942 bp, 314 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sbcE]]'', ''[[yhaL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12833]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yhaM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09930

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12989]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 3'-5' exoribonuclease

* '''Protein family:''' OB DNA-binding domain (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07521 O07521]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09930]

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

=== Additional information===

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

* '''Operon:''' ''[[yhaO]]-[[sbcE]]-[[yhaM]]'' {{PubMed|16267290}}

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

* '''Regulation:'''
** induced by DNA damage ([[LexA]]) {{PubMed|16267290}}
** putatively regulated by [[CcpN]] {{PubMed|19732150}}

* '''Regulatory mechanism:'''
** [[LexA]]: transcription repression {{PubMed|16267290}}

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]

=Your additional remarks=

=References=

<pubmed> 12399495 19553197, 16267290, 16479537,17981983, 15805522 19880604 </pubmed>

[[Category:Protein-coding genes]]

YhaM

2011-06-08T14:20:48Z

Heilers: /* Expression and regulation */

* '''Description:''' [[RNase]], 3'-> 5' exoribonuclease 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhaM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] YhaM
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA degradation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.851
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 942 bp, 314 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sbcE]]'', ''[[yhaL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12833]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yhaM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09930

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12989]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 3'-5' exoribonuclease

* '''Protein family:''' OB DNA-binding domain (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07521 O07521]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09930]

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

=== Additional information===

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

* '''Operon:''' ''[[yhaO]]-[[sbcE]]-[[yhaM]]'' {{PubMed|16267290}}

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

* '''Regulation:'''
** induced by DNA damage ([[LexA]]) {{PubMed|16267290}}
** putatively regulated by [[CcpN]] {{PubMed|19732150}}

* '''Regulatory mechanism:'''
** [[LexA]]: transcription repression {{PubMed|16267290}}

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]

=Your additional remarks=

=References=

<pubmed> 12399495 19553197, 16267290, 16479537,17981983, 15805522 19880604 </pubmed>

[[Category:Protein-coding genes]]

YhaM

2011-06-08T14:16:21Z

Heilers: /* References */

* '''Description:''' [[RNase]], 3'-> 5' exoribonuclease 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhaM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] YhaM
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA degradation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.851
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 942 bp, 314 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sbcE]]'', ''[[yhaL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12833]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yhaM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09930

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12989]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 3'-5' exoribonuclease

* '''Protein family:''' OB DNA-binding domain (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07521 O07521]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09930]

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

=== Additional information===

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

* '''Operon:''' ''[[yhaO]]-[[sbcE]]-[[yhaM]]'' {{PubMed|16267290}}

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

* '''Regulation:'''
** induced by DNA damage ([[LexA]]) {{PubMed|16267290}}

* '''Regulatory mechanism:'''
** [[LexA]]: transcription repression {{PubMed|16267290}}

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]

=Your additional remarks=

=References=

<pubmed> 12399495 19553197, 16267290, 16479537,17981983, 15805522 19880604 </pubmed>

[[Category:Protein-coding genes]]

LicC

2011-04-12T07:54:06Z

Heilers: /* Database entries */

* '''Description:''' lichenan-specific [[PTS|phosphotransferase system]], EIIC component of the [[PTS]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''licC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''celB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || lichenan-specific [[PTS|phosphotransferase system]], EIIC component
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || lichenan uptake and phosphorylation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 8.584
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1356 bp, 452 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[licA]]'', ''[[licB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15884]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:licC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[phosphotransferase systems]]}},
{{SubtiWiki category|[[utilization of specific carbon sources]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38580

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11348]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' [[PTS]] permease, lactose permease (Lac) family [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' [[LicB]]-[[LicC]]

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

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/explore/explore.do?structureId=3QNQ 3QNQ] (EIIC component of diacetylchitobiose specific PTS from ''Bacillus cereus''; 38% identity with LicC) [http://www.ncbi.nlm.nih.gov/pubmed/21471968 PubMed]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P46317 P46317]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38580]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[licB]]-[[licC]]-[[licA]]-[[licH]]'' {{PubMed|8990303}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8990303}}

* '''Regulation:'''
** carbon catabolite repression ([[CcpA]]) {{PubMed|8990303}}
** induction by oligomeric ß-glucosides ([[LicR]]){{PubMed|8990303}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression {{PubMed|8990303}}
** [[LicR]]: transcription activation {{PubMed|8990303}}

* '''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>19087206,8990303,16872404,,10438772,10627040 8990303, </pubmed>

[[Category:Protein-coding genes]]

RNA polymerase

2011-04-08T14:11:02Z

Heilers: /* Other temporary components */

{{CategoryTree
|Parents=
* 3. [[Information processing]]
** 3.2. [[RNA synthesis and degradation]]
** 3.2.1. [[Transcription]]
|Neighbours=
* [[Sigma factors]]
|Related=
* [[protein-protein interactions]]
* [[transcription]]
}}
__TOC__
 

=='''The enzyme responsible for [[transcription]]'''==

==Components of the RNA polymerase==
===Core subunits===
* [[RpoA]]: alpha subunit
* [[RpoB]]: beta subunit
* [[RpoC]]: beta' subunit

* The stoichiometry of the enzyme is [[RpoA]](2)-[[RpoB]]-[[RpoC]]

===[[Sigma factors]]===
* In addition to the housekeeping [[sigma factor]], [[SigA]], there are several other [[sigma factors]] with different promoter recognition specifiity that are active under specific conditions (such as stress or sporulation)

===Small accessory subunits===
* [[RpoE]]: delta subunit
* [[YloH]]: omega subunit

===Other temporary components===
* [[NusA]]: essential elongation factor
* [[Spx]]: transcription regulator, interacts with [[RpoA]]
* [[MgsR]]: transcription regulator orthologous to [[Spx]], interacts with [[RpoA]]

==Back to [[protein-protein interactions]]==

==References==
===Reviews===
<pubmed> 18599813 7708009 18410247 19889534 19489723 18280161 21233849 </pubmed>
===The structure of RNA polymerase===
<pubmed> 12732296 12581657 11297923 19735077 </pubmed>
===Important original publications: {{PubMed|20817769,20724389}} ===
<pubmed> 21350489 </pubmed>

Thi-box

2011-04-03T09:45:14Z

Heilers: /* Important Reviews */

==Important Reviews==

A [[riboswitch]] that controls the expression of the ''[[tenA]]-[[tenI]]-[[thiO]]-[[thiS]]-[[thiG]]-[[thiF]]-[[thiD]]'' and ''[[thiU]]-[[thiV]]-[[thiW]]-[[thiX]]'' operons as well as of the ''[[thiC]]'', ''[[thiT]]'', and ''[[ylmB]]'' genes in response to thiamine. Thiamine pyrophosphate binds the Thi-box resulting in reduced expression.

<pubmed>16356850 12376536 11470904 12376536 17355861</pubmed>

MecA

2011-04-01T14:40:10Z

Heilers: /* Original Publications */

* '''Description:''' buffering protein for development, dampens transitions to spore, biofilm exopolysaccharide and competence expression , targets [[ComK]] to [[ClpC]]-[[ClpP]] degradation machine (in log Phase), inhibits the transcriptional activity of [[Spo0A]]∼P by direct interaction 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mecA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || adaptor protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[ComK]] degradation, regulation of competence
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 4.209
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 654 bp, 218 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yjbE]]'', ''[[coiA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13009]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mecA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[genetic competence]]}},
{{SubtiWiki category|[[proteolysis]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU11520

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10680]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** N-terminal domain (1 ... 120): recruitment of protein substrates {{PubMed|19801546}}
** C-terminal domain (121 ... 218): facilitates assembly of the [[ClpC]]-[[ClpP]] oligomer and acts as a degradation tag {{PubMed|19801546}}

* '''Modification:'''

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

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

* '''Interactions:'''
** [[MecA]]-[[ComK]] {{PubMed|10447896}}
** [[MecA]]-[[ComS]] {{PubMed|10447896}}
** [[ClpC]]-[[MecA]] {{PubMed|10447896}}
** [[MecA]]-[[Spo0A]] {{PubMed|21435029}}

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/3jtp 3JTP] (C-terminal domain) {{PubMed|19801546}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37958 P37958]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU11520]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[mecA]]'' {{PubMed|8412687}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8412687}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP813 (spc), GP814 (aphA3) both available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews: {{PubMed|19609260}}==
==Original Publications==
'''Additonal publications:''' {{PubMed|16525504,12598648,21435029}}
<pubmed>11914365,9000055,17560370,19361434, 9890793,2113920,8817496, , 8412687,11918817, 10447896, 12028382, 8016067, 10361283, 11703662 9535081 19767395 19801546 8016066 19202088 8083167 </pubmed>
[[Category:Protein-coding genes]]

ParB

2011-04-01T14:29:34Z

Heilers: /* References */

* '''Description:''' chromosome positioning near the pole and transport through the polar septum / antagonist of [[Soj]]-dependent inhibition of sporulation initiation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''spo0J''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0JB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || site-specific DNA-binding protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || chromosome positioning before asymmetric septation,

specifying its orientation, and imposing directionality on

its subsequent transport through the septum; required for sporulation

(antagonist of [[Soj]]-dependent inhibition of sporulation initiation)
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 8.417
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 846 bp, 282 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yyaC]]'', ''[[soj]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16133]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:spo0J_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DNA condensation/ segregation]]}},
{{SubtiWiki category|[[sporulation/ other]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40960

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/soj-spo0J.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10054]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' inhibits [[Soj]] dimerization and concomitant DNA-binding activity by stimulating Soj ATPase activity {{PubMed|21235642}}

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' [[Spo0J]]-[[Soj]] {{PubMed|21235642}}

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P26497 P26497]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40960]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[soj]]-[[spo0J]]'' (according to [http://dbtbs.hgc.jp/COG/prom/soj-spo0J.html DBTBS])

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

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

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17462018 16677298 12562803, 10852876, 10482533, 9506522, 8071208, 17932079 19450517 21235642 9663676,11532141,19450516,15659156,18854156,9159397,8866474,9778525,16925562,1900505,9364919,9701805,12950914,,14651647, 19450517, 19450516, 14563866 </pubmed>

[[Category:Protein-coding genes]]

ParA

2011-04-01T14:27:26Z

Heilers: /* Original publications */

* '''Description:''' ATPase, centromere-like function involved in forespore chromosome partitioning / negative regulation of sporulation initiation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''soj''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0JA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || negative regulator of sporulation initiation
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || forespore chromosome partitioning / negative regulation of sporulation initiation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 4.903
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spo0J]]'', ''[[yyaB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16134]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:soj_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DNA condensation/ segregation]]}},
{{SubtiWiki category|[[sporulation/ other]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40970

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/soj-spo0J.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10055]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' regulates [[DNA replication]] initiation by either inhibiting or activating the [[DNA replication]] initiator protein [[DnaA]] {{PubMed|21235642}}; regulation of ''Spo0A'' expression {{PubMed|10852876}}

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** [[Spo0J]] inhibits [[Soj]] dimerization and concomitant DNA-binding activity by stimulating Soj ATPase activity {{PubMed|21235642}}

* '''Interactions:'''
** [[Spo0J]]-[[Soj]] {{PubMed|21235642}}

* '''Localization:'''
** polar/ septal at the cell membrane {{PubMed|20566861}}
** polar localization depends on the proton motive force {{PubMed|20566861}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37522 P37522]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40970]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[soj]]-[[spo0J]]'' (according to [http://dbtbs.hgc.jp/COG/prom/soj-spo0J.html DBTBS])

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

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

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20157337 </pubmed>
==Original publications==
<pubmed>15659156,11532141,19450516,18854156,10619015,8866474,12492861,9701805,12950914,14651647, 19450516 20566861 21235642 10852876 14563866</pubmed>

[[Category:Protein-coding genes]]

ParA

2011-04-01T14:24:39Z

Heilers: /* Basic information/ Evolution */

ParA

2011-04-01T14:22:49Z

Heilers: /* Original publications */

* '''Description:''' ATPase, centromere-like function involved in forespore chromosome partitioning / negative regulation of sporulation initiation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''soj''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0JA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || negative regulator of sporulation initiation
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || forespore chromosome partitioning / negative regulation of sporulation initiation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 4.903
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spo0J]]'', ''[[yyaB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16134]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:soj_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DNA condensation/ segregation]]}},
{{SubtiWiki category|[[sporulation/ other]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40970

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/soj-spo0J.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10055]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' regulates [[DNA replication]] initiation by either inhibiting or activating the [[DNA replication]] initiator protein [[DnaA]] {{PubMed|21235642}}

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** [[Spo0J]] inhibits [[Soj]] dimerization and concomitant DNA-binding activity by stimulating Soj ATPase activity {{PubMed|21235642}}

* '''Interactions:'''
** [[Spo0J]]-[[Soj]] {{PubMed|21235642}}

* '''Localization:'''
** polar/ septal at the cell membrane {{PubMed|20566861}}
** polar localization depends on the proton motive force {{PubMed|20566861}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37522 P37522]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40970]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[soj]]-[[spo0J]]'' (according to [http://dbtbs.hgc.jp/COG/prom/soj-spo0J.html DBTBS])

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

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

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20157337 </pubmed>
==Original publications==
<pubmed>15659156,11532141,19450516,18854156,10619015,8866474,12492861,9701805,12950914,14651647, 19450516 20566861 21235642 10852876</pubmed>

[[Category:Protein-coding genes]]

Spo0A

2011-04-01T14:21:28Z

Heilers: /* Other original Publications */

* '''Description:''' [[phosphorelay]] regulator, initiation of sporulation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''spo0A''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0C, spo0G, spoIIL, sof-1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[phosphorelay]] response regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism],[http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism], [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging],[http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion] '''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 801 bp, 267 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqiG]]'', ''[[spoIVB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14353]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:spo0A_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[Spo0A regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24220

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

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

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

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

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

* '''Localization:'''

=== Database entries ===

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

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

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

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

=== Additional information===

=Expression and regulation=

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

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

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

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=
==Reviews==
<pubmed>19995980 20030732 20157337 11286862 20833318 20955377 </pubmed>
==The [[Spo0A regulon]]==
<pubmed>14651647,15687200, </pubmed>
==Other original Publications==
'''Additonal publications:''' {{PubMed|21326214,21435029}}
<pubmed>14679239, 1569009 20413551 20404177 19528067, 19581368 , 8730857,2106683,3157992, 11254139, 12067336, 10869437, 16385044,9287005, 8127878,9287022, 8231806, 1905258,16452424,2118505,8207022, 12176382, 9733708, 11069677,1391039,12730135, 2437099,8288522,16166384,9495766,2118512,1556084, 18296515,7768874, 3145384, 19114652 20689749 1537790,9658000, 8509330,14762002, 1846779, 2981817, 9477965,8600030, 18840696, 1391039, 14976210, 19207565 11679073 12270811 11112444 18978066 20154131 14712656 17157871 15060025 9685500 10852876</pubmed>

[[Category:Protein-coding genes]]

Spo0A

2011-04-01T14:19:40Z

Heilers: /* Expression and regulation */

Spo0A

2011-04-01T14:00:41Z

Heilers: /* Other original Publications */

* '''Description:''' [[phosphorelay]] regulator, initiation of sporulation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''spo0A''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0C, spo0G, spoIIL, sof-1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[phosphorelay]] response regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism],[http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism], [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging],[http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion] '''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 801 bp, 267 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqiG]]'', ''[[spoIVB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14353]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:spo0A_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[Spo0A regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24220

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

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

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

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

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

* '''Localization:'''

=== Database entries ===

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

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

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

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]
** repressed by casamino acids {{PubMed|15060025}}
** repressed by [[SinR]] ''in vitro'' {{PubMed|9685500}}

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=
==Reviews==
<pubmed>19995980 20030732 20157337 11286862 20833318 20955377 </pubmed>
==The [[Spo0A regulon]]==
<pubmed>14651647,15687200, </pubmed>
==Other original Publications==
'''Additonal publications:''' {{PubMed|21326214,21435029}}
<pubmed>14679239, 1569009 20413551 20404177 19528067, 19581368 , 8730857,2106683,3157992, 11254139, 12067336, 10869437, 16385044,9287005, 8127878,9287022, 8231806, 1905258,16452424,2118505,8207022, 12176382, 9733708, 11069677,1391039,12730135, 2437099,8288522,16166384,9495766,2118512,1556084, 18296515,7768874, 3145384, 19114652 20689749 1537790,9658000, 8509330,14762002, 1846779, 2981817, 9477965,8600030, 18840696, 1391039, 14976210, 19207565 11679073 12270811 11112444 18978066 20154131 14712656 17157871 15060025 9685500</pubmed>

[[Category:Protein-coding genes]]

Spo0A

2011-04-01T13:58:56Z

Heilers: /* Expression and regulation */

* '''Description:''' [[phosphorelay]] regulator, initiation of sporulation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''spo0A''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0C, spo0G, spoIIL, sof-1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[phosphorelay]] response regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism],[http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism], [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging],[http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion] '''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 801 bp, 267 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqiG]]'', ''[[spoIVB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14353]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:spo0A_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[Spo0A regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24220

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

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

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

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

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

* '''Localization:'''

=== Database entries ===

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

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

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

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]
** repressed by casamino acids {{PubMed|15060025}}
** repressed by [[SinR]] ''in vitro'' {{PubMed|9685500}}

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=
==Reviews==
<pubmed>19995980 20030732 20157337 11286862 20833318 20955377 </pubmed>
==The [[Spo0A regulon]]==
<pubmed>14651647,15687200, </pubmed>
==Other original Publications==
'''Additonal publications:''' {{PubMed|21326214,21435029}}
<pubmed>14679239, 1569009 20413551 20404177 19528067, 19581368 , 8730857,2106683,3157992, 11254139, 12067336, 10869437, 16385044,9287005, 8127878,9287022, 8231806, 1905258,16452424,2118505,8207022, 12176382, 9733708, 11069677,1391039,12730135, 2437099,8288522,16166384,9495766,2118512,1556084, 18296515,7768874, 3145384, 19114652 20689749 1537790,9658000, 8509330,14762002, 1846779, 2981817, 9477965,8600030, 18840696, 1391039, 14976210, 19207565 11679073 12270811 11112444 18978066 20154131 14712656 17157871 15060025 </pubmed>

[[Category:Protein-coding genes]]

SinR

2011-04-01T13:54:10Z

Heilers: /* Original publications */

* '''Description:''' transcriptional regulator of post-exponential-phase responses genes 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sinR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sin, flaD ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator of post-exponential-phase responses genes
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 7.177
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 333 bp, 111 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sinI]]'', ''[[tasA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14392]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sinR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[SinR regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24610

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10754]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription repressor of biofilm genes, acts as co-repressor for [[SlrR]] {{PubMed|20351052}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:''' [[SinI]] and [[SlrA]] are antagonists to [[SinR]] {{PubMed|19788541}}, [[SlrR]] is also antagonist of [[SinR]] {{PubMed|20351052}}

* '''Interactions:''' [[SlrA]]-[[SinR]] {{PubMed|19788541}}, [[SlrR]]-[[SinR]] {{PubMed|20351052}}, [[SinR]]-[[ScoC]], [[SinR]]-[[SinI]]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1B0N 1B0N] (complex [[SinR]]-[[SinI]])

* '''UniProt:''' [http://www.uniprot.org/uniprot/P06533 P06533]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24610]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[sinI]]-[[sinR]]'' {{PubMed|3125149}}
** ''[[sinR]]'' {{PubMed|3125149}}

* '''[[Sigma factor]]:'''
** ''[[sinI]]'': [[SigA]] {{PubMed|3125149}}
** ''[[sinR]]'': [[SigA]] {{PubMed|3125149}}

* '''Regulation:'''
** ''[[sinI]]'': repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** ''[[sinI]]'': repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** ''[[sinI]]'': repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]
** ''[[sinI]]'': repressed during vegetative growth ([[SinR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1664536 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1664536 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' TMB079 ''sinR::spec'', GP736 (tetR), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP960 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>20395361 20541494 </pubmed>
==Modelling of the [[SinI]]/[[SinR]] switch==
<pubmed> 21095906 </pubmed>
==Original publications==
'''Additonal publications:''' {{PubMed|21326214}}
<pubmed>8955328,15661000,8878039,16923912,15104138,16430695,16430696,18047568,18430133,11751836,1906467,11751836,7635837,11751836, 19201793, 10547280, 15104138, 9799632 19788541 19898538 3125149 8932324 20351052 20923420 8422983 9685500 </pubmed>

[[Category:Protein-coding genes]]

YqfG

2011-03-04T08:43:20Z

Heilers: /* References */

* '''Description:''' required for rRNA maturation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yqfG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || rRNA maturation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.193
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 471 bp, 157 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dgkA]]'', ''[[yqfF]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14461]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yqfG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[translation]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25320

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11656]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0054 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1TVI 1TVI] orthologue from ''T. maritima'' (38% identity) {{PubMed|15965736}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P46347 P46347]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25320]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=
This protein family is highly conserved in bacteria. In ''E. coli'', its orthologe [http://ecoliwiki.net/colipedia/index.php/ybeY YbeY] is involved in maturation of rRNA. {{PubMed|20807199}}
In S. meliloti, the protein affects sRNA regulation in a similar way as Hfq {{PubMed|21325267}}

=References=
<pubmed> 20807199, 15965736 21325267</pubmed>

[[Category:Protein-coding genes]]

YqfG

2011-03-04T08:42:09Z

Heilers: /* Your additional remarks */

SinR

2011-02-18T09:28:01Z

Heilers: /* Original publications */

* '''Description:''' transcriptional regulator of post-exponential-phase responses genes 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sinR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sin, flaD ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator of post-exponential-phase responses genes
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 7.177
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 333 bp, 111 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sinI]]'', ''[[tasA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14392]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sinR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[SinR regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24610

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10754]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription repressor of biofilm genes, acts as co-repressor for [[SlrR]] {{PubMed|20351052}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:''' [[SinI]] and [[SlrA]] are antagonists to [[SinR]] {{PubMed|19788541}}, [[SlrR]] is also antagonist of [[SinR]] {{PubMed|20351052}}

* '''Interactions:''' [[SlrA]]-[[SinR]] {{PubMed|19788541}}, [[SlrR]]-[[SinR]] {{PubMed|20351052}}, [[SinR]]-[[ScoC]], [[SinR]]-[[SinI]]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1B0N 1B0N] (complex [[SinR]]-[[SinI]])

* '''UniProt:''' [http://www.uniprot.org/uniprot/P06533 P06533]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24610]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[sinI]]-[[sinR]]'' {{PubMed|3125149}}
** ''[[sinR]]'' {{PubMed|3125149}}

* '''[[Sigma factor]]:'''
** ''[[sinI]]'': [[SigA]] {{PubMed|3125149}}
** ''[[sinR]]'': [[SigA]] {{PubMed|3125149}}

* '''Regulation:'''
** ''[[sinI]]'': repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** ''[[sinI]]'': repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** ''[[sinI]]'': repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]
** ''[[sinI]]'': repressed during vegetative growth ([[SinR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1664536 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1664536 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' TMB079 ''sinR::spec'', GP736 (tetR), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP960 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>20395361 20541494 </pubmed>
==Modelling of the [[SinI]]/[[SinR]] switch==
<pubmed> 21095906 </pubmed>
==Original publications==
<pubmed>8955328,15661000,8878039,16923912,15104138,16430695,16430696,18047568,18430133,11751836,1906467,11751836,7635837,11751836, 19201793, 10547280, 15104138, 9799632 19788541 19898538 3125149 8932324 20351052 20923420 8422983 21326214 </pubmed>

[[Category:Protein-coding genes]]

SinI

2011-02-18T09:25:39Z

Heilers: /* Original publications */

* '''Description:''' antagonist of [[SinR]], drives [[SlrR]] from the [[SlrR]](LOW) to the [[SlrR]](HIGH) state 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sinI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || antagonist of [[SinR]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 6.333
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 171 bp, 57 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqhG]]'', ''[[sinR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14391]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sinI_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24600

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10753]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' [[SinR]]-[[SinI]] {{PubMed|9799632}}

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1B0N 1B0N] (complex [[SinR]]-[[SinI]]) {{PubMed|9799632}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P23308 P23308]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24600]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' [[sinI]]-[[sinR]] {{PubMed|3125149}}, [[sinI]]-[[Spo0A]] {{PubMed|21326214}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|3125149}}

* '''Regulation:'''
** activated under conditions that trigger sporulation by ([[Spo0A]]) interaction [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed],{{PubMed|21326214}}
** repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]
** repressed during vegetative growth ([[SinR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1664536 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription activation, in a portion of cells [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1664536 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP959 (spc), available in [[Stülke]] lab
** DS91 (spc) NCIB3610 derivate, available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20541494 </pubmed>
==Modelling of the [[SinI]]/[[SinR]] switch==
<pubmed> 21095906 </pubmed>
==Original publications==
<pubmed>3125149 15661000,18047568,,11751836,1906467,11751836,7635837,11751836, 10547280, 15104138, 9799632 20923420 8422983 21326214</pubmed>

[[Category:Protein-coding genes]]

SinI

2011-02-18T09:24:09Z

Heilers: /* Expression and regulation */

SinI

2011-02-18T09:23:08Z

Heilers: /* Expression and regulation */

* '''Description:''' antagonist of [[SinR]], drives [[SlrR]] from the [[SlrR]](LOW) to the [[SlrR]](HIGH) state 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sinI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || antagonist of [[SinR]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 6.333
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 171 bp, 57 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqhG]]'', ''[[sinR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14391]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sinI_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24600

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10753]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' [[SinR]]-[[SinI]] {{PubMed|9799632}}

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1B0N 1B0N] (complex [[SinR]]-[[SinI]]) {{PubMed|9799632}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P23308 P23308]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24600]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' [[sinI]]-[[sinR]] {{PubMed|3125149}}, [[sinI]]-[[Spo0A]] {{PubMed|21326214}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|3125149}}

* '''Regulation:'''
** activated under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed],{{PubMed|21326214}}
** repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]
** repressed during vegetative growth ([[SinR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1664536 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription activation, in a portion of cells [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1664536 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP959 (spc), available in [[Stülke]] lab
** DS91 (spc) NCIB3610 derivate, available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20541494 </pubmed>
==Modelling of the [[SinI]]/[[SinR]] switch==
<pubmed> 21095906 </pubmed>
==Original publications==
<pubmed>3125149 15661000,18047568,,11751836,1906467,11751836,7635837,11751836, 10547280, 15104138, 9799632 20923420 8422983 </pubmed>

[[Category:Protein-coding genes]]

Spo0A

2011-02-18T09:17:48Z

Heilers: /* Extended information on the protein */

* '''Description:''' [[phosphorelay]] regulator, initiation of sporulation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''spo0A''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0C, spo0G, spoIIL, sof-1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[phosphorelay]] response regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism],[http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism], [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging],[http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion] '''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 801 bp, 267 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqiG]]'', ''[[spoIVB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14353]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:spo0A_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[Spo0A regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24220

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

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

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

* '''Effectors of protein activity:''' the phosphorylation state affects DNA binding activity

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

* '''Localization:'''

=== Database entries ===

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

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

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

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]
** repressed by casamino acids {{PubMed|15060025}}

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=
==Reviews==
<pubmed>19995980 20030732 20157337 11286862 20833318 20955377 </pubmed>
==The [[Spo0A regulon]]==
<pubmed>14651647,15687200, </pubmed>
==Other original Publications==
<pubmed>14679239, 1569009 20413551 20404177 19528067, 19581368 , 8730857,2106683,3157992, 11254139, 12067336, 10869437, 16385044,9287005, 8127878,9287022, 8231806, 1905258,16452424,2118505,8207022, 12176382, 9733708, 11069677,1391039,12730135, 2437099,8288522,16166384,9495766,2118512,1556084, 18296515,7768874, 3145384, 19114652 20689749 1537790,9658000, 8509330,14762002, 1846779, 2981817, 9477965,8600030, 18840696, 1391039, 14976210, 19207565 11679073 12270811 11112444 18978066 20154131 14712656 17157871 15060025 21326214</pubmed>

[[Category:Protein-coding genes]]

Spo0A

2011-02-18T09:14:22Z

Heilers: /* Other original Publications */

* '''Description:''' [[phosphorelay]] regulator, initiation of sporulation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''spo0A''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0C, spo0G, spoIIL, sof-1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[phosphorelay]] response regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism],[http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism], [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging],[http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion] '''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 801 bp, 267 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqiG]]'', ''[[spoIVB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14353]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:spo0A_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[Spo0A regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24220

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

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

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

* '''Effectors of protein activity:''' the phosphorylation state affects DNA binding activity

* '''Interactions:''' [[KinC]]-[[Spo0A]] {{PubMed|19114652}}, [[Spo0A]]-[[Spo0E]] {{PubMed|12067336}}, [[Spo0A]]-[[SigA]] {{PubMed|14976210}}, [[Spo0A]]-[[Spo0B]]

* '''Localization:'''

=== Database entries ===

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

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

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

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]
** repressed by casamino acids {{PubMed|15060025}}

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=
==Reviews==
<pubmed>19995980 20030732 20157337 11286862 20833318 20955377 </pubmed>
==The [[Spo0A regulon]]==
<pubmed>14651647,15687200, </pubmed>
==Other original Publications==
<pubmed>14679239, 1569009 20413551 20404177 19528067, 19581368 , 8730857,2106683,3157992, 11254139, 12067336, 10869437, 16385044,9287005, 8127878,9287022, 8231806, 1905258,16452424,2118505,8207022, 12176382, 9733708, 11069677,1391039,12730135, 2437099,8288522,16166384,9495766,2118512,1556084, 18296515,7768874, 3145384, 19114652 20689749 1537790,9658000, 8509330,14762002, 1846779, 2981817, 9477965,8600030, 18840696, 1391039, 14976210, 19207565 11679073 12270811 11112444 18978066 20154131 14712656 17157871 15060025 21326214</pubmed>

[[Category:Protein-coding genes]]

ABC transporters

2011-02-07T09:46:52Z

Heilers: /* Relevant publications */

{{CategoryTree
|Parents=
* 1. [[Cellular processes]]
** 1.2. [[Transporters]]
|Neighbours=
* 1.2.1. [[ABC transporters]]
* 1.2.2. [[Phosphotransferase systems]]
* 1.2.3. [[Transporters/ other]]
|Related=
[[transport proteins]]
|}}

__TOC__
 
=Importers=
==Uptake of carbon sources==
* [[YurJ]], [[YurM]], [[YurN]], [[YurO]]: uptake of aminosugars
* [[AraN]], [[AraP]], [[AraQ]]: uptake of arabinose
* [[CycB]], [[YvfL]], [[YvfM]]: uptake of cyclodextrin/maltodextrin (probably)
* [[MdxE]], [[MdxF]], [[MdxG]]: uptake of maltodextrin
* [[AmyC]], [[AmyD]], [[MsmE]]: uptake of melibiose (probably)
* [[RbsA]], [[RbsB]], [[RbsC]], [[RbsD]]: uptake of ribose
* ([[YtrB]]-[[YtrE]])-([[YtrC]]-[[YtrD]])-[[YtrF]]: uptake of acetoin

===ATPase subunit of multiple sugar transport systems===
* [[MsmX]]

==Uptake of amino acids==
* [[ArtP]], [[ArtQ]], [[ArtR]]: uptake of arginine
* [[TcyJ]], [[TcyK]], [[TcyL]], [[TcyM]], [[TcyN]]: uptake of cystine
* [[TcyA]], [[TcyB]], [[TcyC]]: uptake of cystine
* [[GlnH]], [[GlnM]], [[GlnP]], [[GlnQ]]: uptake of glutamine
* [[MetN]], [[MetP]], [[MetQ]]: uptake of methionine

==Uptake of peptides==
* [[AppA]], [[AppB]], [[AppC]], [[AppD]], [[AppF]]: uptake of oligopeptides
* [[DppB]], [[DppC]], [[DppD]], [[DppE]], [[YkfD]]: uptake of dipeptides
* [[OppA]], [[OppB]], [[OppC]], [[OppD]], [[OppF]]: uptake of oligopeptides

==Uptake of compatible solutes for osmoprotection==
* [[OpuAA]]-[[OpuAB]]-[[OpuAC]]: [[ABC transporter]] for glycine betaine
* [[OpuBA]]-[[OpuBB]]-[[OpuBC]]-[[OpuBD]]: [[ABC transporter]] for choline
* [[OpuCA]]-[[OpuCB]]-[[OpuCC]]-[[OpuCD]]: [[ABC transporter]] for glycine betaine/ carnitine/ choline

==Uptake of iron/ siderophores==
* [[YusV]]-[[FeuB]]-[[FeuC]]-[[FeuA]]: uptake of the siderophores enterobactin and bacillibactin
* [[FhuC]]-[[FhuB]]-[[FhuG]]-[[FhuD]]-[[YxeB]]: uptake of ferrichrome und ferrioxamine
* [[YclN]]-[[YclO]]-[[YclP]]-[[YclQ]]: uptake of petrobactin
* [[YusV]]-[[YfiZ]]-[[YfhA]]-[[YfiY]]: uptake of the siderophores schizokinen and arthrobactin
* [[YfmF]]-[[YfmD]]-[[YfmE]]-[[YfmC]]-[[YhfQ]]: uptake of iron/citrate

==Uptake of ions==
* [[MntB]]-[[MntA]]-[[MntC]]-[[MntD]]: uptake of manganese
* [[PstBA]]-[[PstBB]]-[[PstS]]-[[PstC]]-[[PstA]]: uptake of phosphate
* [[SsuA]]-[[SsuB]]-[[SsuC]]: uptake of aliphatic sulfonate
* [[YcdI]]-[[YceA]]-[[YcdH]]: uptake of zinc
* [[YvgM]]-[[YvgL]]: uptake of molybdenum (probably)

==Uptake of cofactors==
* [[ThiW]]-([[ThiV]]-[[ThiX]])-[[ThiU]]: uptake of thiamine

==ABC transporters of unknown function==
* [[LplA]]-[[LplB]]-[[LplC]]
* [[YckA]]-[[YckB]]
* [[YesO]]-[[YesP]]-[[YesQ]]
* [[YhjP]]
* [[YjkB]]-[[YjkA]]
* [[YlmA]]
* [[YtcP]]-[[YtcQ]]-[[YteP]]
* [[YtlC]]-[[YtlD]]-[[YtlA]]
* [[YufO]]-[[YufP]]-[[YufQ]]
* [[YvrA]]-[[YvrB]]-[[YvrC]]
* [[YxeM]]-[[YxeN]]-[[YxeO]]

=Exporters=
==Efflux of antibiotics==
* [[VmlR]]: efflux of virginiamycin M and lincomycin
* [[BmrA]]: efflux of multiple antibiotics
* [[YheH]]-[[YheI]]: efflux of multiple antibiotics

==Export of antibiotic substances==
* [[AlbC]]-[[AlbD]]
* [[SunT]]

==Export of toxic peptides==
* [[SkfE]]-[[SkfF]]
* [[YknY]]-[[YknZ]]
* [[BceA]]-[[BceB]]: export of bacitracin, plectasin, mersacidin and actagardine
* [[YxdL]]-[[YxdM]]
* [[PsdA]]-[[PsdB]]: export of lipid II-binding lantibiotics, such as nisin and gallidermin

==Export of cell wall components==
* [[TagG]]-[[TagH]]: export of teichoic acid

==Export of ions==
* [[NatA]]-[[NatB]]: export of Na(+)

==Exporters of unknown function==
* ([[YbxA]]-[[YbaE]])-[[YbaF]]
* [[YcbN]]
* [[YclH]]-[[YclI]]
* [[YdbJ]]-[[YdbK]]
* [[YdiF]]
* [[YfiB]]-[[YfiC]]
* [[YfiL]]-[[YfiM]]-[[YfiN]]
* [[YfmM]]
* [[YfmR]]
* [[YgaD]]
* [[YhaQ]]-[[YhaP]]
* [[YhcG]]-[[YhcE]]
* [[YhcH]]-[[YhcI]]
* [[YknU]]-[[YknV]]
* [[YkpA]]
* [[YthP]]-[[YthQ]]
* [[YvfR]]-[[YvfS]]
* [[YvrO]]-[[YvrN]]
* [[YwjA]]
* [[YxlF]]-[[YxlG]]
* [[YybJ]]-([[YybK]]-[[YybL]])

=Regulatory ABC transporters=
* [[CydC]]-[[CydD]]: required for expression of cytochrome bd
* [[EcsA]]-[[EcsB]]: regulation of the secretion apparatus and of intra-membrane proteolysis
* [[FtsE]]-[[FtsX]]: activation of [[Spo0A]] and initiation of sporulation
* [[YheH]]-[[YheI]]: involved in the signalling pathway to activate [[KinA]] at the onset of sporulation
* [[SufC]]: required for the synthesis of Fe-S clusters
* [[YydI]]-([[YydJ]]-[[YydH]]): control of [[LiaR]]-[[LiaS]] activity

=Relevant publications=
<pubmed> 10092453 1282354 18535149 20497229 21283517</pubmed>

A-box

2011-02-07T09:39:50Z

Heilers: /* References */

'''The A-box is a [[riboswitch ]] that mediates adenine-dependent induction of ''[[pbuE]]'' gene expression'''

==References==
<pubmed> 12787499 ,18072940 19603494 14718920 16931335 16201765 20022916 21283784 </pubmed>

ClpP

2011-01-21T13:49:14Z

Heilers: /* Original Publications */

* '''Description:''' ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''clpP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvdN ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease proteolytic subunit
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.008
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 591 bp, 197 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnQ-Arg]]'', ''[[pgcM]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15459]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:clpP_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[proteolysis]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[heat shock proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34540

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19016]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Hydrolysis of proteins to small peptides in the presence of ATP and magnesium (according to Swiss-Prot) endopeptidase/proteolysis

* '''Protein family:''' peptidase S14 family (according to Swiss-Prot) ClpP (IPR001907) [http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001907 InterPro], (PF00574) [http://pfam.sanger.ac.uk/family?acc=PF00574 PFAM]

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

=== Targets of [[ClpC]]-[[ClpP]]-dependent protein degradation ===
* [[DegU]]-P {{PubMed|20070525}}

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''
** [[ClpE]]-[[ClpP]], [[ClpC]]-[[ClpP]], [[ClpX]]-[[ClpP]]
** [[CtsR]]-[[ClpP]]/[[ClpC]] (degradation of [[CtsR]]) {{PubMed|11179229,16163393,17380125}}
** [[McsB]]-[[ClpP]]/[[ClpC]] (rapid degradation of non-phosphorylated McsB) {{PubMed|20852588}}

* '''Localization:''' cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heat shock, colocalization with [[ClpX]], [[ClpC]] and [[ClpE]] {{PubMed|18786145,18689473}}

[[File:ClpP.jpg‎ ]]

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3KTG 3KTG] {{PubMed|20305655}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80244 P80244]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34540]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.4.21.92 3.4.21.92]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''clpP'' {{PubMed|9643546}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|9643546}}, [[SigB]] {{PubMed|9643546,11544224}}

* '''Regulation:'''
** induced by stress ([[SigB]]) {{PubMed|9643546,11544224}}
** induced by heat ([[CtsR]]) {{PubMed|9987115}}

* '''Regulatory mechanism:'''
** [[CtsR]]: transcription repression {{PubMed|9987115,11179229,16163393,17380125}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** ''clpP::spec'' and ''clpP::cat'', available in the [[Leendert Hamoen]] lab
** GP551 (spc), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' C-terminal GFP fusions (both single copy and as 2th copy in ''amyE'' locus, also as CFP and YFP variants) available in the [[Leendert Hamoen]] lab

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[Leendert Hamoen]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/l.hamoen homepage]

=Your additional remarks=

=References=

==Reviews==
{{PubMed|19609260,19781636}}
==Original Publications==
<pubmed>9643546,10809708,11807061,9987115,14679237,18689476,15317791,17586624,11684022,12923101,17560370, 16899079,19226326 , 20070525,9987115,11544224 14763982 9643546, 19767395 11112444 9535081 18689473 20305655 20852588 </pubmed>
Additional publication: {{PubMed|17380125,12598648,9890793,20049702,20049702}}
[[Category:Protein-coding genes]]

ClpP

2011-01-21T13:48:41Z

Heilers: Undo revision 139660 by Heilers (talk)

ClpP

2011-01-21T13:48:05Z

Heilers: Undo revision 139661 by Heilers (talk)

* '''Description:''' ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''clpP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvdN ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease proteolytic subunit
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.008
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 591 bp, 197 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnQ-Arg]]'', ''[[pgcM]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15459]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:clpP_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[proteolysis]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[heat shock proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34540

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19016]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Hydrolysis of proteins to small peptides in the presence of ATP and magnesium (according to Swiss-Prot) endopeptidase/proteolysis

* '''Protein family:''' peptidase S14 family (according to Swiss-Prot) ClpP (IPR001907) [http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001907 InterPro], (PF00574) [http://pfam.sanger.ac.uk/family?acc=PF00574 PFAM]

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

=== Targets of [[ClpC]]-[[ClpP]]-dependent protein degradation ===
* [[DegU]]-P {{PubMed|20070525}}

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''
** [[ClpE]]-[[ClpP]], [[ClpC]]-[[ClpP]], [[ClpX]]-[[ClpP]]
** [[CtsR]]-[[ClpP]]/[[ClpC]] (degradation of [[CtsR]]) {{PubMed|11179229,16163393,17380125}}
** [[McsB]]-[[ClpP]]/[[ClpC]] (rapid degradation of non-phosphorylated McsB) {{PubMed|20852588}}

* '''Localization:''' cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heat shock, colocalization with [[ClpX]], [[ClpC]] and [[ClpE]] {{PubMed|18786145,18689473}}

[[File:ClpP.jpg‎ ]]

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3KTG 3KTG] {{PubMed|20305655}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80244 P80244]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34540]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.4.21.92 3.4.21.92]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''clpP'' {{PubMed|9643546}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|9643546}}, [[SigB]] {{PubMed|9643546,11544224}}

* '''Regulation:'''
** induced by stress ([[SigB]]) {{PubMed|9643546,11544224}}
** induced by heat ([[CtsR]]) {{PubMed|9987115}}

* '''Regulatory mechanism:'''
** [[CtsR]]: transcription repression {{PubMed|9987115,11179229,16163393,17380125}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** ''clpP::spec'' and ''clpP::cat'', available in the [[Leendert Hamoen]] lab
** GP551 (spc), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' C-terminal GFP fusions (both single copy and as 2th copy in ''amyE'' locus, also as CFP and YFP variants) available in the [[Leendert Hamoen]] lab

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[Leendert Hamoen]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/l.hamoen homepage]

=Your additional remarks=

=References=

==Reviews==
{{PubMed|19609260,19781636}}
==Original Publications==
<pubmed>9643546,10809708,11807061,9987115,14679237,18689476,15317791,17586624,11684022,12923101,17560370, 16899079,19226326 , 20070525,9987115,11544224 14763982 9643546, 19767395 11112444 9535081 18689473 20305655 20852588 20049702 </pubmed>
Additional publication: {{PubMed|17380125,12598648,9890793,20049702}}
[[Category:Protein-coding genes]]

ClpP

2011-01-21T13:46:50Z

Heilers: /* Original Publications */

* '''Description:''' ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''clpP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvdN ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease proteolytic subunit
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.008
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 591 bp, 197 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnQ-Arg]]'', ''[[pgcM]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15459]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:clpP_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[proteolysis]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[heat shock proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34540

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19016]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Hydrolysis of proteins to small peptides in the presence of ATP and magnesium (according to Swiss-Prot) endopeptidase/proteolysis

* '''Protein family:''' peptidase S14 family (according to Swiss-Prot) ClpP (IPR001907) [http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001907 InterPro], (PF00574) [http://pfam.sanger.ac.uk/family?acc=PF00574 PFAM]

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

=== Targets of [[ClpC]]-[[ClpP]]-dependent protein degradation ===
* [[DegU]]-P {{PubMed|20070525}}

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''
** [[ClpE]]-[[ClpP]], [[ClpC]]-[[ClpP]], [[ClpX]]-[[ClpP]]
** [[CtsR]]-[[ClpP]]/[[ClpC]] (degradation of [[CtsR]]) {{PubMed|11179229,16163393,17380125}}
** [[McsB]]-[[ClpP]]/[[ClpC]] (rapid degradation of non-phosphorylated McsB) {{PubMed|20852588}}

* '''Localization:''' cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heat shock, colocalization with [[ClpX]], [[ClpC]] and [[ClpE]] {{PubMed|18786145,18689473}}

[[File:ClpP.jpg‎ ]]

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3KTG 3KTG] {{PubMed|20305655}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80244 P80244]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34540]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.4.21.92 3.4.21.92]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''clpP'' {{PubMed|9643546}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|9643546}}, [[SigB]] {{PubMed|9643546,11544224}}

* '''Regulation:'''
** induced by stress ([[SigB]]) {{PubMed|9643546,11544224}}
** induced by heat ([[CtsR]]) {{PubMed|9987115}}

* '''Regulatory mechanism:'''
** [[CtsR]]: transcription repression {{PubMed|9987115,11179229,16163393,17380125}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** ''clpP::spec'' and ''clpP::cat'', available in the [[Leendert Hamoen]] lab
** GP551 (spc), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' C-terminal GFP fusions (both single copy and as 2th copy in ''amyE'' locus, also as CFP and YFP variants) available in the [[Leendert Hamoen]] lab

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[Leendert Hamoen]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/l.hamoen homepage]

=Your additional remarks=

=References=

==Reviews==
{{PubMed|19609260,19781636}}
==Original Publications==
<pubmed>9643546,10809708,11807061,9987115,14679237,18689476,15317791,17586624,11684022,12923101,17560370, 20049702, 16899079,19226326 , 20070525,9987115,11544224 14763982 9643546, 19767395 11112444 9535081 18689473 20305655 20852588 </pubmed>
Additional publication: {{PubMed|17380125,12598648,9890793,20049702}}
[[Category:Protein-coding genes]]

ClpP

2011-01-21T13:44:53Z

Heilers: /* Original Publications */

* '''Description:''' ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''clpP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvdN ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease proteolytic subunit
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.008
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 591 bp, 197 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnQ-Arg]]'', ''[[pgcM]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15459]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:clpP_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[proteolysis]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[heat shock proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34540

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19016]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Hydrolysis of proteins to small peptides in the presence of ATP and magnesium (according to Swiss-Prot) endopeptidase/proteolysis

* '''Protein family:''' peptidase S14 family (according to Swiss-Prot) ClpP (IPR001907) [http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001907 InterPro], (PF00574) [http://pfam.sanger.ac.uk/family?acc=PF00574 PFAM]

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

=== Targets of [[ClpC]]-[[ClpP]]-dependent protein degradation ===
* [[DegU]]-P {{PubMed|20070525}}

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''
** [[ClpE]]-[[ClpP]], [[ClpC]]-[[ClpP]], [[ClpX]]-[[ClpP]]
** [[CtsR]]-[[ClpP]]/[[ClpC]] (degradation of [[CtsR]]) {{PubMed|11179229,16163393,17380125}}
** [[McsB]]-[[ClpP]]/[[ClpC]] (rapid degradation of non-phosphorylated McsB) {{PubMed|20852588}}

* '''Localization:''' cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heat shock, colocalization with [[ClpX]], [[ClpC]] and [[ClpE]] {{PubMed|18786145,18689473}}

[[File:ClpP.jpg‎ ]]

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3KTG 3KTG] {{PubMed|20305655}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80244 P80244]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34540]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.4.21.92 3.4.21.92]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''clpP'' {{PubMed|9643546}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|9643546}}, [[SigB]] {{PubMed|9643546,11544224}}

* '''Regulation:'''
** induced by stress ([[SigB]]) {{PubMed|9643546,11544224}}
** induced by heat ([[CtsR]]) {{PubMed|9987115}}

* '''Regulatory mechanism:'''
** [[CtsR]]: transcription repression {{PubMed|9987115,11179229,16163393,17380125}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** ''clpP::spec'' and ''clpP::cat'', available in the [[Leendert Hamoen]] lab
** GP551 (spc), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' C-terminal GFP fusions (both single copy and as 2th copy in ''amyE'' locus, also as CFP and YFP variants) available in the [[Leendert Hamoen]] lab

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[Leendert Hamoen]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/l.hamoen homepage]

=Your additional remarks=

=References=

==Reviews==
{{PubMed|19609260,19781636}}
==Original Publications==
<pubmed>9643546,10809708,11807061,9987115,14679237,18689476,15317791,17586624,11684022,12923101,17560370, 16899079,19226326 , 20070525,9987115,11544224 14763982 9643546, 19767395 11112444 9535081 18689473 20305655 20852588 20049702 </pubmed>
Additional publication: {{PubMed|17380125,12598648,9890793,20049702}}
[[Category:Protein-coding genes]]

YqfG

2010-11-04T13:43:25Z

Heilers: /* References */

* '''Description:''' required for rRNA maturation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yqfG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || rRNA maturation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.193
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 471 bp, 157 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dgkA]]'', ''[[yqfF]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14461]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yqfG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25320

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11656]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0054 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1TVI 1TVI] orthologue from ''T. maritima'' (38% identity) {{PubMed|15965736}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P46347 P46347]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25320]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=
This protein family is highly conserved in bacteria. In ''E. coli'', its orthologe [http://ecoliwiki.net/colipedia/index.php/ybeY YbeY] is involved in maturation of rRNA. {{PubMed|20807199}}

=References=
<pubmed> 20807199, 15965736</pubmed>

[[Category:Protein-coding genes]]

YqfG

2010-11-04T13:42:11Z

Heilers: /* Database entries */

* '''Description:''' required for rRNA maturation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yqfG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || rRNA maturation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.193
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 471 bp, 157 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dgkA]]'', ''[[yqfF]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14461]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yqfG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25320

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11656]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0054 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1TVI 1TVI] orthologue from ''T. maritima'' (38% identity) {{PubMed|15965736}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P46347 P46347]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25320]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=
This protein family is highly conserved in bacteria. In ''E. coli'', its orthologe [http://ecoliwiki.net/colipedia/index.php/ybeY YbeY] is involved in maturation of rRNA. {{PubMed|20807199}}

=References=
<pubmed> 20807199 </pubmed>

[[Category:Protein-coding genes]]

YqfG

2010-11-04T13:38:39Z

Heilers: /* Database entries */

* '''Description:''' required for rRNA maturation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yqfG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || rRNA maturation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.193
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 471 bp, 157 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dgkA]]'', ''[[yqfF]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14461]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yqfG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25320

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11656]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0054 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1TVI 1TVI] orthologue from ''T. maritima'' (38% identity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P46347 P46347]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25320]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=
This protein family is highly conserved in bacteria. In ''E. coli'', its orthologe [http://ecoliwiki.net/colipedia/index.php/ybeY YbeY] is involved in maturation of rRNA. {{PubMed|20807199}}

=References=
<pubmed> 20807199 </pubmed>

[[Category:Protein-coding genes]]