SubtiWiki - User contributions [en]

SspB

2012-04-05T09:04:52Z

Cdiethm: /* Biological materials */

* '''Description:''' small acid-soluble spore protein (major beta-type SASP) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sspB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small acid-soluble spore protein (major beta-type SASP)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protection of spore DNA
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 4.791
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 201 bp, 67 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yheF]]'', ''[[yheE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12814]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sspB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU09750

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10787]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' alpha/beta-type SASP 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/P04832 P04832]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''sspB'' {{PubMed|3009398}}

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

* '''Regulation:'''
** expressed during sporulation in the forespore ([[SigG]], [[SpoVT]]) {{PubMed|15699190,8755877}}

* '''Regulatory mechanism:'''
** [[SpoVT]]: transcription activation {{PubMed|8755877}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' GP996 (cat, based on pSG1151), available in the [[Stülke]] lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>16707666,1900507,2456528,3009398,11092849,7608092,15458366, 19542328 8755877</pubmed>

[[Category:Protein-coding genes]]

PGP1080

2011-11-30T09:46:56Z

Cdiethm: Created page with "'''pGP1080: click to enlarge''' '''General comments''' * Integrative plasmid for the fusion of GFP tag to the C-terminus of a protei..."

[[File:pGP1080.jpg|250px|thumb|right|'''pGP1080: click to enlarge''']]

'''General comments'''

* Integrative [[plasmid]] for the fusion of GFP tag to the C-terminus of a protein, keeping the control of the expression under its natural promotor, allows express of the downstream gene by the P(spac) promoter
* constructed in [[Jörg Stülke]]'s lab (C. Diethmaier)

* ''E.coli'': low copy plasmid, select for ampicillin
* ''B. subtilis'': no ori, select for erythromycin/lincomycin

* based on pMUTIN-FLAG

'''Hints for the usage'''
* amplify the last 300bp of your gene of interest
* skip the stop codon of the gene in the reverse primer
* take care that the integration is in-frame
* do not use the XmaIII site for cloning, as GFP is inserted via this restriction site

File:PGP1080.jpg

2011-11-30T09:39:19Z

Cdiethm:

YsbB

2011-11-11T09:11:55Z

Cdiethm: /* Biological materials */

* '''Description:''' putative peptidoglycan hydrolase, probably involved in cell wall turnover 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ysbB''
|-
|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
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 9.81
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 693 bp, 231 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yscB]]'', ''[[ysbA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14850]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ysbB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell wall degradation/ turnover]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28900

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12312]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' LrgB subfamily (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/P94516 P94516]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28900]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ysbB]]'' {{PubMed|8969504}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1554 (''ysbAB''::''spc''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 8969504 </pubmed>
[[Category:Protein-coding genes]]

YsbA

2011-11-11T09:11:02Z

Cdiethm: /* Biological materials */

* '''Description:''' putative anti-holin 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ysbA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''lrgA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || putative anti-holin
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 15 kDa, 9.825
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 438 bp, 146 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysbB]]'', ''[[lytT]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14851]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ysbA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28910

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12311]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P94515 P94515]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28910]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1554 (''ysbAB''::''spc''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 15659658 17452642</pubmed>
[[Category:Protein-coding genes]]

MgsA

2011-11-07T09:03:26Z

Cdiethm: /* Biological materials */

* '''Description:''' methylglyoxal synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mgsA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypjF, jojF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || methylglyoxal synthase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || bypass of glycolysis
|-
|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/MgsA MgsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/lys_threo.html Lys, Thr], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 4.919
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 411 bp, 137 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bshB1]]'', ''[[dapB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14164]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mgsA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU22480

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11211]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Glycerone phosphate = methylglyoxal + phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** non-phosphorylated [[Crh]] interacts with [[MgsA]] to inhibit its activity {{PubMed|21992469}}

* '''[[SubtInteract|Interactions]]:'''
** [[Crh]]-[[MgsA]] (only non-phosphorylated [[Crh]] interacts with [[MgsA]]) {{PubMed|21992469}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1b93 1B93] (from ''Escherichia coli'', 50% identity, 73% similarity) {{PubMed|10368300}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42980 P42980]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU22480]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.3.3 4.2.3.3]

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP67 (''mgsA''::''tet''), available in [[Stülke]] lab
** GP84 (''mgsA''::''pX2''(''cat'')), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1301 (N-terminal Strep-tag, purification from ''E. coli'', in [[pGP172]]), available in [[Stülke]] lab
** pGP1180 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pGP1181 (C-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP382]]), available in [[Stülke]] lab
** pGP2207 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP1459]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP86 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=
[[Boris Görke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]

=Your additional remarks=

=References=
<pubmed> 10368300 21992469 20308541 </pubmed>

[[Category:Protein-coding genes]]

RpsJ

2011-11-07T09:01:01Z

Cdiethm: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rpsJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tetA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[ribosomal protein]] S10 (BS13)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[translation]]
|-
|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/RpsJ RpsJ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 10.207
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 306 bp, 102 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybaC]]'', ''[[rplC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11891]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:rpsJ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01150

===Phenotypes of a mutant ===

essential [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+BG19008]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' [[ribosomal protein]] S10P family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

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

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

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

=== Additional information===

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

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

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

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

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

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

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

Crh

2011-11-07T08:58:12Z

Cdiethm: /* Biological materials */

* '''Description:''' "Catabolite repression [[HPr]]-like protein", control of flux through the harmful methylglyoxal pathway, minor cofactor of the [[CcpA]] transcription factor 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''crh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvcM''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || catabolite repression [[HPr]]-like protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of carbon flux
|-
|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/Crh Crh]
|-
|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''' || 9,2 kDa, 4.70
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 255 bp, 85 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvcN]]'', ''[[yvcL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15479]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:crh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34740

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12403]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' [[PtsH|HPr]] family

* '''Paralogous protein(s):''' [[PtsH|HPr]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' [[PtsH|HPr]] domain (1–85)

* '''Modification:''' phosphorylation on Ser46 by [[HprK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]

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

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

* '''[[SubtInteract|Interactions]]:'''
** Crh-[[GapA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
** Crh-[[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12972249 PubMed]
** [[HprK]]-Crh [http://www.ncbi.nlm.nih.gov/sites/entrez/12009882 PubMed]
** [[Crh]]-[[MgsA]] (only non-phosphorylated [[Crh]] interacts with [[MgsA]]) {{PubMed|21992469}}

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

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/explore.do?structureId=2AK7 2AK7] (dimeric Crh-Ser46-P)
** [http://www.rcsb.org/pdb/explore.do?structureId=1ZVV 1ZVV] ([[CcpA]]-Crh-DNA complex)
** [http://www.rcsb.org/pdb/explore.do?structureId=2RLZ 2RLZ] (dimer)
** [http://www.rcsb.org/pdb/explore.do?structureId=1MU4 1MU4]
** [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=24634 NCBI], dimer
** [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=64943 NCBI], [[CcpA]]-Crh-DNA complex
** [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326 NCBI], dimeric phosphor-Crh
** [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39567 NCBI]
* '''UniProt:''' [http://www.uniprot.org/uniprot/O06976 O06976]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34740]

=== Additional information===

Crh does not possess the phosphorylation site used for [[PTS]] phosphotransfer (His-15 in [[PtsH]]), it can only be phosphorylated on Ser-46

=Expression and regulation=

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

* '''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:''' Crh is weakly expressed. This results in part from a poorly conserved ribosomal binding site of the mRNA. [http://www.ncbi.nlm.nih.gov/sites/entrez/15126459 PubMed]

=Biological materials =

* '''Mutant:''' GP860 (aphA3), QB7097 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP641 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pGP734 (C-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP382]]), available in [[Stülke]] lab

* '''lacZ fusion:''' see ''[[yvcI]]''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''[[crh]]'', ''crh(Ser46Asp)'', ''crh(Ser46Ala)'' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Boris Görke| Görke]] lab

* '''FLAG-tag construct:
** GP69 (spc, based on [[pGP1331]]), available in the [[Boris Görke]] and [[Stülke]] labs
** pGP1200 ''crh''(Ser46Ala) (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:''' available in [[Boris Görke| Görke]] lab

=Labs working on this gene/protein=

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

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

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

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

=Your additional remarks=

=References=

<pubmed>12972249 9973552 9237995 16272399 15126459 10217795 17142398 16316990, 12009882 10589728 12670692 11916384 11361076 11361074 18320329 18284240 16411239 21992469</pubmed>

[[Category:Protein-coding genes]]

MgsA

2011-11-07T08:53:35Z

Cdiethm: /* Biological materials */

* '''Description:''' methylglyoxal synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mgsA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypjF, jojF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || methylglyoxal synthase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || bypass of glycolysis
|-
|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/MgsA MgsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/lys_threo.html Lys, Thr], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 4.919
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 411 bp, 137 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bshB1]]'', ''[[dapB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14164]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mgsA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU22480

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11211]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Glycerone phosphate = methylglyoxal + phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** non-phosphorylated [[Crh]] interacts with [[MgsA]] to inhibit its activity {{PubMed|21992469}}

* '''[[SubtInteract|Interactions]]:'''
** [[Crh]]-[[MgsA]] (only non-phosphorylated [[Crh]] interacts with [[MgsA]]) {{PubMed|21992469}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1b93 1B93] (from ''Escherichia coli'', 50% identity, 73% similarity) {{PubMed|10368300}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42980 P42980]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU22480]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.3.3 4.2.3.3]

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP67 (''mgsA''::''tet''), available in [[Stülke]] lab
** GP84 (''mgsA''::''pX2''(''cat'')), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1301 (N-terminal Strep-tag, purification from ''E. coli'', in [[pGP172]]), available in [[Stülke]] lab
** pGP1180 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pGP1181 (C-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP382]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP86 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=
[[Boris Görke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]

=Your additional remarks=

=References=
<pubmed> 10368300 21992469 20308541 </pubmed>

[[Category:Protein-coding genes]]

Crh

2011-11-07T08:49:49Z

Cdiethm: /* Biological materials */

* '''Description:''' "Catabolite repression [[HPr]]-like protein", control of flux through the harmful methylglyoxal pathway, minor cofactor of the [[CcpA]] transcription factor 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''crh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvcM''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || catabolite repression [[HPr]]-like protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of carbon flux
|-
|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/Crh Crh]
|-
|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''' || 9,2 kDa, 4.70
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 255 bp, 85 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvcN]]'', ''[[yvcL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15479]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:crh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34740

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12403]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' [[PtsH|HPr]] family

* '''Paralogous protein(s):''' [[PtsH|HPr]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' [[PtsH|HPr]] domain (1–85)

* '''Modification:''' phosphorylation on Ser46 by [[HprK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]

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

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

* '''[[SubtInteract|Interactions]]:'''
** Crh-[[GapA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
** Crh-[[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12972249 PubMed]
** [[HprK]]-Crh [http://www.ncbi.nlm.nih.gov/sites/entrez/12009882 PubMed]
** [[Crh]]-[[MgsA]] (only non-phosphorylated [[Crh]] interacts with [[MgsA]]) {{PubMed|21992469}}

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

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/explore.do?structureId=2AK7 2AK7] (dimeric Crh-Ser46-P)
** [http://www.rcsb.org/pdb/explore.do?structureId=1ZVV 1ZVV] ([[CcpA]]-Crh-DNA complex)
** [http://www.rcsb.org/pdb/explore.do?structureId=2RLZ 2RLZ] (dimer)
** [http://www.rcsb.org/pdb/explore.do?structureId=1MU4 1MU4]
** [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=24634 NCBI], dimer
** [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=64943 NCBI], [[CcpA]]-Crh-DNA complex
** [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326 NCBI], dimeric phosphor-Crh
** [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39567 NCBI]
* '''UniProt:''' [http://www.uniprot.org/uniprot/O06976 O06976]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34740]

=== Additional information===

Crh does not possess the phosphorylation site used for [[PTS]] phosphotransfer (His-15 in [[PtsH]]), it can only be phosphorylated on Ser-46

=Expression and regulation=

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

* '''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:''' Crh is weakly expressed. This results in part from a poorly conserved ribosomal binding site of the mRNA. [http://www.ncbi.nlm.nih.gov/sites/entrez/15126459 PubMed]

=Biological materials =

* '''Mutant:''' GP860 (aphA3), QB7097 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP641 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pGP734 (C-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP382]]), available in [[Stülke]] lab

* '''lacZ fusion:''' see ''[[yvcI]]''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''[[crh]]'', ''crh(Ser46Asp)'', ''crh(Ser46Ala)'' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Boris Görke| Görke]] lab

* '''FLAG-tag construct:''' GP69 (spc, based on [[pGP1331]]), available in the [[Boris Görke]] and [[Stülke]] labs

* '''Antibody:''' available in [[Boris Görke| Görke]] lab

=Labs working on this gene/protein=

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

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

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

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

=Your additional remarks=

=References=

<pubmed>12972249 9973552 9237995 16272399 15126459 10217795 17142398 16316990, 12009882 10589728 12670692 11916384 11361076 11361074 18320329 18284240 16411239 21992469</pubmed>

[[Category:Protein-coding genes]]

ThiC

2011-11-07T08:42:12Z

Cdiethm: /* Biological materials */

* '''Description:''' biosynthesis of the pyrimidine moiety of thiamine 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''thiC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''thiA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of thiamine
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/thiamin.html Thiamin]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 5.262
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1770 bp, 590 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ygaJ]]'', ''[[ygaK]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12707]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:thiC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU08790

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11246]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated on Ser-565, Ser-586 and Tyr-589 {{PubMed|20509597}}

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/1g6c 1G6C]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P45740 P45740]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU08790]

* '''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:'''

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

* '''Regulation:'''
** repressed by thiamine and 2-methyl-4-amino-5-hydroxymethylpyrimidine {{PubMed|9370266}}
** repressed by thiamine ([[Thi-box]]) {{PubMed|12376536}}

* '''Regulatory mechanism:'''
** [[Thi-box]]: [[RNA switch]] {{PubMed|12376536}}

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>19348578 10382260 </pubmed>

==Original publications==
<pubmed>16291685 9370266 20509597 12376536</pubmed>
[[Category:Protein-coding genes]]

MgsA

2011-11-07T08:38:17Z

Cdiethm: /* Biological materials */

* '''Description:''' methylglyoxal synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mgsA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypjF, jojF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || methylglyoxal synthase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || bypass of glycolysis
|-
|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/MgsA MgsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/lys_threo.html Lys, Thr], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 4.919
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 411 bp, 137 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bshB1]]'', ''[[dapB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14164]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mgsA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU22480

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11211]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Glycerone phosphate = methylglyoxal + phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** non-phosphorylated [[Crh]] interacts with [[MgsA]] to inhibit its activity {{PubMed|21992469}}

* '''[[SubtInteract|Interactions]]:'''
** [[Crh]]-[[MgsA]] (only non-phosphorylated [[Crh]] interacts with [[MgsA]]) {{PubMed|21992469}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1b93 1B93] (from ''Escherichia coli'', 50% identity, 73% similarity) {{PubMed|10368300}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42980 P42980]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU22480]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.3.3 4.2.3.3]

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP67 (''mgsA''::''tet''), available in [[Stülke]] lab
** GP84 (''mgsA''::''pX2''(''cat'')), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1301 (N-terminal Strep-tag, purification from ''E. coli'', in [[pGP172]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP86 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=
[[Boris Görke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]

=Your additional remarks=

=References=
<pubmed> 10368300 21992469 20308541 </pubmed>

[[Category:Protein-coding genes]]

BshA

2011-11-02T12:42:46Z

Cdiethm: /* Biological materials */

* '''Description:''' L-malic acid glycosyltransferase, involved in bacillithiol synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''bshA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''jojH, ypjH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || L-malic acid glycosyltransferase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of bacillithiol
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 6.149
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1131 bp, 377 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cca]]'', ''[[bshB1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14162]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ypjH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[miscellaneous metabolic pathways]]}},
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU22460

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11213]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' UDP-GlcNAc + L-malate = GlcNAc(α1→2)L-malate {{PubMed|20308541}}; also uses D-malate as a substrate, but with much lower affinity {{PubMed|20308541}}

* '''Protein family:''' NamA 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/explore.do?structureId=3MBO 3MBO] (from ''B. anthracis'') {{PubMed|20799687}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42982 P42982]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU22460]

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' ''bshA::mls'' available in [[John_Helmann]] lab
** GP88 (''ypjH''::''pX2''(''cat'')), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 20308541 19578333 </pubmed>
'''Additional references: ''' {{PubMed|20799687}}
[[Category:Protein-coding genes]]

BshB1

2011-11-02T12:41:50Z

Cdiethm: /* Biological materials */

* '''Description:''' N-acetylglucosamin-malate deacetylase, involved in bacillithiol synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''bshB1''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''jojG, ypjG ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || N-acetylglucosamin-malate deacetylase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of bacillithiol
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/lys_threo.html Lys, Thr]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 6.343
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 672 bp, 224 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bshA]]'', ''[[mgsA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14163]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ypjG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[miscellaneous metabolic pathways]]}},
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU22470

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11212]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' GlcNAc-Mal -> GlcN-Mal + Ac

* '''Protein family:'''

* '''Paralogous protein(s):''' [[BshB2]]

=== 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/P42981 P42981]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU22470]

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' ''bshB1'' null mutant and ''[[bshB1]]'' / ''[[bshB2]]'' double null mutant available in [[John Helmann]] lab
** GP87 (''ypjG''::''pX2''(''cat'')), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 20308541 19578333 </pubmed>
[[Category:Protein-coding genes]]

MgsA

2011-11-02T12:40:18Z

Cdiethm: /* Biological materials */

* '''Description:''' methylglyoxal synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mgsA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypjF, jojF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || methylglyoxal synthase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || bypass of glycolysis
|-
|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/MgsA MgsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/lys_threo.html Lys, Thr], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 4.919
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 411 bp, 137 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bshB1]]'', ''[[dapB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14164]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mgsA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU22480

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11211]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Glycerone phosphate = methylglyoxal + phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** non-phosphorylated [[Crh]] interacts with [[MgsA]] to inhibit its activity {{PubMed|21992469}}

* '''[[SubtInteract|Interactions]]:'''
** [[Crh]]-[[MgsA]] (only non-phosphorylated [[Crh]] interacts with [[MgsA]]) {{PubMed|21992469}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1b93 1B93] (from ''Escherichia coli'', 50% identity, 73% similarity) {{PubMed|10368300}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42980 P42980]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU22480]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.3.3 4.2.3.3]

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP67 (''mgsA''::''tet''), available in [[Stülke]] lab
** GP84 (''mgsA''::''pX2''(''cat'')), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP86 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=
[[Boris Görke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]

=Your additional remarks=

=References=
<pubmed> 10368300 21992469 20308541 </pubmed>

[[Category:Protein-coding genes]]

MgsA

2011-11-02T12:38:38Z

Cdiethm: /* Biological materials */

* '''Description:''' methylglyoxal synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mgsA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypjF, jojF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || methylglyoxal synthase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || bypass of glycolysis
|-
|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/MgsA MgsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/lys_threo.html Lys, Thr], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 4.919
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 411 bp, 137 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bshB1]]'', ''[[dapB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14164]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mgsA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU22480

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11211]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Glycerone phosphate = methylglyoxal + phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** non-phosphorylated [[Crh]] interacts with [[MgsA]] to inhibit its activity {{PubMed|21992469}}

* '''[[SubtInteract|Interactions]]:'''
** [[Crh]]-[[MgsA]] (only non-phosphorylated [[Crh]] interacts with [[MgsA]]) {{PubMed|21992469}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1b93 1B93] (from ''Escherichia coli'', 50% identity, 73% similarity) {{PubMed|10368300}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42980 P42980]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU22480]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.3.3 4.2.3.3]

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP67 (''mgsA''::''tet''), available in [[Stülke]] lab
** GP84 (''mgsA''::''pX2''(''cat'')), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[Boris Görke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]

=Your additional remarks=

=References=
<pubmed> 10368300 21992469 20308541 </pubmed>

[[Category:Protein-coding genes]]

HprK

2011-11-02T12:36:04Z

Cdiethm: /* Biological materials */

* '''Description:''' [[ptsH|HPr]] [[protein kinases and phosphatases|kinase]]/ phosphorylase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hprK''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ptsK, yvoB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[ptsH|HPr]] [[protein kinases and phosphatases|kinase]]/ phosphorylase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || carbon catabolite repression, phosphorylation of [[ptsH|HPr]] and [[Crh]] proteins at Ser46
|-
|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/HPrK HprK]
|-
|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], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 4.906
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 930 bp, 310 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lgt]]'', ''[[nagA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15505]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:hprK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35000

===Phenotypes of a mutant ===

no carbon catabolite repression

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14125]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + [[ptsH|HPr]] = ADP + P-Ser-HPr (according to Swiss-Prot)

* '''Protein family:''' HPrK/P 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]]:'''
** HprK-[[PtsH| HPr]]
** HprK-[[Crh]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12009882 PubMed]

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1KKM 1KKM] (complex of Lactobacillus casei HprK with B. subtilis HPr-Ser-P), [http://www.rcsb.org/pdb/explore.do?structureId=1KKL 1KKL] (complex of Lactobacillus casei HprK with B. subtilis HPr)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34483 O34483]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35000]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[hprK]]-[[lgt]]-[[yvoD]]-[[yvoE]]-[[yvoF]]'' {{PubMed|9465101}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP202 (spc), GP858 (aphA3), GP82 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP642, available in [[Stülke]] lab
** for expression/ purification of mutant HprK-G158A from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP650, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP205, available in [[Stülke]] lab
** for expression, purification of the N-terminal in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP218, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP201 (in [[pAC5]]) available in [[Stülke]] lab, pGP202 (in [[pAC6]]) available in [[Stülke]] lab

* '''GFP fusion:'''

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

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

=Labs working on this gene/protein=

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

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

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

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

=Your additional remarks=

=References=
==Reviews==
<pubmed>12837773 15023355 18628769 </pubmed>

==General Analysis, Physiology==
<pubmed>9570401 9465101 12123463 18757537 22001508 </pubmed>

==Structural Analysis of HPrK==
<pubmed>11904409 12589763 12359875 17878158 </pubmed>

==Enzymatic Properties, Mutation Analysis==
<pubmed>12359880 11483496 12055300 10636874 12411438 11796714 12009882 12779331 </pubmed>
==HprK as a Target For Antimicrobial Compounds==
<pubmed>15084125, </pubmed>

[[Category:Protein-coding genes]]

MgsA

2011-11-02T12:31:20Z

Cdiethm: /* Biological materials */

* '''Description:''' methylglyoxal synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mgsA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypjF, jojF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || methylglyoxal synthase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || bypass of glycolysis
|-
|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/MgsA MgsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/lys_threo.html Lys, Thr], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 4.919
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 411 bp, 137 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bshB1]]'', ''[[dapB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14164]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mgsA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU22480

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11211]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Glycerone phosphate = methylglyoxal + phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** non-phosphorylated [[Crh]] interacts with [[MgsA]] to inhibit its activity {{PubMed|21992469}}

* '''[[SubtInteract|Interactions]]:'''
** [[Crh]]-[[MgsA]] (only non-phosphorylated [[Crh]] interacts with [[MgsA]]) {{PubMed|21992469}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1b93 1B93] (from ''Escherichia coli'', 50% identity, 73% similarity) {{PubMed|10368300}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42980 P42980]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU22480]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.3.3 4.2.3.3]

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP67 (''mgsA''::''tet''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[Boris Görke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]

=Your additional remarks=

=References=
<pubmed> 10368300 21992469 20308541 </pubmed>

[[Category:Protein-coding genes]]

TapA

2011-11-02T10:50:20Z

Cdiethm: /* Biological materials */

* '''Description:''' required for the anchoring of the [[TasA]] amyloid fibers to the cell and for the initiation of fiber polymerization, minor fiber component
 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tapA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqhD, yqxM ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[TasA]] anchoring/assembly protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|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/TapA TapA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 6.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sipW]]'', ''[[yqzG]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14395]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqxM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24640

===Phenotypes of a mutant ===
The mutants are able to form a biofilm in the presence of D-amino acids {{PubMed|20431016}}

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqxM-sipW-tasA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11076]

=== 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:''' D-amino acids lead to disappearance of TapA from the cell wall {{PubMed|21477127}}

* '''[[SubtInteract|Interactions]]:'''
** [[TapA]]-[[TasA]] {{PubMed|21477127}}

* '''[[Localization]]:'''
** attached to the cell surface (on the outside of the cell), associated with peptidoglycan {{PubMed|21477127}}
** secretion requires SipW

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P40949 P40949]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24640]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[tapA]]-[[sipW]]-[[tasA]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]

* '''Regulation:'''
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10464223,17720793 PubMed]

* '''Regulatory mechanism:'''
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10464223,17720793 PubMed]
** [[SinR]]: transcription repression {{PubMed|16430695}}

* '''Additional information:'''
** induction by sequestration of [[SinR]] by [[SinI]] or [[SlrA]] {{PubMed|15661000,19788541}} or by SlrR {{PubMed|20351052}}
** the ''[[tapA]]-[[sipW]]-[[tasA]]'' operon is not expressed in ''[[rny]]'' and ''[[ymdB]]'' mutants {{PubMed|21856853,21815947}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:''' pGP1926 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 21488983 </pubmed>
==Original publications==
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big>
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
<big>Flagellin Expression and Biofilm Formation.''' </big>
<big>J Bacteriol.: 2011, 193(21):5997-6007. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]

<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>18763711,19193632,17005971 19779461 19820159 20418391 20525796 20572937,21803996 21843271 </pubmed>
<pubmed>18430133,18047568,18647168, 20351052,16430695,10464223,17720793, 19605685 20431016 10559173 21477127 </pubmed>

[[Category:Protein-coding genes]]

YmdB

2011-11-02T10:31:32Z

Cdiethm: /* Biological materials */

* '''Description:''' putative phosphatase/ phosphodiesterase, controls bistable gene expression 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ymdB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || putative phosphatase/ phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of bistable gene expression
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29,1 kDa, 6.50
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rny]]'', ''[[spoVS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13570]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ymdB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16970

===Phenotypes of a mutant ===

* strong overexpression of ''[[hag]]'' {{PubMed|21856853}}
* defective in [[biofilm formation]] {{PubMed|21856853}}
* the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[[slrR]]'' {{PubMed|21856853}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13421]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP (the ''Deinococcus'' ortholog) {{PubMed|17847097}}

* '''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.pdb.org/pdb/explore/explore.do?structureId=1T70 1T70] (the protein of ''Deinococcus radiodurans'', 44% identity) {{PubMed|17847097}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31775 O31775]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16970]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[rny]]-[[ymdB]]'' (weak readthrough transcription) {{PubMed|21856853}}

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

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there {{PubMed|21856853}}

=Biological materials =

* '''Mutant:'''
** GP583 (spc), available in [[Stülke]] lab
** GP922 (cat), available in [[Stülke]] lab
** GP921 (spc) NCIB3610 derivate, available in [[Stülke]] lab
** GP969 (''[[ymdB]]''(E39Q)-cat) inactive enzyme, available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP1041, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1919, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1040, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP1917, available in [[Stülke]] lab
** GP970 (''[[ymdB]]''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP1018 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big>
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
<big>Flagellin Expression and Biofilm Formation.''' </big>
J Bacteriol.: 2011, 193(21):5997-6007.
[http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]

==Functional and structural analysis of orthologs in other organisms==
<pubmed> 19376879 17847097 </pubmed>

[[Category:Protein-coding genes]]

YmdB

2011-11-02T10:25:28Z

Cdiethm: /* Biological materials */

* '''Description:''' putative phosphatase/ phosphodiesterase, controls bistable gene expression 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ymdB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || putative phosphatase/ phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of bistable gene expression
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29,1 kDa, 6.50
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rny]]'', ''[[spoVS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13570]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ymdB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16970

===Phenotypes of a mutant ===

* strong overexpression of ''[[hag]]'' {{PubMed|21856853}}
* defective in [[biofilm formation]] {{PubMed|21856853}}
* the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[[slrR]]'' {{PubMed|21856853}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13421]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP (the ''Deinococcus'' ortholog) {{PubMed|17847097}}

* '''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.pdb.org/pdb/explore/explore.do?structureId=1T70 1T70] (the protein of ''Deinococcus radiodurans'', 44% identity) {{PubMed|17847097}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31775 O31775]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16970]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[rny]]-[[ymdB]]'' (weak readthrough transcription) {{PubMed|21856853}}

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

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there {{PubMed|21856853}}

=Biological materials =

* '''Mutant:'''
** GP583 (spc), available in [[Stülke]] lab
** GP922 (cat), available in [[Stülke]] lab
** GP921 (spc) NCIB3610 derivate, available in [[Stülke]] lab
** GP969 (''[[ymdB]]''(E39Q)-cat) inactive enzyme, available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP1041, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1040, available in [[Stülke]] lab
** GP970 (''[[ymdB]]''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP1018 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big>
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
<big>Flagellin Expression and Biofilm Formation.''' </big>
J Bacteriol.: 2011, 193(21):5997-6007.
[http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]

==Functional and structural analysis of orthologs in other organisms==
<pubmed> 19376879 17847097 </pubmed>

[[Category:Protein-coding genes]]

Hag

2011-11-02T10:17:51Z

Cdiethm: /* Biological materials */

* '''Description:''' flagellin protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hag''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || flagellin protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[motility and chemotaxis]]
|-
|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/Hag Hag]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 4.782
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 912 bp, 304 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvyC]]'', ''[[csrA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15553]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:hag_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[motility and chemotaxis]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35360

===Phenotypes of a mutant ===

No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10655]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

* '''Paralogous protein(s):''' [[YvzB]] (C-terminal domain of Hag)

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[FlhA]]-[[Hag]] {{PubMed|20534509}}
** [[FlhA]]-([[FliS]]-[[Hag]]) {{PubMed|20534509}}
** [[FliS]]-[[Hag]] {{PubMed|20534509}}
** [[FliW]]-[[Hag]] {{PubMed|21895793}}

* '''[[Localization]]:'''
** extracellular (no signal peptide), major component of the secretome [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P02968 P02968]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35360]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[hag]]'' {{PubMed|2498284}}

* '''[[Sigma factor]]:''' [[SigD]] {{PubMed|2498284}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12730172 PubMed]

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12730172 PubMed]
** [[CsrA]]: translation inhibition {{PubMed|17555441}}
** [[ScoC]]: transcription repression {{PubMed|19118355}}

* '''Additional information:'''
** the ''[[hag]]'' gene is strongly overexpressed in a ''[[ymdB]]'' mutant (loss of bistable gene expression) {{PubMed|21856853}}

=Biological materials =

* '''Mutant:''' GP901 (aphA3), GP902 (tet), both available in [[Stülke]] lab

* '''Expression vector:'''
** expression in ''B. subtilis'', in [[pBQ200]]: pGP1089, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP1035 (in [[pAC6]]), pGP755 (in [[pAC7]]), there is also a series of promoter deletion variants in [[pAC6]] and [[pAC7]], all available in [[Stülke]] lab

* '''GFP fusion:''' BP494 (bglS:: (hag-promoter-cfp-aphA3)), BP496 (amyE:: (hag-promoter-iyfp-cat)), available in [[Stülke]] lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|21602220}}
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big>
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
<big>Flagellin Expression and Biofilm Formation.''' </big>
<big>J Bacteriol.: 2011, 193(21):5997-6007. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]

<pubmed>2498284,9648743,9096206,7708689,19202088, 18763711, 21895793 10809682 19118355 17555441 20534509 </pubmed>
[[Category:Protein-coding genes]]

YlxF

2011-11-02T10:15:30Z

Cdiethm: /* Biological materials */

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ylxF''
|-
|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
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 9.745
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 639 bp, 213 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fliJ]]'', ''[[fliK]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13499]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ylxF_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16260

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10246]

=== 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/P23454 P23454]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16260]

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

=== Additional information===

=Expression and regulation=
* '''Operon:'''
** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[ylxG]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[ylxH]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|9657996,8157612,15175317}}
** ''[[ylxF]]-[[fliK]]-[[ylxG]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[ylxH]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|20233303}}

* '''[[Sigma factor]]:'''
** ''[[flgB]]'': [[SigA]] {{PubMed|9657996}}, [[SigD]] {{PubMed|9657996}}
** ''[[ylxF]]'': [[SigD]] {{PubMed|20233303}}

* '''Regulation:'''
** repressed under conditions that trigger sporulation ([[Spo0A]]) {{PubMed|14651647}}

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression {{PubMed|14651647}}
** [[CodY]]: transcription repression {{PubMed|12730172}}
** [[DegU]] (non-phosphorylated): transcription activation {{PubMed|17850253}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:''' pGP1088 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>14651647, 9657996,8157612,15175317 20233303 17850253</pubmed>

[[Category:Protein-coding genes]]

SinR

2011-11-02T10:12:59Z

Cdiethm: /* Biological materials */

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

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

__TOC__

 

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

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

=The [[SinR regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24610

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** DNA-binding N-terminal domain (aa 1-69) {{PubMed|21708175}}
** [[SinI]]-binding C-terminal domain (aa 74-111) {{PubMed|21708175}}

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[SlrA]]-[[SinR]] {{PubMed|19788541}}
** [[SlrR]]-[[SinR]] {{PubMed|20351052}}
** [[SinR]]-[[ScoC]]
** [[SinR]]-[[SinI]] {{PubMed|9799632}}

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

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/explore.do?structureId=3QQ6 3QQ6] (N-terminal domain, aa 1-69) {{PubMed|21708175}}
** [http://www.rcsb.org/pdb/explore.do?structureId=2YAL 2YAL] (C-terminal domain, aa 74-111) {{PubMed|21708175}}
** [http://www.rcsb.org/pdb/explore.do?structureId=1B0N 1B0N] (complex [[SinR]]-[[SinI]]) {{PubMed|9799632}}

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

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

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

=== Additional information===

=Expression and regulation=

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

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

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

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

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:'''
** N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]: pGP1083 , available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>20395361 20541494 </pubmed>
==Modelling of the [[SinI]]/[[SinR]] switch==
<pubmed> 21095906 </pubmed>
==Original publications==
'''Additonal publications:''' {{PubMed|21326214,21708175}}
<pubmed>8955328,15661000,8878039,16923912,15104138,16430695,16430696,18047568,18430133,11751836,1906467,11751836,7635837,11751836, 19201793, 10547280, 15104138, 9799632 19788541 19898538 3125149 8932324 20351052 20923420 8422983 9685500 9158733 </pubmed>

[[Category:Protein-coding genes]]

SacT

2011-11-02T10:09:41Z

Cdiethm: /* Biological materials */

* '''Description:''' [[PRD-containing transcription factors|transcriptional antiterminator]] for the ''[[sacP]]-[[sacA]]-[[ywdA]]'' operon 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sacT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-47d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[PRD-containing transcription factors|transcriptional antiterminator]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of sucrose utilization
|-
|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/SacT SacT]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.587
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 828 bp, 276 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywcJ]]'', ''[[ywcI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15833]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sacT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[SacT regulon]]: ''[[sacP]]-[[sacA]]-[[ywdA]]''=
=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38070

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10593]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' binding to the mRNA of the ''[[sacP]]-[[sacA]]'' operon, causes transcription antitermination (in presence of sucrose and absence of glucose)

* '''Protein family:''' [[PRD-containing transcription factors|transcriptional antiterminator]] bglG family (according to Swiss-Prot) BglG family of antiterminators

* '''Paralogous protein(s):''' [[LicT]], [[SacY]], [[GlcT]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[PtsH]]-[[SacT]]

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P26212 P26212]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38070]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[sacT]]'' {{PubMed|9353933}}

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

* '''Regulation:'''
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP429 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression, purification of both PRDs in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP166, available in [[Stülke]] lab
** for expression, purification of PRD-1 in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP426, available in [[Stülke]] lab
** for expression, purification of PRD-2 in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP427, available in [[Stülke]] lab
** for expression, purification of PRD-1 in ''E. coli'' with N-terminal His-tag and thrombin cleavage site, in [[pGP570]]: pGP439, available in [[Stülke]] lab
** for expression, purification of PRD-2 in ''E. coli'' with N-terminal His-tag and thrombin cleavage site, in [[pGP570]]: pGP440, available in [[Stülke]] lab
** for expression, purification of the RNA-binding domain in ''E. coli'' with N-terminal His-tag and thrombin cleavage site, in [[pGP570]]: pGP571, available in [[Stülke]] lab
** for expression of the RNA-binding domain in ''B. subtilis'', in [[pBQ200]]: pGP446, available in [[Stülke]] lab
** for expression, purification of [[sacT]]-full length in ''B. subtilis'' with C-terminal Strep-tag, in [[pGP382]]: pGP1064, available in [[Stülke]] lab
** for expression, purification of [[sacT]]-full length in ''B. subtilis'' with N-terminal Strep-tag, in [[pGP380]]: pGP1068, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12107147 2163394 1577686 8702561 1279678, 21278164 </pubmed>

[[Category:Protein-coding genes]]

SacT

2011-11-02T10:07:15Z

Cdiethm: /* Biological materials */

* '''Description:''' [[PRD-containing transcription factors|transcriptional antiterminator]] for the ''[[sacP]]-[[sacA]]-[[ywdA]]'' operon 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sacT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-47d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[PRD-containing transcription factors|transcriptional antiterminator]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of sucrose utilization
|-
|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/SacT SacT]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.587
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 828 bp, 276 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywcJ]]'', ''[[ywcI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15833]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sacT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[SacT regulon]]: ''[[sacP]]-[[sacA]]-[[ywdA]]''=
=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38070

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10593]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' binding to the mRNA of the ''[[sacP]]-[[sacA]]'' operon, causes transcription antitermination (in presence of sucrose and absence of glucose)

* '''Protein family:''' [[PRD-containing transcription factors|transcriptional antiterminator]] bglG family (according to Swiss-Prot) BglG family of antiterminators

* '''Paralogous protein(s):''' [[LicT]], [[SacY]], [[GlcT]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[PtsH]]-[[SacT]]

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P26212 P26212]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38070]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[sacT]]'' {{PubMed|9353933}}

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

* '''Regulation:'''
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP429 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression, purification of both PRDs in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP166, available in [[Stülke]] lab
** for expression, purification of PRD-1 in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP426, available in [[Stülke]] lab
** for expression, purification of PRD-2 in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP427, available in [[Stülke]] lab
** for expression, purification of PRD-1 in ''E. coli'' with N-terminal His-tag and thrombin cleavage site, in [[pGP570]]: pGP439, available in [[Stülke]] lab
** for expression, purification of PRD-2 in ''E. coli'' with N-terminal His-tag and thrombin cleavage site, in [[pGP570]]: pGP440, available in [[Stülke]] lab
** for expression, purification of the RNA-binding domain in ''E. coli'' with N-terminal His-tag and thrombin cleavage site, in [[pGP570]]: pGP571, available in [[Stülke]] lab
** for expression of the RNA-binding domain in ''B. subtilis'', in [[pBQ200]]: pGP446, available in [[Stülke]] lab
** for expression, purification of [[sacT]]-full length in ''B. subtilis'' with N-terminal Strep-tag, in [[pGP382]]: pGP1064, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12107147 2163394 1577686 8702561 1279678, 21278164 </pubmed>

[[Category:Protein-coding genes]]

SpoVS

2011-11-02T10:03:24Z

Cdiethm: /* Biological materials */

* '''Description:''' required for dehydratation of the spore core and assembly of the coat, mutation increases [[SigD]]-dependent gene expression, might act via [[SinR]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''spoVS''
|-
|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''' || spore coat assembly, spore core dehydratation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 6.475
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 258 bp, 86 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ymdB]]'', ''[[tdh]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13571]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:spoVS_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16980

===Phenotypes of a mutant ===
increased [[SigD]]-dependent gene expression, this might occur via [[SinR]] {{PubMed|16428420}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11245]

=== 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/P45693 P45693]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16980]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[spoVS]]'' {{PubMed|7559352}}

* '''[[Sigma factor]]:''' [[SigH]] {{PubMed|7559352}}

* '''Regulation:'''
** expressed at the onset of stationary phase ([[SigH]]) {{PubMed|7559352}}

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>7559352,18562273 16428420 , 20525796 </pubmed>

[[Category:Protein-coding genes]]

Hag

2011-11-02T10:01:17Z

Cdiethm: /* Biological materials */

* '''Description:''' flagellin protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hag''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || flagellin protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[motility and chemotaxis]]
|-
|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/Hag Hag]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 4.782
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 912 bp, 304 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvyC]]'', ''[[csrA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15553]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:hag_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[motility and chemotaxis]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35360

===Phenotypes of a mutant ===

No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10655]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

* '''Paralogous protein(s):''' [[YvzB]] (C-terminal domain of Hag)

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[FlhA]]-[[Hag]] {{PubMed|20534509}}
** [[FlhA]]-([[FliS]]-[[Hag]]) {{PubMed|20534509}}
** [[FliS]]-[[Hag]] {{PubMed|20534509}}
** [[FliW]]-[[Hag]] {{PubMed|21895793}}

* '''[[Localization]]:'''
** extracellular (no signal peptide), major component of the secretome [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P02968 P02968]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35360]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[hag]]'' {{PubMed|2498284}}

* '''[[Sigma factor]]:''' [[SigD]] {{PubMed|2498284}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12730172 PubMed]

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12730172 PubMed]
** [[CsrA]]: translation inhibition {{PubMed|17555441}}
** [[ScoC]]: transcription repression {{PubMed|19118355}}

* '''Additional information:'''
** the ''[[hag]]'' gene is strongly overexpressed in a ''[[ymdB]]'' mutant (loss of bistable gene expression) {{PubMed|21856853}}

=Biological materials =

* '''Mutant:''' GP901 (aphA3), GP902 (tet), both available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:''' pGP1035 (in [[pAC6]]), pGP755 (in [[pAC7]]), there is also a series of promoter deletion variants in [[pAC6]] and [[pAC7]], all available in [[Stülke]] lab

* '''GFP fusion:''' BP494 (bglS:: (hag-promoter-cfp-aphA3)), BP496 (amyE:: (hag-promoter-iyfp-cat)), available in [[Stülke]] lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|21602220}}
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big>
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
<big>Flagellin Expression and Biofilm Formation.''' </big>
<big>J Bacteriol.: 2011, 193(21):5997-6007. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]

<pubmed>2498284,9648743,9096206,7708689,19202088, 18763711, 21895793 10809682 19118355 17555441 20534509 </pubmed>
[[Category:Protein-coding genes]]

Hag

2011-11-02T10:00:21Z

Cdiethm: /* Biological materials */

* '''Description:''' flagellin protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hag''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || flagellin protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[motility and chemotaxis]]
|-
|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/Hag Hag]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 4.782
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 912 bp, 304 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvyC]]'', ''[[csrA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15553]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:hag_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[motility and chemotaxis]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35360

===Phenotypes of a mutant ===

No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10655]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

* '''Paralogous protein(s):''' [[YvzB]] (C-terminal domain of Hag)

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[FlhA]]-[[Hag]] {{PubMed|20534509}}
** [[FlhA]]-([[FliS]]-[[Hag]]) {{PubMed|20534509}}
** [[FliS]]-[[Hag]] {{PubMed|20534509}}
** [[FliW]]-[[Hag]] {{PubMed|21895793}}

* '''[[Localization]]:'''
** extracellular (no signal peptide), major component of the secretome [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P02968 P02968]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35360]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[hag]]'' {{PubMed|2498284}}

* '''[[Sigma factor]]:''' [[SigD]] {{PubMed|2498284}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12730172 PubMed]

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12730172 PubMed]
** [[CsrA]]: translation inhibition {{PubMed|17555441}}
** [[ScoC]]: transcription repression {{PubMed|19118355}}

* '''Additional information:'''
** the ''[[hag]]'' gene is strongly overexpressed in a ''[[ymdB]]'' mutant (loss of bistable gene expression) {{PubMed|21856853}}

=Biological materials =

* '''Mutant:''' GP901 (aphA3), GP902 (tet), both available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:''' pGP1035 (in [[pAC6]]), pGP755 (in [[pAC7]]), there is also a series of promoter deletion variants in [[pAC6]] and [[pAC7]], all available in [[Stülke]] lab

* '''GFP fusion:''' BP494 (bglS:: (hag-promoter-cfp-ahpA3)), BP496 (amyE:: (hag-promoter-iyfp-cat)), available in [[Stülke]] lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|21602220}}
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big>
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
<big>Flagellin Expression and Biofilm Formation.''' </big>
<big>J Bacteriol.: 2011, 193(21):5997-6007. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]

<pubmed>2498284,9648743,9096206,7708689,19202088, 18763711, 21895793 10809682 19118355 17555441 20534509 </pubmed>
[[Category:Protein-coding genes]]

Hag

2011-11-02T09:59:09Z

Cdiethm: /* Biological materials */

* '''Description:''' flagellin protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hag''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || flagellin protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[motility and chemotaxis]]
|-
|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/Hag Hag]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 4.782
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 912 bp, 304 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvyC]]'', ''[[csrA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15553]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:hag_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[motility and chemotaxis]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35360

===Phenotypes of a mutant ===

No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10655]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

* '''Paralogous protein(s):''' [[YvzB]] (C-terminal domain of Hag)

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[FlhA]]-[[Hag]] {{PubMed|20534509}}
** [[FlhA]]-([[FliS]]-[[Hag]]) {{PubMed|20534509}}
** [[FliS]]-[[Hag]] {{PubMed|20534509}}
** [[FliW]]-[[Hag]] {{PubMed|21895793}}

* '''[[Localization]]:'''
** extracellular (no signal peptide), major component of the secretome [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P02968 P02968]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35360]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[hag]]'' {{PubMed|2498284}}

* '''[[Sigma factor]]:''' [[SigD]] {{PubMed|2498284}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12730172 PubMed]

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12730172 PubMed]
** [[CsrA]]: translation inhibition {{PubMed|17555441}}
** [[ScoC]]: transcription repression {{PubMed|19118355}}

* '''Additional information:'''
** the ''[[hag]]'' gene is strongly overexpressed in a ''[[ymdB]]'' mutant (loss of bistable gene expression) {{PubMed|21856853}}

=Biological materials =

* '''Mutant:''' GP901 (aphA3), GP902 (tet), both available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:''' pGP1035 (in [[pAC6]]), pGP755 (in [[pAC7]]), there is also a series of promoter deletion variants in [[pAC6]] and [[pAC7]], all available in [[Stülke]] lab

* '''GFP fusion:''' BP494 (bglS:: (hag-promoter-gfpmut3-ahpA3)), BP496 (amyE:: (hag-promoter-cfp-cat)), available in [[Stülke]] lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|21602220}}
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big>
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
<big>Flagellin Expression and Biofilm Formation.''' </big>
<big>J Bacteriol.: 2011, 193(21):5997-6007. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]

<pubmed>2498284,9648743,9096206,7708689,19202088, 18763711, 21895793 10809682 19118355 17555441 20534509 </pubmed>
[[Category:Protein-coding genes]]

GdpP

2011-11-02T09:48:12Z

Cdiethm: /* Biological materials */

* '''Description:''' cyclic dinucleotide phosphodiesterase
 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yybT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || cyclic dinucleotide phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of sporulation initiation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 74 kDa, 4.865
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1977 bp, 659 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rplI]]'', ''[[yybS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16088]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yybT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40510

===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+BG10010]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' cyclic dinucleotide phosphodiesterase, hydrolysis of di-cyclic AMP {{PubMed|19901023}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** N-terminal domain that shares minimum sequence homology with Per-ARNT-Sim (PAS) domains {{PubMed|21257773}}

* '''Modification:'''

* '''Cofactor(s):''' b-type heme with 1:1 stoichiometry {{PubMed|21257773}}

* '''Effectors of protein activity:'''
** ppGpp inhibits cyclic dinucleotide phosphodiesterase activity {{PubMed|19901023}}
** Heme binding suppresses phosphodiesterase activity {{PubMed|21257773}}

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37484 P37484]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40510]

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' YA188 ''[[yybT]]::spc'', available in [[Stülke]] lab
** GP998 (''[[yybT]]''::''spc''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 19901023 21257773 21566650</pubmed>
==YybT homologs in other organisms==
<pubmed> 18502872 </pubmed>
[[Category:Protein-coding genes]]

DisA

2011-11-02T09:45:32Z

Cdiethm: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''disA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yacK''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA integrity scanning protein, has diadenylate cyclase activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of sporulation initiation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/DisA DisA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.569
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1080 bp, 360 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[radA]]'', ''[[yacL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11864]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yacK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell division]]}},
{{SubtiWiki category|[[metabolism of signalling nucleotides]]}},
{{SubtiWiki category|[[sporulation/ other]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},
{{SubtiWiki category|[[heat shock proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00880

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10150]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' synthesizes the small molecule cyclic diadenosine monophosphate (c-di-AMP) {{PubMed|21566650}}

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[RacA]]-[[DisA]]

* '''[[Localization]]:'''
** see a [http://download.cell.com/mmcs/journals/0092-8674/PIIS0092867406005034.mmc12.avi video] showing the movement of DisA in the cell (in real time) [http://www.ncbi.nlm.nih.gov/pubmed/16713562 PubMed]

=== Database entries ===

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

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37573 P37573]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00880]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]
** ''disA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]

* '''[[Sigma factor]]:'''
** ''[[ctsR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]
** ''disA'': [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]

* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed], induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Regulatory mechanism:''' [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' YA5 ''[[disA]]::tet'', available in [[Stülke]] lab
** GP987 (''[[disA]]''::''tet''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

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

[[Category:Protein-coding genes]]

CdaR

2011-11-02T09:38:47Z

Cdiethm: /* Biological materials */

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ybbR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 4.719
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1449 bp, 483 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbP]]'', ''[[glmM]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11952]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ybbR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01760

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

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

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

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

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

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

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

[[Category:Protein-coding genes]]

CdaA

2011-11-02T09:33:19Z

Cdiethm: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ybbP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbQ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 8.074
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 819 bp, 273 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbM]]'', ''[[ybbR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11951]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbP_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01750

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

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

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

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

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

=Biological materials =

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

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

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

[[Category:Protein-coding genes]]

CdaS

2011-11-02T09:28:05Z

Cdiethm: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yojJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.367
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 621 bp, 207 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yojK]]'', ''[[yojI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13835]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:yojJ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19430

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

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

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

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

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

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

YmdB

2011-11-02T09:18:45Z

Cdiethm: /* Biological materials */

* '''Description:''' putative phosphatase/ phosphodiesterase, controls bistable gene expression 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ymdB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || putative phosphatase/ phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of bistable gene expression
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29,1 kDa, 6.50
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rny]]'', ''[[spoVS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13570]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ymdB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16970

===Phenotypes of a mutant ===

* strong overexpression of ''[[hag]]'' {{PubMed|21856853}}
* defective in [[biofilm formation]] {{PubMed|21856853}}
* the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[[slrR]]'' {{PubMed|21856853}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13421]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP (the ''Deinococcus'' ortholog) {{PubMed|17847097}}

* '''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.pdb.org/pdb/explore/explore.do?structureId=1T70 1T70] (the protein of ''Deinococcus radiodurans'', 44% identity) {{PubMed|17847097}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31775 O31775]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16970]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[rny]]-[[ymdB]]'' (weak readthrough transcription) {{PubMed|21856853}}

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

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there {{PubMed|21856853}}

=Biological materials =

* '''Mutant:'''
** GP583 (spc), available in [[Stülke]] lab
** GP922 (cat), available in [[Stülke]] lab
** GP921 (spc) NCIB3610 derivate, available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP1041, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1040, available in [[Stülke]] lab
** GP970 (''[[ymdB]]''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP1018 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big>
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
<big>Flagellin Expression and Biofilm Formation.''' </big>
J Bacteriol.: 2011, 193(21):5997-6007.
[http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]

==Functional and structural analysis of orthologs in other organisms==
<pubmed> 19376879 17847097 </pubmed>

[[Category:Protein-coding genes]]

SlrR

2011-11-02T09:13:02Z

Cdiethm: /* Biological materials */

* '''Description:''' transcriptional activator of competence development and sporulation genes, represses [[SigD]]-dependent flagellar genes, antagonist of [[SlrA]] and [[SinR]], has LexA-like autocleavage activity 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''slrR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yveJ, slr''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription regulator, [[SlrA]] antagonist
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of initiation of [[biofilm formation]] and of autolysis
|-
|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/SlrR SlrR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 9.63
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 456 bp, 152 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsA]]'', ''[[pnbA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15443]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:slr_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[SlrR regulon]]:=
* ''[[lytA]]-[[lytB]]-[[lytC]]'', ''[[lytF]]''

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34380

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11858]

=== Additional information===
* overexpression of ''slrR'' suppresses the phenotype of a [[ymdB]] mutant {{PubMed|21856853}}

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** [[SlrR]] binds to and inhibits the activity of [[SlrA]], [[SlrA]] indirectly stimulates the synthesis of [[SlrR]] by interacting with [[SinR]]. [[SlrR]] can bind to [[SinR]] and [[SinR]] directly represses the transcription of [[SlrR]]. [[SlrR]] indirectly derepresses its own gene. The heterocomplex of [[SlrR]]-[[SinR]] is a repressor of autolysin and motility genes and inhibits the repressor function of [[SinR]]. {{PubMed|19788541,20923420,20351052}}
** repression of transcription of ''[[lytA]]-[[lytB]]-[[lytC]]'' and ''[[lytF]]'' {{PubMed|20351052}}
** autocleavage {{PubMed|20923420}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** subject to self-cleavage via a LexA-like autopeptidase, this involves [[ClpC]] {{PubMed|20923420}}

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

* '''Effectors of protein activity:''' interaction with [[SinR]] triggers binding of SlrR to the promoters of ''[[lytA]]-[[lytB]]-[[lytC]]'' and ''[[lytF]]'', resulting in their repression {{PubMed|20351052}}

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P71049 P71049]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34380]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''
** [[Abh]]: transcription activation {{PubMed|19767430}}
** [[SinR]]: transcription repression {{PubMed|19788541}}
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''
** induction by sequestration of [[SinR]] by [[SinI]], [[SlrA]] {{PubMed|15661000,19788541}} or by SlrR itself {{PubMed|20351052}}
** the ''[[slrR]]'' gene is not expressed in a ''[[ymdB]]'' mutant {{PubMed|21856853}}

=Biological materials =

* '''Mutant:'''
** GP955 (''slrR''-''[[pnbA]]''::''cat''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20541494 </pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|20817675}}
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big>
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
<big>Flagellin Expression and Biofilm Formation.''' </big>
<big>J Bacteriol.: 2011, 193(21):5997-6007. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]

<pubmed>18763711,19193632,17005971 19779461 19820159 20418391 20525796 20572937,21803996 21843271 </pubmed>
<pubmed>18430133,18647168, 19767430, 19788541 20351052 20923420 </pubmed>

[[Category:Protein-coding genes]]

SlrR

2011-11-02T09:03:48Z

Cdiethm: /* Biological materials */

* '''Description:''' transcriptional activator of competence development and sporulation genes, represses [[SigD]]-dependent flagellar genes, antagonist of [[SlrA]] and [[SinR]], has LexA-like autocleavage activity 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''slrR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yveJ, slr''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription regulator, [[SlrA]] antagonist
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of initiation of [[biofilm formation]] and of autolysis
|-
|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/SlrR SlrR]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 9.63
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 456 bp, 152 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsA]]'', ''[[pnbA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15443]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:slr_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[SlrR regulon]]:=
* ''[[lytA]]-[[lytB]]-[[lytC]]'', ''[[lytF]]''

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34380

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11858]

=== Additional information===
* overexpression of ''slrR'' suppresses the phenotype of a [[ymdB]] mutant {{PubMed|21856853}}

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** [[SlrR]] binds to and inhibits the activity of [[SlrA]], [[SlrA]] indirectly stimulates the synthesis of [[SlrR]] by interacting with [[SinR]]. [[SlrR]] can bind to [[SinR]] and [[SinR]] directly represses the transcription of [[SlrR]]. [[SlrR]] indirectly derepresses its own gene. The heterocomplex of [[SlrR]]-[[SinR]] is a repressor of autolysin and motility genes and inhibits the repressor function of [[SinR]]. {{PubMed|19788541,20923420,20351052}}
** repression of transcription of ''[[lytA]]-[[lytB]]-[[lytC]]'' and ''[[lytF]]'' {{PubMed|20351052}}
** autocleavage {{PubMed|20923420}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** subject to self-cleavage via a LexA-like autopeptidase, this involves [[ClpC]] {{PubMed|20923420}}

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

* '''Effectors of protein activity:''' interaction with [[SinR]] triggers binding of SlrR to the promoters of ''[[lytA]]-[[lytB]]-[[lytC]]'' and ''[[lytF]]'', resulting in their repression {{PubMed|20351052}}

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P71049 P71049]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34380]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''
** [[Abh]]: transcription activation {{PubMed|19767430}}
** [[SinR]]: transcription repression {{PubMed|19788541}}
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''
** induction by sequestration of [[SinR]] by [[SinI]], [[SlrA]] {{PubMed|15661000,19788541}} or by SlrR itself {{PubMed|20351052}}
** the ''[[slrR]]'' gene is not expressed in a ''[[ymdB]]'' mutant {{PubMed|21856853}}

=Biological materials =

* '''Mutant:'''
** GP955 (''[[slrR]]''-''pnbA''::''cat''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20541494 </pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|20817675}}
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big>
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
<big>Flagellin Expression and Biofilm Formation.''' </big>
<big>J Bacteriol.: 2011, 193(21):5997-6007. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]

<pubmed>18763711,19193632,17005971 19779461 19820159 20418391 20525796 20572937,21803996 21843271 </pubmed>
<pubmed>18430133,18647168, 19767430, 19788541 20351052 20923420 </pubmed>

[[Category:Protein-coding genes]]

PnbA

2011-11-02T09:02:12Z

Cdiethm: /* Biological materials */

* '''Description:''' para-nitrobenzyl esterase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pnbA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''estB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || para-nitrobenzyl esterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || lipid degradation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 4.776
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1467 bp, 489 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[slrR]]'', ''[[padC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15444]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pnbA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34390

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11844]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Triacylglycerol + H2O = diacylglycerol + a carboxylate (according to Swiss-Prot)

* '''Protein family:''' type-B carboxylesterase/lipase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-189 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1C7J 1C7J]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37967 P37967]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34390]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.1.3 3.1.1.3] 3.1.1.1]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''
** repressed during logarithmic growth ([[AbrB]]) {{PubMed|18840696}}

* '''Regulatory mechanism:'''
** [[AbrB]]: transcription repression {{PubMed|18840696}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP951 (''pnbA''::''cat''), available in [[Stülke]] lab
** GP955 (''[[slrR]]''-''pnbA''::''cat''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>7828905,21574267,17218307, </pubmed>

[[Category:Protein-coding genes]]

PnbA

2011-11-02T08:59:45Z

Cdiethm: /* Biological materials */

* '''Description:''' para-nitrobenzyl esterase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pnbA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''estB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || para-nitrobenzyl esterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || lipid degradation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 4.776
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1467 bp, 489 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[slrR]]'', ''[[padC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15444]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pnbA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34390

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11844]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Triacylglycerol + H2O = diacylglycerol + a carboxylate (according to Swiss-Prot)

* '''Protein family:''' type-B carboxylesterase/lipase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-189 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1C7J 1C7J]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37967 P37967]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34390]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.1.3 3.1.1.3] 3.1.1.1]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''
** repressed during logarithmic growth ([[AbrB]]) {{PubMed|18840696}}

* '''Regulatory mechanism:'''
** [[AbrB]]: transcription repression {{PubMed|18840696}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP951 (''pnbA''::''cat''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>7828905,21574267,17218307, </pubmed>

[[Category:Protein-coding genes]]

SigD

2011-11-02T08:57:19Z

Cdiethm: /* Biological materials */

* '''Description:''' [[RNA polymerase]] [[sigma factor]] SigD 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''flaB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNA polymerase]] [[sigma factor]] SigD
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of flagella, motility, chemotaxis and autolysis
|-
|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/SigD SigD]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.167
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cheD]]'', ''[[swrB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13520]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sigD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[SigD regulon]]=
=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16470

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10751]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' sigma-70 factor family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:''' interaction with [[FlgM]] inhibits SigD activity {{PubMed|10207036}}

* '''[[SubtInteract|Interactions]]:'''
** [[SigD]]-[[FlgM]] {{PubMed|10207036}}, [[SigD]]-([[RpoB]]-[[RpoC]])

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P10726 P10726]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16470]

* '''E.C. number:'''
=== Additional information===

=Expression and regulation=
* '''Operon:'''
** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[ylxG]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[ylxH]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|9657996,8157612,15175317}}
** ''[[ylxF]]-[[fliK]]-[[ylxG]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[ylxH]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|20233303}}
** ''[[sigD]]-[[swrB]]'' {{PubMed|9335309}}

* '''[[Sigma factor]]:'''
** ''[[flgB]]'': [[SigA]] {{PubMed|9657996}}, [[SigD]] {{PubMed|9657996}}
** ''[[ylxF]]'': [[SigD]] {{PubMed|20233303}}
** ''[[sigD]]'': [[SigA]] {{PubMed|9335309}}

* '''Regulation:'''
** ''[[flgB]]'' promoter: repressed under conditions that trigger sporulation ([[Spo0A]]) {{PubMed|14651647}}

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression {{PubMed|14651647}}
** [[CodY]]: transcription repression {{PubMed|12730172}}
** [[DegU]] (non-phosphorylated): transcription activation {{PubMed|17850253}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP948 (ermC, based on [[pGP1087]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20233302 </pubmed>
==The [[SigD regulon]]==
<pubmed>15033535,2111808,</pubmed>
==Original publications==
<pubmed>8955328,7708689,9648743,8169223,9096206,15175317,2498284,16357223,3127378,9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 </pubmed>
'''Additional publications:''' {{PubMed|21097624}}
[[Category:Protein-coding genes]]

SigD

2011-11-02T08:56:07Z

Cdiethm: /* Biological materials */

* '''Description:''' [[RNA polymerase]] [[sigma factor]] SigD 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''flaB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNA polymerase]] [[sigma factor]] SigD
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of flagella, motility, chemotaxis and autolysis
|-
|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/SigD SigD]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.167
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cheD]]'', ''[[swrB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13520]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sigD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[SigD regulon]]=
=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16470

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10751]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' sigma-70 factor family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:''' interaction with [[FlgM]] inhibits SigD activity {{PubMed|10207036}}

* '''[[SubtInteract|Interactions]]:'''
** [[SigD]]-[[FlgM]] {{PubMed|10207036}}, [[SigD]]-([[RpoB]]-[[RpoC]])

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P10726 P10726]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16470]

* '''E.C. number:'''
=== Additional information===

=Expression and regulation=
* '''Operon:'''
** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[ylxG]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[ylxH]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|9657996,8157612,15175317}}
** ''[[ylxF]]-[[fliK]]-[[ylxG]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[ylxH]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|20233303}}
** ''[[sigD]]-[[swrB]]'' {{PubMed|9335309}}

* '''[[Sigma factor]]:'''
** ''[[flgB]]'': [[SigA]] {{PubMed|9657996}}, [[SigD]] {{PubMed|9657996}}
** ''[[ylxF]]'': [[SigD]] {{PubMed|20233303}}
** ''[[sigD]]'': [[SigA]] {{PubMed|9335309}}

* '''Regulation:'''
** ''[[flgB]]'' promoter: repressed under conditions that trigger sporulation ([[Spo0A]]) {{PubMed|14651647}}

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression {{PubMed|14651647}}
** [[CodY]]: transcription repression {{PubMed|12730172}}
** [[DegU]] (non-phosphorylated): transcription activation {{PubMed|17850253}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP948 (ermC, based on [[pGP1085]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20233302 </pubmed>
==The [[SigD regulon]]==
<pubmed>15033535,2111808,</pubmed>
==Original publications==
<pubmed>8955328,7708689,9648743,8169223,9096206,15175317,2498284,16357223,3127378,9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 </pubmed>
'''Additional publications:''' {{PubMed|21097624}}
[[Category:Protein-coding genes]]

DisA

2011-06-09T11:26:09Z

Cdiethm: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''disA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yacK''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA integrity scanning protein, has diadenylate cyclase activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of sporulation initiation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.569
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1080 bp, 360 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[radA]]'', ''[[yacL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11864]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yacK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell division]]}},
{{SubtiWiki category|[[metabolism of signalling nucleotides]]}},
{{SubtiWiki category|[[sporulation/ other]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, W, X, Y)]]}},
{{SubtiWiki category|[[heat shock proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00880

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10150]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' synthesizes the small molecule cyclic diadenosine monophosphate (c-di-AMP) {{PubMed|21566650}}

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' [[RacA]]-[[DisA]]

* '''Localization:''' see a [http://download.cell.com/mmcs/journals/0092-8674/PIIS0092867406005034.mmc12.avi video] showing the movement of DisA in the cell (in real time) [http://www.ncbi.nlm.nih.gov/pubmed/16713562 PubMed]

=== Database entries ===

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

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37573 P37573]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00880]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]
** ''disA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]

* '''[[Sigma factor]]:'''
** ''[[ctsR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]
** ''disA'': [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]

* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed], induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Regulatory mechanism:''' [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' YA5 ''[[disA]]::tet'', available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

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

[[Category:Protein-coding genes]]

GdpP

2011-06-09T11:25:17Z

Cdiethm: /* Biological materials */

* '''Description:''' cyclic dinucleotide phosphodiesterase,
 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yybT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || cyclic dinucleotide phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of sporulation initiation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 74 kDa, 4.865
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1977 bp, 659 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rplI]]'', ''[[yybS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16088]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yybT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40510

===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+BG10010]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' cyclic dinucleotide phosphodiesterase, hydrolysis of di-cyclic AMP {{PubMed|19901023}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** N-terminal domain that shares minimum sequence homology with Per-ARNT-Sim (PAS) domains {{PubMed|21257773}}

* '''Modification:'''

* '''Cofactor(s):''' b-type heme with 1:1 stoichiometry {{PubMed|21257773}}

* '''Effectors of protein activity:'''
** ppGpp inhibits cyclic dinucleotide phosphodiesterase activity {{PubMed|19901023}}
** Heme binding suppresses phosphodiesterase activity {{PubMed|21257773}}

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37484 P37484]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40510]

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' YA188 ''[[yybT]]::spc'', available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 19901023 21257773 21566650
</pubmed>
[[Category:Protein-coding genes]]

GdpP

2011-06-09T11:23:30Z

Cdiethm: /* Biological materials */

* '''Description:''' cyclic dinucleotide phosphodiesterase,
 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yybT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || cyclic dinucleotide phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of sporulation initiation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 74 kDa, 4.865
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1977 bp, 659 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rplI]]'', ''[[yybS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16088]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yybT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40510

===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+BG10010]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' cyclic dinucleotide phosphodiesterase, hydrolysis of di-cyclic AMP {{PubMed|19901023}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** N-terminal domain that shares minimum sequence homology with Per-ARNT-Sim (PAS) domains {{PubMed|21257773}}

* '''Modification:'''

* '''Cofactor(s):''' b-type heme with 1:1 stoichiometry {{PubMed|21257773}}

* '''Effectors of protein activity:'''
** ppGpp inhibits cyclic dinucleotide phosphodiesterase activity {{PubMed|19901023}}
** Heme binding suppresses phosphodiesterase activity {{PubMed|21257773}}

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37484 P37484]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40510]

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

=== Additional information===

=Expression and regulation=

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

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' YA188 ''yybT::spc'', available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 19901023 21257773 21566650
</pubmed>
[[Category:Protein-coding genes]]

DisA

2011-06-09T11:21:48Z

Cdiethm: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''disA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yacK''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA integrity scanning protein, has diadenylate cyclase activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of sporulation initiation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.569
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1080 bp, 360 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[radA]]'', ''[[yacL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11864]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yacK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell division]]}},
{{SubtiWiki category|[[metabolism of signalling nucleotides]]}},
{{SubtiWiki category|[[sporulation/ other]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, W, X, Y)]]}},
{{SubtiWiki category|[[heat shock proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00880

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10150]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' synthesizes the small molecule cyclic diadenosine monophosphate (c-di-AMP) {{PubMed|21566650}}

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' [[RacA]]-[[DisA]]

* '''Localization:''' see a [http://download.cell.com/mmcs/journals/0092-8674/PIIS0092867406005034.mmc12.avi video] showing the movement of DisA in the cell (in real time) [http://www.ncbi.nlm.nih.gov/pubmed/16713562 PubMed]

=== Database entries ===

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

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37573 P37573]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00880]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]
** ''disA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]

* '''[[Sigma factor]]:'''
** ''[[ctsR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]
** ''disA'': [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]

* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed], induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Regulatory mechanism:''' [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' YA5 ''disA::tet'', available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

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

[[Category:Protein-coding genes]]

SlrR

2011-03-31T11:49:31Z

Cdiethm: /* Basic information/ Evolution */

* '''Description:''' transcriptional activator of competence development and sporulation genes, represses [[SigD]]-dependent flagellar genes, antagonist of [[SlrA]] and [[SinR]], has LexA-like autocleavage activity 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''slrR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yveJ, slr''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription regulator, [[SlrA]] antagonist
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of initiation of [[biofilm formation]] and of autolysis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 9.63
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 456 bp, 152 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsA]]'', ''[[pnbA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15443]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:slr_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The [[SlrR regulon]]:=
* ''[[lytA]]-[[lytB]]-[[lytC]]'', ''[[lytF]]''

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34380

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11858]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** [[SlrR]] binds to and inhibits the activity of [[SlrA]], [[SlrA]] indirectly stimulates the synthesis of [[SlrR]] by interacting with [[SinR]]. [[SlrR]] can bind to [[SinR]] and [[SinR]] directly represses the transcription of [[SlrR]]. [[SlrR]] indirectly derepresses its own gene. The heterocomplex of [[SlrR]]-[[SinR]] is a repressor of autolysin and motility genes and inhibits the repressor function of [[SinR]]. {{PubMed|19788541}}{{PubMed| 20923420}}{{PubMed| 20351052}}
** repression of transcription of ''[[lytA]]-[[lytB]]-[[lytC]]'' and ''[[lytF]]'' {{PubMed|20351052}}
** autocleavage {{PubMed|20923420}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** subject to self-cleavage via a LexA-like autopeptidase, this involves [[ClpC]] {{PubMed|20923420}}

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

* '''Effectors of protein activity:''' interaction with [[SinR]] triggers binding of SlrR to the promoters of ''[[lytA]]-[[lytB]]-[[lytC]]'' and ''[[lytF]]'', resulting in their repression {{PubMed|20351052}}

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

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P71049 P71049]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34380]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''
** [[Abh]]: transcription activation {{PubMed|19767430}}
** [[SinR]]: transcription repression {{PubMed|19788541}}
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''
** induction by sequestration of [[SinR]] by [[SinI]], [[SlrA]] {{PubMed|15661000,19788541}} or by SlrR itself {{PubMed|20351052}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20541494 </pubmed>
==Original publications==
'''Additional publications:''' {{PubMed|20817675}}
<pubmed>18430133,18647168, 19767430, 19788541 20351052 20923420 </pubmed>

[[Category:Protein-coding genes]]

SinR

2011-01-04T14:12:06Z

Cdiethm:

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

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

__TOC__

 

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

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

=The [[SinR regulon]]=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24610

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

* '''Localization:'''

=== Database entries ===

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

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

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

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

=== Additional information===

=Expression and regulation=

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

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

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

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

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

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

[[Category:Protein-coding genes]]

SinI

2011-01-04T14:05:25Z

Cdiethm:

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

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

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24600

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

* '''Localization:'''

=== Database entries ===

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

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

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

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

=== Additional information===

=Expression and regulation=

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

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

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

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

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

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

[[Category:Protein-coding genes]]

SinI

2010-08-19T07:19:16Z

Cdiethm: /* Biological materials */

* '''Description:''' antagonist of [[SinR]] 

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

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24600

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' [[SinR]]-[[SinI]]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

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

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

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

=== Additional information===

=Expression and regulation=

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

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

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

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

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20541494 </pubmed>
==Original publications==
<pubmed>3125149 15661000,18047568,,11751836,1906467,11751836,7635837,11751836, 10547280, 15104138, 9799632 </pubmed>

[[Category:Protein-coding genes]]