SubtiWiki - User contributions [en]

YybN

2012-12-10T08:17:05Z

Awiechert:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yybN''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40580 yybN]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 9.532
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 435 bp, 145 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yyzL]]'', ''[[yybM]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16095]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yybN_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=yybN_4173114_4173551_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yybN_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40580

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10017]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37490 P37490]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40580]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[yybN]]-[[yybM]]-[[yybL]]-[[yybK]]-[[yybJ]]'' (according to [[http://dbtbs.hgc.jp/COG/prom/yybNMLKJ.html DBTBS]])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yybN_4173114_4173551_1 yybN] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''
** repressed by [[Rok]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15743949 PubMed]

* '''Regulatory mechanism:'''
** [[Rok]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15743949 PubMed]

* '''Additional information:'''
** the mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed|20525796}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>15743949, 20525796 </pubmed>

[[Category:Protein-coding genes]]

CotF

2012-12-05T13:41:29Z

Awiechert:

* '''Description:''' spore coat protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cotF''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || spore coat protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance of the spore
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40530 cotF]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 18 kDa, 7.374
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 480 bp, 160 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yyzH]]'', ''[[hypR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16090]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:cotF_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=cotF_4167110_4167592_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:cotF_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40530

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10012]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' cotF 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]]:'''
** inner spore coat {{PubMed|19933362}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P23261 P23261]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40530]

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

=== Additional information===

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cotF_4167110_4167592_1 cotF] {{PubMed|22383849}}

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

* '''Regulation:'''
** expressed late during sporulation in the mother cell ([[SigK]], [[SpoIIID]]) {{PubMed|15699190,15383836}}

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1S106 ( ''cotF''::''cat''), {{PubMed|1708381}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S106&Search=1S106 BGSC]
** 1S107 ( ''cotF''::''cat''), {{PubMed|1708381}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S107&Search=1S107 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>1708381, 19933362, 15699190,15383836</pubmed>

[[Category:Protein-coding genes]]

YybS

2012-12-05T13:40:53Z

Awiechert:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yybS''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40520 yybS]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 9.946
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 927 bp, 309 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gdpP]]'', ''[[yyzH]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16089]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yybS_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=yybS_4165659_4166588_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yybS_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40520

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10011]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37485 P37485]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40520]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yybS]]-[[gdpP]]-[[rplI]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yybST-rplI.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yybS_4165659_4166588_-1 yybS] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** The mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed|20525796}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>20525796 </pubmed>
[[Category:Protein-coding genes]]

HtrC

2012-12-05T13:36:56Z

Awiechert:

* '''Description:''' similar to serine protease HtrA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yyxA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yycK ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40360 yyxA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 5.315
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1200 bp, 400 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yyzO]]'', ''[[walJ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16073]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yyxA_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=htrC_4147567_4148769_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yyxA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40360

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11054]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' peptidase S1B family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39668 P39668]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40360]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[walR]]-[[walK]]-[[yycH]]-[[yycI]]-[[walJ]]-[[yyxA]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9829949 PubMed]

''[[yyxA]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9829949 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=htrC_4147567_4148769_-1 yyxA] {{PubMed|22383849}}

* '''Sigma factor:''' for ''[[yyxA]]'': [[SigG]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9829949 PubMed]

* '''Regulation:''' expressed during vegetative growth, repressed during stationary phase [http://www.ncbi.nlm.nih.gov/sites/entrez/9829949 PubMed]

''yyxA'' transcript expressed during sporulation [http://www.ncbi.nlm.nih.gov/sites/entrez/9829949 PubMed]

* '''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>9829949,21630458, </pubmed>
[[Category:Protein-coding genes]]

RocR

2012-12-05T13:34:15Z

Awiechert:

* '''Description:''' [[transcription factors activating transcription at SigL-dependent promoters |transcriptional activator]] of arginine utilization operons 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rocR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[transcription factors activating transcription at SigL-dependent promoters |transcriptional activator]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional activator of arginine utilization operons
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40350 rocR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/RocR RocR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52.6 kDa, 6.08
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1383 bp, 461 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocD]]'', ''[[yyzO]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16072]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:rocR_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=rocR_4145747_4147132_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:rocR_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
* {{SubtiWiki category|[[utilization of amino acids]]}},
{{SubtiWiki category|[[transcription factors and their control]]}}
* see also: [[glutamate metabolism]]

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

=The [[RocR regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40350

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10723]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription activation at [[SigL]]-dependent promoters of ''[[rocA|rocABC]]'', ''[[rocD|rocDEF]]'', and ''[[rocG]]''

* '''Protein family:''' [[SigL | Sigma-54]] interacting transcription activator

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
**[[SigL | Sigma-54]] factor interaction domain (143–372)
**2x nucleotid-binding domain (171–178),(233–242)
**HTH motif (434–453)

* '''Modification:'''

* '''Cofactor(s):''' ornithine or citrulline are required for RocR-dependent transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/9194709 PubMed]

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

* '''[[SubtInteract|Interactions]]:'''
** RocR-[[SigL]]

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P38022 P38022]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40350]

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rocR_4145747_4147132_1 rocR] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]

* '''Regulation:''' autoregulation by [[RocR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]

* '''Regulatory mechanism:''' autorepression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' QB5533 (aphA3), from [[Michel Debarbouille]], available in [[Stülke]] lab
** 1A911 ( ''rocR''::''kan''), {{PubMed|16585774}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A911&Search=1A911 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]

=Your additional remarks=

=References=

<pubmed>12634342 8113162,9194709 21965396 </pubmed>

[[Category:Protein-coding genes]]

YycQ

2012-12-05T13:33:19Z

Awiechert:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yycQ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40260 yycQ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 10.678
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 246 bp, 82 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yyzG]]'', ''[[yycP]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16063]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yycQ_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=yycQ_4137362_4137610_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yycQ_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40260

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11470]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45605 Q45605]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40260]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yycO]]-[[yycP]]-[[yycQ]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yycOPQ.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yycQ_4137362_4137610_-1 yycQ] {{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]]

YycR

2012-12-05T13:32:56Z

Awiechert:

* '''Description:''' similar to formaldehyde dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yycR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40250 yycR]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 5.787
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1224 bp, 408 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yycS]]'', ''[[yyzG]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16062]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yycR_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=yycR_4135798_4137024_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yycR_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40250

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11471]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45604 Q45604]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40250]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yycR_4135798_4137024_-1 yycR] {{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]]

YycS

2012-12-05T13:31:44Z

Awiechert:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yycS''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40240 yycS]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 15 kDa, 4.508
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 411 bp, 137 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yyzF]]'', ''[[yycR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16061]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yycS_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=yycS_4135351_4135764_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yycS_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40240

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11472]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45603 Q45603]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40240]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yycS_4135351_4135764_1 yycS] {{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]]

YydA

2012-12-05T13:31:11Z

Awiechert:

* '''Description:''' similar to pseudouridine methyltransferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yydA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || similar to pseudouridine methyltransferase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || may be involved in maturation of 23S rRNA
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40230 yydA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 9.314
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 477 bp, 159 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yydB]]'', ''[[yyzF]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16060]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yydA_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=yydA_4134436_4134915_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yydA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40230

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11474]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methylpseudouridine (according to Swiss-Prot)

* '''Protein family:''' RNA methyltransferase rlmH 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:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1TO0 1TO0]

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45601 Q45601]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40230]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yydA_4134436_4134915_-1 yydA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''
** [[DnaA]]: transcription repression {{PubMed|17932079}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|20817755}}
<pubmed> 17932079 18755836 18755835 </pubmed>
[[Category:Protein-coding genes]]

YydJ

2012-12-05T12:04:23Z

Awiechert:

* '''Description:''' [[ABC transporter]] (resistance), permease, export of [[YydF]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yydJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[ABC transporter]] (resistance), permease
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[LiaR]]-[[LiaS]] activity
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40140 yydJ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/YydJ YydJ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 9.469
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 720 bp, 240 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yyzN]]'', ''[[yydI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16051]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yydJ_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=yydJ_4124220_4124942_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yydJ_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ABC transporters]]}},
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40140

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11483]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[YydI]]-([[YydJ]]-[[YydH]]) {{PubMed|10092453}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45592 Q45592]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40140]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yydF]]-[[yydG]]-[[yydH]]-[[yydI]]-[[yydJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yydJ_4124220_4124942_-1 yydJ] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]

* '''Regulation:''' activated after transition to stationary phase([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
** repressed by [[Rok]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15743949 PubMed]
** strongly repressed in response to glucose starvation in M9 medium {{PubMed|23033921}}

* '''Regulatory mechanism:'''
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
** [[Rok]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15743949 PubMed]

* '''Additional information:'''
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}}

=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> 23106164</pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|23033921}}
<big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J'' </big>
<big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big>
<big>Mol Microbiol. 2011 81(6): 1459-1473. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21815947 PubMed:21815947]
<pubmed>10092453,,17921301,15743949,17921301, </pubmed>

[[Category:Protein-coding genes]]

YydK

2012-12-05T12:00:09Z

Awiechert:

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yydK''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator ([[GntR family]])
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40130 yydK]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 5.194
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 708 bp, 236 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yyzE]]'', ''[[yyzN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16050]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yydK_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=yydK_4123193_4123903_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yydK_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40130

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11484]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

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

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45591 Q45591]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40130]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yydK_4123193_4123903_1 yydK] {{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]]

HutP

2012-12-05T11:56:19Z

Awiechert:

* '''Description:''' transcriptional antiterminator of the ''[[hutH|hut]]'' operon 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hutP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hutP1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional antiterminator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of histidine utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU39340 hutP]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/histidine.html His]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 6.057
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 453 bp, 151 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxzL]]'', ''[[hutH]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15970]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:hutP_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=hutP_4041483_4041938_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:hutP_expression.png|500px]]
|-
|}

__TOC__
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of amino acids]]}},
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[RNA binding regulators]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[CodY regulon]]}}
=The [[HutP regulon]]: ''[[hutH]]-[[hutU]]-[[hutI]]-[[hutG]]-[[hutM]]''=
=The gene=

=== Basic information ===

* '''Locus tag:''' BSU39340

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10666]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3BOY 3BOY] (complex bound to the hut mRNA), [http://www.rcsb.org/pdb/explore.do?structureId=1WPT 1WPT]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P10943 P10943]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU39340]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[hutP]]-[[hutH]]-[[hutU]]-[[hutI]]-[[hutG]]-[[hutM]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10746760 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hutP_4041483_4041938_1 hutP] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|8071225}}

* '''Regulation:'''
** repressed by glucose ([[CcpA]]) {{PubMed|8071225}}
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8682780 PubMed]

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression {{PubMed|8071225}}
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/8682780 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>17395359 16427271 22933560 </pubmed>

==Original publications==
<pubmed>12903241,8682780, 8071225 10217782 18083814 22900538 </pubmed>

[[Category:Protein-coding genes]]

Abn2

2012-12-05T11:55:41Z

Awiechert:

* '''Description:''' endo-1,5-alpha-L-arabinosidase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''abn2''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || endo-1,5-alpha-L-arabinosidase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU39330 abn2]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 7.371
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiB]]'', ''[[yxzL]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yxiA_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yxiA_protein.txt Protein sequence]'''
|-
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
|-
|colspan="2" | '''Genetic context''' [[Image:yxiA_context.gif]]
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of specific carbon sources]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11130]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' glycosyl hydrolase 43 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' With linear-alpha-1,5-l-arabinan as the preferred substrate, the enzyme exhibited an apparent K(m) of 2.0 mg ml(-1) and V(max) of 0.25 mmol min(-1) mg(-1) at pH 7.0 and 50°C. [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]

* '''Domains:'''

* '''Modification:'''

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

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

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

* '''[[Localization]]:''' extracellular (signal peptide) {{PubMed|18957862,18408032}}

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=2X8F 2X8F] {{PubMed|20883454}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42293 P42293]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU39330]

* '''E.C. number:''' 3.2.1.99

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''abn2'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]

* '''[[Sigma factor]]:''' [[SigA]], [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]

* '''Regulation:''' repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], expression is stimulated by arabinose and pectin and repressed by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, unknown [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Isabel de Sa-Nogueira]], Lisboa, Portugal [http://www.itqb.unl.pt/research/biology/microbial-genetics homepage]

=Your additional remarks=

=References=

<pubmed>18607095,,18408032,18957862 12850135 18408032 </pubmed>
'''Additional references:''' {{PubMed|20883454}}
[[Category:Protein-coding genes]]

NupG

2012-12-05T11:52:21Z

Awiechert:

* '''Description:''' purine nucleoside transporter 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''nupG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxjA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || purine nucleoside transporter
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || purine uptake
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU39020 nupG]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 7.757
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1191 bp, 397 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxjB]]'', ''[[yxiT/1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15928]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yxjA_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=yxjA_4005752_4006945_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:nupG_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transporters/ other]]}},
{{SubtiWiki category|[[biosynthesis/ acquisition of nucleotides]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU39020

===Phenotypes of a mutant ===
* a ''[[nupN]] [[nupG]]'' double mutant is unable to utilize externally provided guanosine {{PubMed|21926227}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11150]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' SLC28A transporter 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 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42312 P42312]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU39020]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''nupG''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yxjA_4005752_4006945_1 nupG] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''
** expression activated by glucose (4.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** repressed by hypoxanthine and guanine, [[PurR]]-independent, [[G-box]][http://www.ncbi.nlm.nih.gov/sites/entrez/12923093 PubMed]

* '''Regulatory mechanism:''' [[G-box]]: transcriptional termination/ antitermination [[riboswitch]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12923093 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>12923093,,12850135 18763711 12923093, 21926227</pubmed>

[[Category:Protein-coding genes]]

DltA

2012-12-05T11:25:42Z

Awiechert:

* '''Description:''' D-alanyl-D-alanine carrier protein ligase, alanylation of teichoic acid provides some resistance against positively charged antimicrobial peptides 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''dltA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-5r, dae ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || D-alanyl-D-alanine carrier protein ligase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of teichoic acid
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU38500 dltA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 55 kDa, 4.929
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1509 bp, 503 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywzH]]'', ''[[dltB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15876]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:dltA_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=dltA_3952275_3953786_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:dltA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

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

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[SigD regulon]]}},
{{SubtiWiki regulon|[[SigM regulon]]}},
{{SubtiWiki regulon|[[SigX regulon]]}},
{{SubtiWiki regulon|[[Spo0A regulon]]}},
{{SubtiWiki regulon|[[stringent response]]}},
{{SubtiWiki regulon|[[YvrHb regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38500

===Phenotypes of a mutant ===
** increased sensitivity to lysozyme {{PubMed|21856855}}
=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10551]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate) (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3E7X 3E7X]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39581 P39581]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38500]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.1.1.13 6.1.1.13]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[dltA]]-[[dltB]]-[[dltC]]-[[dltD]]-[[dltE]]'' {{PubMed|7797557}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dltA_3952275_3953786_1 dltA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigD]] {{PubMed|7797557}}, [[SigM]] {{PubMed|18179421}}, [[SigX]] {{PubMed|14762009}}

* '''Regulation:'''
** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed|11948165}}
** repressed under conditions that trigger sporulation ([[Spo0A]]) {{PubMed|7797557}}
** expression is reduced in a [[SigV]] mutant {{PubMed|21926231}}

* '''Regulatory mechanism:'''
** activated by [[YvrHb]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
** [[Spo0A]]: transcription repression {{PubMed|7797557}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|21856855,21926231}}
<pubmed>14762009,15955059,18784082,,7797557, 19324056, 16306698 </pubmed>

[[Category:Protein-coding genes]]

MenA

2012-12-05T11:24:46Z

Awiechert:

* '''Description:''' probable 1,4-dihydroxy-2-naphthoate octaprenyltransferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''menA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywaB, ipa-6d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || probable 1,4-dihydroxy-2-naphthoate octaprenyltransferase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of menaquinone
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU38490 menA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/menaquinone.html Menaquinone]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 9.32
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 933 bp, 311 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywaC]]'', ''[[ywzH]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15875]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:menA_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=menA_3950726_3951661_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:menA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38490

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10552]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' menA 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 ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39582 P39582]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38490]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=menA_3950726_3951661_-1 menA] {{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> 9353933</pubmed>
[[Category:Protein-coding genes]]

PdxK

2012-12-05T11:22:51Z

Awiechert:

* '''Description:''' pyridoxine, pyridoxal, and pyridoxamine kinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pdxK''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywdB, ipa-52r, thiD''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || pyridoxine, pyridoxal, and pyridoxamine kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of pyridoxal phosphate
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU38020 pdxK]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.922
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 813 bp, 271 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywzG]]'', ''[[ywdA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13028]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:thiD_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=pdxK_3900963_3901778_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:pdxK_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38020

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10598]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2IB5 2IB5]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39610 P39610]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38020]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.4.7 2.7.4.7]

=== 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:''' ''pdxK'' {{PubMed|3100393}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdxK_3900963_3901778_1 pdxK] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''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]

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17012797,14973012,3100393 , </pubmed>

[[Category:Protein-coding genes]]

CsbD

2012-12-05T11:19:14Z

Awiechert:

* '''Description:''' general stress protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''csbD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywmG ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || survival of salt stress and at low temperatures
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU36670 csbD]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 9.689
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 186 bp, 62 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywzF]]'', ''[[ywmF]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15684]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:csbD_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=csbD_3770104_3770292_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:csbD_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36670

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12478]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0337 (csbD) family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P70964 P70964]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36670]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[ywmF]]-[[csbD]]'' {{PubMed|10376822}}
** ''[[csbD]]'' {{PubMed|10376822}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=csbD_3770104_3770292_-1 csbD] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[csbD]]'': [[SigB]] {{PubMed|10376822,15805528}}

* '''Regulation:'''
** ''csbD'': induced by stress ([[SigB]]) {{PubMed|10376822,15805528}}

* '''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>10376822,,15805528, </pubmed>

[[Category:Protein-coding genes]]

UreA

2012-12-05T11:18:12Z

Awiechert:

* '''Description:''' urease (gamma subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ureA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || urease (gamma subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of urea as alternative nitrogen source
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU36660 ureA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/UreA UreA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/purines_catabolism.html Purine catabolism], [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Alternative nitrogen sources]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 4.98
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 315 bp, 105 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ureB]]'', ''[[ywzE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15683]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ureA_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=ureA_3768791_3769108_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ureA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of nitrogen sources other than amino acids]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[GlnR regulon]]}},
{{SubtiWiki regulon|[[PucR regulon]]}},
{{SubtiWiki regulon|[[SigH regulon]]}},
{{SubtiWiki regulon|[[TnrA regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36660

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11981]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Urea + H2O = CO2 + 2 NH3 (according to Swiss-Prot)

* '''Protein family:''' urease gamma subunit 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]]:'''
** [[UreA]]-[[UreB]]-[[UreC]]

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2FVH 2FVH] (from ''Mycobacterium tuberculosis'', 57% identity, 62% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P75030 P75030]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36660]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.1.5 3.5.1.5]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[ureA]]-[[ureB]]-[[ureC]]'' {{PubMed|9287005}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ureA_3768791_3769108_-1 ureA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|9287005}}, [[SigH]] {{PubMed|9287005}}

* '''Regulation:'''
** induced by nitrogen limitation ([[GlnR]], [[TnrA]]) {{PubMed|9287005}}
** induced in the presence of purine nucleotides (inducer: allantoin) ([[PucR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12374841 PubMed]
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) {{PubMed|9287005,12618455}}

* '''Regulatory mechanism:'''
** [[GlnR]]: transcription repression {{PubMed|9287005}}
** [[TnrA]]: transcription activation {{PubMed|9287005}}
** [[PucR]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12374841 PubMed]
** [[CodY]]: transcription repression {{PubMed|9287005,12618455}}

* '''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>12374841,18083814,12618455,9287005,9287005,12374841,9287005,1670935, </pubmed>

[[Category:Protein-coding genes]]

YwqB

2012-12-05T11:17:20Z

Awiechert:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywqB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU36270 ywqB]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 63 kDa, 7.616
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1608 bp, 536 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywzD]]'', ''[[ywqA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15644]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ywqB_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=ywqB_3733852_3735462_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ywqB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36270

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12506]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96714 P96714]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36270]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywqB_3733852_3735462_1 ywqB] {{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]]

TkmA

2012-12-05T11:16:50Z

Awiechert:

* '''Description:''' transmembrane modulator of [[PtkA]] activity, activates [[PtkA]] autophosphorylation and substrate phosphorylation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tkmA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || modulator of [[PtkA]] activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of protein tyrosine phosphorylation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU36260 tkmA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/TkmA TkmA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 4.61
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 744 bp, 248 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptkA]]'', ''[[ywzD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15643]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ywqC_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=ywqC_3732525_3733271_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tkmA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36260

===Phenotypes of a mutant ===
the mutant exhibits a defect in [[biofilm formation]] {{PubMed|20815827}}
=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12507]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transmembrane activation of [[PtkA]] protein tyrosine kinase activity

* '''Protein family:''' cpsC/capA family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96715 P96715]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36260]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[tkmA]]-[[ptkA]]-[[ptpZ]]-[[ugd]]'' {{PubMed|20815827,12970183}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywqC_3732525_3733271_-1 tkmA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|20815827}}

* '''Regulation:'''

* '''Regulatory mechanism:'''
** [[DegU]]-P: transcription repression {{PubMed|20815827}}
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|20817675}}
<pubmed>12970183, 20815827 </pubmed>

[[Category:Protein-coding genes]]

TagH

2012-12-05T11:15:49Z

Awiechert:

* '''Description:''' [[ABC transporter]] for teichoic acid translocation (ATP-binding protein) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tagH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[ABC transporter]] for teichoic acid translocation (ATP-binding protein)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of teichoic acid
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU35700 tagH]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/TagH TagH]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 59 kDa, 9.447
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1581 bp, 527 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvzE]]'', ''[[tagG]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15587]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:tagH_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=tagH_3673564_3675147_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tagH_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35700

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11191]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + H2O + teichoic acid(In) = ADP + phosphate + teichoic acid(Out) (according to Swiss-Prot)

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[TagG]]-[[TagH]] {{PubMed|10092453}}

* '''[[Localization]]:''' membrane associated (via [[TagG]]) {{PubMed|10092453}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42954 P42954]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35700]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.6.3.40 3.6.3.40]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tagH_3673564_3675147_-1 tagH] {{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>18156271,10092453,7565096,21280653 , </pubmed>

[[Category:Protein-coding genes]]

GgaA

2012-12-05T11:14:40Z

Awiechert:

* '''Description:''' galactosamine-containing minor teichoic acid biosynthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ggaA''
|-
|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''' || biosynthesis of teichoic acid
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU35690 ggaA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 9.055
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ggaB]]'', ''[[yvzI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15586]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ggaA_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=ggaA_3670035_3671375_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ggaA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35690

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11367]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' glycosyltransferase 2 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-85 {{PubMed|22517742}}

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P46917 P46917]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35690]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ggaA]]-[[ggaB]]'' {{PubMed|16735734}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ggaA_3670035_3671375_-1 ggaA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|16735734}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** An [[ncRNA|antisense RNA]] is predicted for''[[ggaA]]'' {{PubMed|20525796}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>16735734,20525796, 22517742</pubmed>

[[Category:Protein-coding genes]]

GgaB

2012-12-05T11:13:47Z

Awiechert:

* '''Description:''' galactosamine-containing minor teichoic acid biosynthesis, membrane protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ggaB''
|-
|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''' || biosynthesis of teichoic acid
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU35680 ggaB]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 106 kDa, 9.482
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2700 bp, 900 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvzH]]'', ''[[ggaA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15585]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ggaB_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=ggaB_3667209_3669911_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ggaB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35680

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11192]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' glycosyltransferase 2 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P46918 P46918]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35680]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ggaA]]-[[ggaB]]'' {{PubMed|16735734}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ggaB_3667209_3669911_-1 ggaB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|16735734}}

* '''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>16735734,, </pubmed>

[[Category:Protein-coding genes]]

GtaB

2012-12-05T11:12:38Z

Awiechert:

* '''Description:''' UTP-glucose-1-phosphate uridylyltransferase, general stress protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gtaB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || UTP-glucose-1-phosphate uridylyltransferase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of teichoic acid
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU35670 gtaB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 4.913
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 876 bp, 292 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mnaA]]'', ''[[yvzH]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15584]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:gtaB_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=gtaB_3665629_3666507_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:gtaB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall synthesis]]}},
{{SubtiWiki category|[[lipid metabolism/ other]]}},
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35670

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10402]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' UTP + alpha-D-glucose 1-phosphate = diphosphate + UDP-glucose (according to Swiss-Prot)

* '''Protein family:''' UDPGP type 2 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-76 {{PubMed|22517742}}
** phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?pdbId=2E3D 2E3D] (from ''E. coli'', 44% identity, 61% similarity) {{PubMed|17322528}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q05852 Q05852]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35670]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.9 2.7.7.9]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''gtaB'' {{PubMed|8320212}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gtaB_3665629_3666507_1 gtaB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|8320212}}, [[SigB]] {{PubMed|8320212,11544224}}

* '''Regulation:'''
** induced by stress ([[SigB]]) {{PubMed|8320212,11544224}}

* '''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>8320212,2846750,22517742,16493705 11544224, </pubmed>

[[Category:Protein-coding genes]]

CtpB

2012-12-05T11:04:38Z

Awiechert:

* '''Description:''' carboxy-terminal processing serine protease, cleaves [[SpoIVFA]], this results in processing of pro-[[SigK]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ctpB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvjB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || carboxy-terminal processing serine protease, cleaves SpoIVFA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[SigK]] activation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU35240 ctpB]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 8.641
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1440 bp, 480 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[swrAA/2]]'', ''[[ftsX]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15541]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yvjB_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=ctpB_3622356_3623798_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ctpB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[proteolysis]]}},
{{SubtiWiki category|[[sigma factors and their control]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35240

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14110]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O35002 O35002]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35240]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ctpB_3622356_3623798_-1 ctpB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigE]] {{PubMed|15699190}}, [[SigG]] {{PubMed|15699190,16497325}}

* '''Regulation:''' expressed during sporulation ([[SigE]], [[SigG]]) {{PubMed|15699190,16497325}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1S129 ( ''ctpB''::''tet''), {{PubMed|14526016}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S129&Search=1S129 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>14526016, 17557826, 16818230 15699190,16497325</pubmed>

[[Category:Protein-coding genes]]

YvcN

2012-12-05T11:03:12Z

Awiechert:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yvcN''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU34730 yvcN]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.582
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvzJ]]'', ''[[crh]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15478]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yvcN_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=yvcN_3568527_3569291_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yvcN_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34730

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12404]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' arylamine N-acetyltransferase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O06977 O06977]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34730]

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

=== Additional information===
The gene is annotated in KEGG as an ortholog of EC 2.3.1.5 and is marked in Swiss-Prot as “uncharacterized acetyltransferase” (EC 2.3.1.-). No EC annotation is available in MetaCyc.No literature/ experimental evidence supporting the annotation is available. {{PubMed|19935659}}

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvcN_3568527_3569291_-1 yvcN] {{PubMed|22383849}}

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

* '''Regulation:''' very weak stimuation of expression by citrate and succinate [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>9237995 16272399, </pubmed>

[[Category:Protein-coding genes]]

PsdR

2012-12-05T11:02:13Z

Awiechert:

* '''Description:''' [[two-component systems|two-component]] response regulator, induction of ''[[psdA]]-[[psdB]]'' in response to lipid II-binding lantibiotics, such as nisin and gallidermin 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''psdR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvcP ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[two-component systems|two-component]] response regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance against toxic peptides
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU34720 psdR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/PsdR PsdR]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 4.676
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 711 bp, 237 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[psdS]]'', ''[[yvzJ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15477]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yvcP_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=yvcP_3567422_3568135_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:psdR_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

= This gene is a member of the following [[regulons]] =
=The [[PsdR regulon]]: ''[[psdA]]-[[psdB]]''=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34720

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12405]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' OmpR family of two-component response regulators

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated by [[PsdS]] on an Asp residue

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

* '''Effectors of protein activity:''' phosphorylation likely affects DNA-binding activity

* '''[[SubtInteract|Interactions]]:'''
** [[PsdR]]-[[PsdS]]

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O06978 O06978]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34720]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[psdR]]-[[psdS]]-[[psdA]]-[[psdB]]'' {{PubMed|21078927}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvcP_3567422_3568135_-1 psdR] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|21078927}}

* '''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=
'''Additional publications:''' {{PubMed|21078927}}
<pubmed>10094672,18394148,14651641 21283517</pubmed>

[[Category:Protein-coding genes]]

YusN

2012-12-05T10:56:28Z

Awiechert:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yusN''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32860 yusN]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 4.495
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 330 bp, 110 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuzM]]'', ''[[mdtR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15275]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yusN_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=yusN_3374001_3374333_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yusN_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU32860

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14026]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32180 O32180]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32860]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yusN_3374001_3374333_1 yusN] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigG]] {{PubMed|16497325}}

* '''Regulation:''' expressed during sporulation in the forespore ([[SigG]]) {{PubMed|16497325}}

* '''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>16497325 </pubmed>
[[Category:Protein-coding genes]]

FadM

2012-12-05T10:55:17Z

Awiechert:

* '''Description:''' fatty acid degradation, similar to proline dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fadM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yusM''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid degradation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32850 fadM]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_deg.html Fatty acid degradation]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 9.377
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 906 bp, 302 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuzL]]'', ''[[yuzM]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15274]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yusM_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=fadM_3372740_3373648_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:fadM_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of lipids]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU32850

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14025]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32179 O32179]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32850]

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

=== Additional information===

=Expression and regulation=
* '''Operon:'''
** ''[[fadM]]-[[fadN]]-[[fadA]]-[[fadE]]'' {{PubMed|17189250}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fadM_3372740_3373648_-1 fadM] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''
** ''[[fadM]]'': induced by long-chain fatty acids ([[FadR]]) {{PubMed|17189250}}

* '''Regulatory mechanism:'''
** [[FadR]]: transcription repression {{PubMed|17189250}}
** [[SdpR]]: transcription activation {{PubMed|12817086}}

* '''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>17189250,,12817086, </pubmed>

[[Category:Protein-coding genes]]

FadM

2012-12-05T10:52:44Z

Awiechert:

* '''Description:''' fatty acid degradation, similar to proline dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fadM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yusM''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid degradation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32850 fadM]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_deg.html Fatty acid degradation]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 9.377
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 906 bp, 302 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuzL]]'', ''[[yusN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15274]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yusM_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=fadM_3372740_3373648_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:fadM_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of lipids]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU32850

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14025]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32179 O32179]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32850]

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

=== Additional information===

=Expression and regulation=
* '''Operon:'''
** ''[[fadM]]-[[fadN]]-[[fadA]]-[[fadE]]'' {{PubMed|17189250}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fadM_3372740_3373648_-1 fadM] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''
** ''[[fadM]]'': induced by long-chain fatty acids ([[FadR]]) {{PubMed|17189250}}

* '''Regulatory mechanism:'''
** [[FadR]]: transcription repression {{PubMed|17189250}}
** [[SdpR]]: transcription activation {{PubMed|12817086}}

* '''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>17189250,,12817086, </pubmed>

[[Category:Protein-coding genes]]

FadN

2012-12-05T10:19:03Z

Awiechert:

* '''Description:''' 3-hydroxyacyl-CoA dehydrogenase (acetoacetyl-CoA) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fadN''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yusL''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 3-hydroxyacyl-CoA dehydrogenase (acetoacetyl-CoA)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid degradation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32840 fadN]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_deg.html Fatty acid degradation]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 89 kDa, 6.53
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2445 bp, 815 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fadA]]'', ''[[yuzL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15273]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yusL_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=fadN_3370025_3372472_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:fadN_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of lipids]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU32840

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14024]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH (according to Swiss-Prot)

* '''Protein family:''' 3-hydroxyacyl-CoA dehydrogenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32178 O32178]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32840]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.35 1.1.1.35]

=== Additional information===

=Expression and regulation=
* '''Operon:'''
** ''[[fadM]]-[[fadN]]-[[fadA]]-[[fadE]]'' {{PubMed|17189250}}
** ''[[fadN]]-[[fadA]]-[[fadE]]'' {{PubMed|17189250}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fadN_3370025_3372472_-1 fadN] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[fadN]]'': [[SigA]] {{PubMed|17189250}}

* '''Regulation:'''
** ''[[fadN]]'': induced by long-chain fatty acids ([[FadR]]) {{PubMed|17189250}}
** ''[[fadN]]'': subject to carbon catabolite repression ([[CcpA]]-[[PtsH|HPr(Ser-P)]] {{PubMed|12850135,21398533}}
** strongly induced in response to glucose starvation in M9 medium {{PubMed|23033921}}

* '''Regulatory mechanism:'''
** [[FadR]]: transcription repression {{PubMed|17189250}}
** [[SdpR]]: transcription activation {{PubMed|12817086}}
** [[CcpA]]-[[PtsH|HPr(Ser-P)]]: transcription repression {{PubMed|21398533}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|23033921,21398533}}
<pubmed>12817086,12850135 17189250, 17919287</pubmed>

[[Category:Protein-coding genes]]

SufB

2012-12-05T09:54:21Z

Awiechert:

* '''Description:''' synthesis of Fe-S-clusters 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sufB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' yurU''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of iron-sulfur clusters
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32670 sufB]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 4.958
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1395 bp, 465 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuzN]]'', ''[[sufU]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15256]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yurU_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=sufB_3355593_3356990_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sufB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU32670

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14007]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32162 O32162]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32670]

* '''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:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sufB_3355593_3356990_-1 sufB] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''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]

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 17981983 20097860 </pubmed>
[[Category:Protein-coding genes]]

GlxB

2012-12-05T09:53:18Z

Awiechert:

* '''Description:''' similar to methylglyoxalase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yurT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32660 yurT]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 4.609
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 381 bp, 127 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yurS]]'', ''[[yuzN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15255]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yurT_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=yurT_3354551_3354934_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yurT_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU32660

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14006]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32161 O32161]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32660]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yurT_3354551_3354934_-1 yurT] {{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]]

PucE

2012-12-05T09:42:54Z

Awiechert:

* '''Description:''' xanthine dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pucE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yurB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || xanthine dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || purine utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32470 pucE]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/purines_catabolism.html Purine catabolism], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 18 kDa, 6.127
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 519 bp, 173 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuzJ]]'', ''[[pucD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15237]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pucE_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=pucE_3335751_3336272_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:pucE_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU32470

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13988]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Xanthine + NAD+ + H2O = urate + NADH (according to Swiss-Prot)

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JRO 1JRO] (from ''Rhodobacter capsulatus'', 43% identity, 58% similarity) {{PubMed|11796116}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32143 O32143]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32470]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[pucA]]-[[pucB]]-[[pucC]]-[[pucD]]-[[pucE]]'' {{PubMed|12823818}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pucE_3335751_3336272_-1 pucE] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|12029039}}

* '''Regulation:'''
** induced in the presence of purine nucleotides (effector: allantoin) ([[PucR]]) {{PubMed|12029039}}

* '''Regulatory mechanism:'''
** [[PucR]]: transcription activaton {{PubMed|12029039}}

* '''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>11344136,,12029039,12823818, </pubmed>

[[Category:Protein-coding genes]]

PucM

2012-12-05T09:42:06Z

Awiechert:

* '''Description:''' uricase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pucM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yunM ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || uricase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || purine utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32460 pucM]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/purines_catabolism.html Purine catabolism], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 5.082
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 363 bp, 121 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pucL]]'', ''[[yuzJ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15236]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pucM_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=pucM_3334646_3334990_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:pucM_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU32460

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13987]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 5-hydroxyisourate + H2O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate (according to Swiss-Prot)

* '''Protein family:''' 5-hydroxyisourate hydrolase subfamily (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2H0E 2H0E]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32142 O32142]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32460]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.2.17 3.5.2.17]

=== Additional information===

=Expression and regulation=
* '''Operon:'''
** ''[[pucR]]-[[pucJ]]-[[pucK]]-[[pucL]]-[[pucM]]'' {{PubMed|12823818}}
** ''[[pucJ]]-[[pucK]]-[[pucL]]-[[pucM]]'' {{PubMed|12029039}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pucM_3334646_3334990_1 pucM] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[pucJ]]'': [[SigA]] {{PubMed|12029039}}

* '''Regulation:'''
** expressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) {{PubMed|12823818}}
** induced in the presence of purine nucleotides (inducer: allantoin) ([[PucR]]) {{PubMed|12029039}}

* '''Regulatory mechanism:'''
** [[TnrA]]: transcription activation {{PubMed|12823818}}
** [[PucR]]: transcription activation {{PubMed|12029039}}

* '''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>11344136,12823818,12029039,16782815 ,20168977 </pubmed>

[[Category:Protein-coding genes]]

DhbF

2012-12-05T09:38:18Z

Awiechert:

* '''Description:''' involved in 2,3-dihydroxybenzoate biosynthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''dhbF''
|-
|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''' || biosynthesis of the siderophore bacillibactin
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU31960 dhbF]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 263 kDa, 4.737
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 7134 bp, 2378 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybdZ]]'', ''[[dhbB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15186]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:dhbF_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=dhbF_3280519_3287655_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:dhbF_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[acquisition of iron]]}},
{{SubtiWiki category|[[iron metabolism]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU31960

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11243]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' ATP-dependent AMP-binding enzyme family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-988 AND Ser-996 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

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

* '''[[Localization]]:'''
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P45745 P45745]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31960]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[dhbA]]-[[dhbC]]-[[dhbE]]-[[dhbB]]-[[dhbF]]'' {{PubMed|8921902}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dhbF_3280519_3287655_-1 dhbF] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|8550523}}

* '''Regulation:'''
** induced by iron starvation ([[Fur]]) {{PubMed|12354229}}

* '''Regulatory mechanism:'''
** [[Fur]]: transcription repression {{PubMed|12354229}}
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|20817675}}
<big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J'' </big>
<big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big>
<big>Mol Microbiol. 2011 81(6): 1459-1473. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21815947 PubMed:21815947]
<pubmed>11112781,11790741,12354229,18763711 17218307,8921902 8550523 </pubmed>

[[Category:Protein-coding genes]]

YugP

2012-12-05T09:30:11Z

Awiechert:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yugP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU31310 yugP]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 9.164
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 675 bp, 225 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yugS]]'', ''[[yuzI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15120]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yugP_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=yugP_3217496_3218173_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yugP_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU31310

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12370]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O05248 O05248]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31310]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yugP_3217496_3218173_-1 yugP] {{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]]

YugU

2012-12-05T09:29:31Z

Awiechert:

* '''Description:''' general stress protein, survival of ethanol stress 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yugU''
|-
|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''' || survival of ethanol stress
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU31280 yugU]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 6.59
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 426 bp, 142 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuzH]]'', ''[[yugT]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15106]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yugU_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=yugU_3213854_3214252_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yugU_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU31280

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12373]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0047 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:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O05243 O05243]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31280]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yugU_3213854_3214252_-1 yugU] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]

* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]

* '''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>15805528, </pubmed>

[[Category:Protein-coding genes]]

Tgl

2012-12-05T09:28:12Z

Awiechert:

* '''Description:''' spore associated transglutaminase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tgl''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yuxF, yugV ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || spore associated transglutaminase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || introduction of crosslinks in the spore coat protein [[GerQ]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU31270 tgl]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 6.687
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 735 bp, 245 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mcpB]]'', ''[[yuzH]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15105]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:tgl_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=tgl_3212591_3213328_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tgl_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU31270

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10946]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Protein glutamine + alkylamine = protein N(5)-alkylglutamine + NH3 (according to Swiss-Prot), temperature-dependent modification of the coat proteins such as [[GerQ]] (together with [[YabG]]) {{PubMed|16751597}}

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P40746 P40746]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31270]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.2.13 2.3.2.13]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[tgl]]'' {{PubMed|9274030}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tgl_3212591_3213328_1 tgl] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigK]] {{PubMed|15699190,12501297}}

* '''Regulation:'''
** expressed late during sporulation in the mother cell ([[SigK]]) {{PubMed|15699190,12501297}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1S122 ( ''tgl''::''erm''), {{PubMed|15317760}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S122&Search=1S122 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Adriano Henriques]], Lisbon, Portugal [http://www.itqb.unl.pt/research/biology/microbial-development homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed>19797877 </pubmed>
==Original Publications==
<pubmed>18249137,,12501297,16267299,11193401, 16751597 9274030 15699190</pubmed>
[[Category:Protein-coding genes]]

YtkA

2012-12-05T09:26:12Z

Awiechert:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ytkA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yznA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU30660 ytkA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 15 kDa, 4.744
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 435 bp, 145 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytzI]]'', ''[[luxS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15044]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ytkA_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=ytkA_3136938_3137375_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ytkA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU30660

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11027]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P40768 P40768]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30660]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytkA_3136938_3137375_-1 ytkA] {{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]]

Dps

2012-12-05T09:25:43Z

Awiechert:

* '''Description:''' iron storage protein, general stress protein, resistance against ethanol stress and survival at low temperatures 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''dps''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ytkB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || mini-ferritin
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || iron storage
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU30650 dps]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 4.444
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 435 bp, 145 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytkC]]'', ''[[ytzI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15043]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:dps_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=dps_3136238_3136675_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:dps_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[acquisition of iron]]}},
{{SubtiWiki category|[[iron metabolism]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU30650

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12584]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80879 P80879]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30650]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[dps]]'' {{PubMed|9393687}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dps_3136238_3136675_-1 dps] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigB]] {{PubMed|9393687,15805528}}

* '''Regulation:'''
** induced by stress ([[SigB]]) {{PubMed|9393687,15805528}}

* '''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=
==Reviews==
<pubmed>15222465 </pubmed>
==Original publications==
<pubmed>9393687,9013563 ,15805528, </pubmed>

[[Category:Protein-coding genes]]

AcsA

2012-12-05T09:20:52Z

Awiechert:

* '''Description:''' acetyl-CoA synthetase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''acsA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || acetyl-CoA synthetase)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of acetate, fatty acids
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29680 acsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 64 kDa, 5.547
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1716 bp, 572 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytzK]]'', ''[[acuA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14946]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:acsA_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=acsA_3038213_3039931_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:acsA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29680

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10370]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA (according to Swiss-Prot)

* '''Protein family:''' ATP-dependent AMP-binding enzyme family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' acetylated on Lys-549 by [[AcuA]], this results in inactivation [http://www.ncbi.nlm.nih.gov/sites/entrez/18487328 PubMed], deacetylated by [[SrtN]] and [[AcuC]] deacetylates (and thereby activates) [[AcsA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19136592 PubMed]

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39062 P39062]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29680]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.1 6.2.1.1]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[acsA]]'' {{PubMed|7934817}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=acsA_3038213_3039931_-1 acsA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|7913927}}

* '''Regulation:'''
** repressed by glucose (4.5-fold) ([[CcpA]]) {{PubMed|7913927,12850135}}
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) {{PubMed|12618455,18083814}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression {{PubMed|7913927}}
** [[CodY]]: transcription repression {{PubMed|12618455,18083814}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1212 (''acsA''::''kan''), available in [[Stülke]] lab
* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15316652 15491124 15221478 </pubmed>

==Original publications==
<pubmed>7934817,7913927,18083814,17303131,12618455,19136592, 18487328, 12850135 16855235 22900538</pubmed>

[[Category:Protein-coding genes]]

TyrS

2012-12-05T09:19:50Z

Awiechert:

* '''Description:''' tyrosyl-tRNA synthetase (major) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tyrS''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || tyrosyl-tRNA synthetase (major)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29670 tyrS]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 5.213
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1266 bp, 422 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpsD]]'', ''[[ytzK]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14945]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:tyrS_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=tyrS_3036603_3037871_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tyrS_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29670

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10371]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1N53 1N53] (the [[T-box]] antiterminator RNA) [http://www.ncbi.nlm.nih.gov/sites/entrez/12547201 PubMed], [http://www.rcsb.org/pdb/explore.do?structureId=1JH3 1JH3] (C-terminal domain, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/explore.do?structureId=3TS1 3TS1] (complex with tyrosyl adenylate intermediate, Geobacillus stearothermophilus)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P22326 P22326]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29670]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[tyrS]]'' {{PubMed|1735721}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tyrS_3036603_3037871_-1 tyrS] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|1735721}}

* '''Regulation:'''
** induced by tyrosine limitation ([[T-box]]) {{PubMed|19258532}}

* '''Regulatory mechanism:'''
** [[T-box]]: [[RNA switch]], transcriptional antitermination {{PubMed|19258532}}

* '''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>19258532,10546897 </pubmed>
==Original publications==
<pubmed>9098057,12547201,11842119,10943892,9282752,8045882,8348614,1735721,8289305,20110252 , 21333656 </pubmed>

[[Category:Protein-coding genes]]

YsxE

2012-12-05T09:17:10Z

Awiechert:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ysxE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU28100 ysxE]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.635
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1023 bp, 341 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yszA]]'', ''[[spoVID]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14770]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ysxE_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=ysxE_2869964_2870989_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ysxE_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28100

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10347]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37964 P37964]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28100]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[spoVID]]-[[ysxE]]'' {{PubMed|15699190,8449878}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ysxE_2869964_2870989_-1 ysxE] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigE]] {{PubMed|15699190,8449878}}

* '''Regulation:'''
** expressed early during sporulation in the mother cell ([[SigE]]) {{PubMed|15699190,8449878}}
** repressed by casamino acids {{PubMed|12107147}}

* '''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> 15699190,8449878 12107147</pubmed>
[[Category:Protein-coding genes]]

ValS

2012-12-05T09:16:05Z

Awiechert:

* '''Description:''' valyl-tRNA synthetase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''valS''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || valyl-tRNA synthetase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU28090 valS]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging], [http://subtiwiki.uni-goettingen.de/pathways/folate_biosynthesis.html Folate]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 101 kDa, 4.868
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2640 bp, 880 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[folC]]'', ''[[yszA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14769]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:valS_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=valS_2866664_2869306_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:valS_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28090

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10321]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val) (according to Swiss-Prot)

* '''Protein family:''' ValS type 1 subfamily (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1IYW 1IYW] (from ''Thermus thermophilus'', 41% identity, 60% similarity) {{PubMed|12554880}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q05873 Q05873]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28090]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.1.1.9 6.1.1.9]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[valS]]-[[folC]]'' {{PubMed|9098041}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=valS_2866664_2869306_-1 valS] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|9098041}}

* '''Regulation:'''
** induced by valine limitation ([[T-box]]) {{PubMed|9098041,19258532}}

* '''Regulatory mechanism:'''
** [[T-box]]: [[riboswitch]], transcription termination/antitermination {{PubMed|9098041,19258532}}

* '''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>19258532,, </pubmed>
==Original Publications==
<pubmed>,9098041, </pubmed>

[[Category:Protein-coding genes]]

YrbD

2012-12-05T09:13:40Z

Awiechert:

* '''Description:''' sodium/proton-dependent alanine transporter 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yrbD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || sodium/proton-dependent alanine transporter
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of alanine
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU27810 yrbD]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/ala_gly_ser.html Ala, Gly, Ser]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 9.383
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1452 bp, 484 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrzT]]'', ''[[yrbC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14741]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yrbD_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=yrbD_2841611_2843065_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yrbD_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU27810

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13784]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32060 O32060]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU27810]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yrbD_2841611_2843065_1 yrbD] {{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]]

RuvB

2012-12-05T09:12:31Z

Awiechert:

* '''Description:''' Holliday junction DNA helicase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ruvB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || Holliday junction DNA helicase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || recombination
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU27730 ruvB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/RuvB RuvB]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 5.152
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1002 bp, 334 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrzS]]'', ''[[ruvA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14733]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ruvB_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=ruvB_2835150_2836154_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ruvB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU27730

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12669]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' ruvB 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]]:'''
** [[RecU]]-[[RuvB]] {{PubMed|21600217}}
** [[RuvA]]-[[RuvB]]

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32055 O32055]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU27730]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[ruvA]]-[[ruvB]]'' {{PubMed|16267290}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ruvB_2835150_2836154_-1 ruvB] {{PubMed|22383849}}

* '''Sigma factor:'''

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

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1A896 (no resistance), {{PubMed|16020779}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A896&Search=1A896 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>16267290, </pubmed>

[[Category:Protein-coding genes]]

QueA

2012-12-05T09:04:04Z

Awiechert:

* '''Description:''' S-adenosylmethionine tRNA ribosyltransferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''queA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || S-adenosylmethionine tRNA ribosyltransferase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU27720 queA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 38 kDa, 5.047
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1026 bp, 342 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tgt]]'', ''[[yrzS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14732]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:queA_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=queA_2833899_2834927_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:queA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU27720

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12662]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' S-adenosylmethionine + 7-aminomethyl-7-deazaguanosine = methionine + adenine + epoxyqueuosine (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1YY3 1YY3]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32054 O32054]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU27720]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=queA_2833899_2834927_-1 queA] {{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>10739928,,17083917, </pubmed>

[[Category:Protein-coding genes]]

YrrD

2012-12-05T09:03:02Z

Awiechert:

* '''Description:''' forespore-specific sporulation protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yrrD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || forespore-specific sporulation protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU27470 yrrD]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 7.104
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 522 bp, 174 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrzR]]'', ''[[yrrC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14688]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yrrD_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=yrrD_2805704_2806228_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yrrD_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU27470

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13790]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34402 O34402]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU27470]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''yrrD'' {{PubMed|16497325}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yrrD_2805704_2806228_-1 yrrD] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigG]] {{PubMed|16497325}}

* '''Regulation:'''
** expressed late during sporulation in the forespore ([[SigG]]) {{PubMed|16497325}}

* '''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> 16497325</pubmed>
[[Category:Protein-coding genes]]