SubtiWiki - User contributions [en]

SkfA

2015-02-03T15:57:49Z

JGerwig: /* Biological materials */

SkfA

2015-02-03T15:56:58Z

JGerwig: /* Biological materials */

* '''Description:''' spore killing factor 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''skfA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybcO''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || spore killing factor
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || killing of sister cells
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01910 skfA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SkfA SkfA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 10.648
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 165 bp, 55 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybcM]]'', ''[[skfB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01910 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ybcO_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=skfA_213941_214108_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:skfA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01910]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
{{SubtiWiki category|[[prophage 1]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01910

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01910&redirect=T BSU01910]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12713]

=== 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:''' the mature SKF is cyclic 26-amino acid peptide that is posttranslationally modified with one disulfide and one cysteine thioether bridged to the alpha-position of a methionine {{PubMed|20805502}}, the thioether bond is generated by [[SkfB]] {{PubMed|23282011}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[SkfA]]-[[SkfB]] {{PubMed|23282011}}

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01910&redirect=T BSU01910]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31422 O31422]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01910]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=skfA_213941_214108_1 skfA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/16452424 PubMed]

* '''Regulation:'''
** repressed by glucose (33-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** expressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
** induced by phosphate starvation ([[PhoP]]) [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
** induced by rhamnogalacturonan [http://www.ncbi.nlm.nih.gov/sites/entrez/17449691 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
** [[PhoP]]: transcription activation [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]

* '''Additional information:'''
** Northern blotting during during phosphate limitation showed an intense 0.25 kb ''[[skfA]]''-specific transcript, and a weaker 6.5 kb ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' transcript.
** The ''[[skfA]]'' transcript is stabilized by a stem-loop structure in the ''[[skfA]]-[[skfB]]'' intergenic region. [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
** The mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''
** GP1645 ''[[ymdB]]''::''spc'' P''skf-gfp'' (''spc'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>20955377 </pubmed>
==Original Publications==
'''Additional publications:''' {{PubMed|23282011,20805502}}
<pubmed>12884008,15812018,14651647,15687200, 17720793, 12850135,12817086,16816204,17449691,18840696 </pubmed>

[[Category:Protein-coding genes]]

ComGA

2015-02-03T15:56:16Z

JGerwig: /* Biological materials */

* '''Description:''' late competence protein, traffic ATPase, binds and transports transforming DNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''comGA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || traffic ATPase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[genetic competence]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730 comGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=ComGA ComGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ComGA ComGA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 8.893
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1068 bp, 356 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[comGB]]'', ''[[corA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24730 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24730 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24730 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:comGA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:comGA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24730

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10483]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' binds and transports transforming DNA

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-28, Arg-71- and Arg-330 {{PubMed|22517742}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[ComGA]]-[[ComGB]] {{PubMed|15083159}}
** [[ComGA]]-[[ComFA]] {{PubMed|17630974}}
** [[ComEC]]-[[ComGA]] {{PubMed|17630974}}
** [[Maf]]-[[ComGA]] {{PubMed|21564336}}

* '''[[Localization]]:'''
** peripheral membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/9723928 PubMed]
** localizes to cell poles in competent cells [http://www.ncbi.nlm.nih.gov/pubmed/16009133 PubMed]
** localizes to one cell pole {{PubMed|21278288}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P25953 P25953]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24730]

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

=== Additional information===
* ComGA stability depends on [[Maf]] {{PubMed|21564336}}

=Expression and regulation=

* '''Operon:''' ''[[comGA]]-[[comGB]]-[[comGC]]-[[comGD]]-[[comGE]]-[[comGF]]-[[comGG]]-[[yqzE]]'' {{PubMed|2507524}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 comGA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|2507524}}

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

* '''Regulatory mechanism:'''
** [[ComK]]: transcription activation {{PubMed|8196543}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''
**GP1640 ''trpC2'' ''[[ymdB]]''::''spc'' P''comG-gfp'' (''cat''), available in [[ Jörg Stülke]]'s lab
**GP1643 P''comG-gfp'' (''cat'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15083159 </pubmed>
==Original publications==
<pubmed>11814663,9422590,16009133,11298275,17630974,9723928,21278288,12107147, 8196543 2507524 21564336 21707789 22517742</pubmed>

[[Category:Protein-coding genes]]

ComGA

2015-02-03T15:53:58Z

JGerwig: /* Biological materials */

* '''Description:''' late competence protein, traffic ATPase, binds and transports transforming DNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''comGA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || traffic ATPase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[genetic competence]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730 comGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=ComGA ComGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ComGA ComGA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 8.893
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1068 bp, 356 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[comGB]]'', ''[[corA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24730 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24730 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24730 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:comGA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:comGA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24730

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10483]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' binds and transports transforming DNA

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-28, Arg-71- and Arg-330 {{PubMed|22517742}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[ComGA]]-[[ComGB]] {{PubMed|15083159}}
** [[ComGA]]-[[ComFA]] {{PubMed|17630974}}
** [[ComEC]]-[[ComGA]] {{PubMed|17630974}}
** [[Maf]]-[[ComGA]] {{PubMed|21564336}}

* '''[[Localization]]:'''
** peripheral membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/9723928 PubMed]
** localizes to cell poles in competent cells [http://www.ncbi.nlm.nih.gov/pubmed/16009133 PubMed]
** localizes to one cell pole {{PubMed|21278288}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P25953 P25953]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24730]

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

=== Additional information===
* ComGA stability depends on [[Maf]] {{PubMed|21564336}}

=Expression and regulation=

* '''Operon:''' ''[[comGA]]-[[comGB]]-[[comGC]]-[[comGD]]-[[comGE]]-[[comGF]]-[[comGG]]-[[yqzE]]'' {{PubMed|2507524}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 comGA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|2507524}}

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

* '''Regulatory mechanism:'''
** [[ComK]]: transcription activation {{PubMed|8196543}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''
**GP1640 ''trpC2'' ''[[ymdB]]''::''spc'' ''comG-gfp'' (''cat''), available in [[ Jörg Stülke]]'s lab
**GP1643 ''comG-gfp'' (''cat'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15083159 </pubmed>
==Original publications==
<pubmed>11814663,9422590,16009133,11298275,17630974,9723928,21278288,12107147, 8196543 2507524 21564336 21707789 22517742</pubmed>

[[Category:Protein-coding genes]]

ComGA

2015-02-03T15:53:27Z

JGerwig: /* Biological materials */

* '''Description:''' late competence protein, traffic ATPase, binds and transports transforming DNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''comGA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || traffic ATPase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[genetic competence]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730 comGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=ComGA ComGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ComGA ComGA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 8.893
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1068 bp, 356 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[comGB]]'', ''[[corA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24730 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24730 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24730 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:comGA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:comGA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24730

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10483]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' binds and transports transforming DNA

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-28, Arg-71- and Arg-330 {{PubMed|22517742}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[ComGA]]-[[ComGB]] {{PubMed|15083159}}
** [[ComGA]]-[[ComFA]] {{PubMed|17630974}}
** [[ComEC]]-[[ComGA]] {{PubMed|17630974}}
** [[Maf]]-[[ComGA]] {{PubMed|21564336}}

* '''[[Localization]]:'''
** peripheral membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/9723928 PubMed]
** localizes to cell poles in competent cells [http://www.ncbi.nlm.nih.gov/pubmed/16009133 PubMed]
** localizes to one cell pole {{PubMed|21278288}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P25953 P25953]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24730]

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

=== Additional information===
* ComGA stability depends on [[Maf]] {{PubMed|21564336}}

=Expression and regulation=

* '''Operon:''' ''[[comGA]]-[[comGB]]-[[comGC]]-[[comGD]]-[[comGE]]-[[comGF]]-[[comGG]]-[[yqzE]]'' {{PubMed|2507524}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 comGA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|2507524}}

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

* '''Regulatory mechanism:'''
** [[ComK]]: transcription activation {{PubMed|8196543}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''
**GP1640 ''trpC2'' ''[[ymdB]]''::spc ''comG-gfp'' (''cat''), available in [[ Jörg Stülke]]'s lab
**GP1643 ''comG-gfp'' (''cat'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15083159 </pubmed>
==Original publications==
<pubmed>11814663,9422590,16009133,11298275,17630974,9723928,21278288,12107147, 8196543 2507524 21564336 21707789 22517742</pubmed>

[[Category:Protein-coding genes]]

SkfA

2015-02-03T15:52:43Z

JGerwig: /* Biological materials */

* '''Description:''' spore killing factor 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''skfA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybcO''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || spore killing factor
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || killing of sister cells
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01910 skfA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SkfA SkfA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 10.648
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 165 bp, 55 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybcM]]'', ''[[skfB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01910 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ybcO_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=skfA_213941_214108_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:skfA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01910]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
{{SubtiWiki category|[[prophage 1]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01910

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01910&redirect=T BSU01910]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12713]

=== 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:''' the mature SKF is cyclic 26-amino acid peptide that is posttranslationally modified with one disulfide and one cysteine thioether bridged to the alpha-position of a methionine {{PubMed|20805502}}, the thioether bond is generated by [[SkfB]] {{PubMed|23282011}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[SkfA]]-[[SkfB]] {{PubMed|23282011}}

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01910&redirect=T BSU01910]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31422 O31422]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01910]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=skfA_213941_214108_1 skfA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/16452424 PubMed]

* '''Regulation:'''
** repressed by glucose (33-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** expressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
** induced by phosphate starvation ([[PhoP]]) [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
** induced by rhamnogalacturonan [http://www.ncbi.nlm.nih.gov/sites/entrez/17449691 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
** [[PhoP]]: transcription activation [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]

* '''Additional information:'''
** Northern blotting during during phosphate limitation showed an intense 0.25 kb ''[[skfA]]''-specific transcript, and a weaker 6.5 kb ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' transcript.
** The ''[[skfA]]'' transcript is stabilized by a stem-loop structure in the ''[[skfA]]-[[skfB]]'' intergenic region. [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
** The mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''
** GP1645 ''[[ymdB]]''::''spc'' ''skf-gfp'' (''spc'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>20955377 </pubmed>
==Original Publications==
'''Additional publications:''' {{PubMed|23282011,20805502}}
<pubmed>12884008,15812018,14651647,15687200, 17720793, 12850135,12817086,16816204,17449691,18840696 </pubmed>

[[Category:Protein-coding genes]]

SkfA

2015-02-03T15:52:18Z

JGerwig: /* Biological materials */

* '''Description:''' spore killing factor 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''skfA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybcO''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || spore killing factor
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || killing of sister cells
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01910 skfA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SkfA SkfA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 10.648
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 165 bp, 55 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybcM]]'', ''[[skfB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01910 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ybcO_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=skfA_213941_214108_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:skfA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01910]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
{{SubtiWiki category|[[prophage 1]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01910

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01910&redirect=T BSU01910]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12713]

=== 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:''' the mature SKF is cyclic 26-amino acid peptide that is posttranslationally modified with one disulfide and one cysteine thioether bridged to the alpha-position of a methionine {{PubMed|20805502}}, the thioether bond is generated by [[SkfB]] {{PubMed|23282011}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[SkfA]]-[[SkfB]] {{PubMed|23282011}}

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01910&redirect=T BSU01910]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31422 O31422]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01910]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=skfA_213941_214108_1 skfA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/16452424 PubMed]

* '''Regulation:'''
** repressed by glucose (33-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** expressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
** induced by phosphate starvation ([[PhoP]]) [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
** induced by rhamnogalacturonan [http://www.ncbi.nlm.nih.gov/sites/entrez/17449691 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
** [[PhoP]]: transcription activation [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]

* '''Additional information:'''
** Northern blotting during during phosphate limitation showed an intense 0.25 kb ''[[skfA]]''-specific transcript, and a weaker 6.5 kb ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' transcript.
** The ''[[skfA]]'' transcript is stabilized by a stem-loop structure in the ''[[skfA]]-[[skfB]]'' intergenic region. [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
** The mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''
** GP1645 ''[[ymdB]]''::''spc'' ''skf-gfp'' (''spc'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>20955377 </pubmed>
==Original Publications==
'''Additional publications:''' {{PubMed|23282011,20805502}}
<pubmed>12884008,15812018,14651647,15687200, 17720793, 12850135,12817086,16816204,17449691,18840696 </pubmed>

[[Category:Protein-coding genes]]

SkfA

2015-02-03T15:51:50Z

JGerwig: /* Biological materials */

* '''Description:''' spore killing factor 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''skfA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybcO''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || spore killing factor
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || killing of sister cells
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01910 skfA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SkfA SkfA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 10.648
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 165 bp, 55 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybcM]]'', ''[[skfB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01910 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ybcO_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=skfA_213941_214108_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:skfA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01910]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
{{SubtiWiki category|[[prophage 1]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01910

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01910&redirect=T BSU01910]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12713]

=== 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:''' the mature SKF is cyclic 26-amino acid peptide that is posttranslationally modified with one disulfide and one cysteine thioether bridged to the alpha-position of a methionine {{PubMed|20805502}}, the thioether bond is generated by [[SkfB]] {{PubMed|23282011}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[SkfA]]-[[SkfB]] {{PubMed|23282011}}

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

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01910&redirect=T BSU01910]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31422 O31422]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01910]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=skfA_213941_214108_1 skfA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/16452424 PubMed]

* '''Regulation:'''
** repressed by glucose (33-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** expressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
** induced by phosphate starvation ([[PhoP]]) [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
** induced by rhamnogalacturonan [http://www.ncbi.nlm.nih.gov/sites/entrez/17449691 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
** [[PhoP]]: transcription activation [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]

* '''Additional information:'''
** Northern blotting during during phosphate limitation showed an intense 0.25 kb ''[[skfA]]''-specific transcript, and a weaker 6.5 kb ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' transcript.
** The ''[[skfA]]'' transcript is stabilized by a stem-loop structure in the ''[[skfA]]-[[skfB]]'' intergenic region. [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
** The mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''
** GP1645 ''[[ymdB]]''::spc ''skf-gfp'' (spc) in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>20955377 </pubmed>
==Original Publications==
'''Additional publications:''' {{PubMed|23282011,20805502}}
<pubmed>12884008,15812018,14651647,15687200, 17720793, 12850135,12817086,16816204,17449691,18840696 </pubmed>

[[Category:Protein-coding genes]]

ComGA

2015-02-03T15:48:20Z

JGerwig: /* Biological materials */

* '''Description:''' late competence protein, traffic ATPase, binds and transports transforming DNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''comGA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || traffic ATPase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[genetic competence]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730 comGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=ComGA ComGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ComGA ComGA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 8.893
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1068 bp, 356 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[comGB]]'', ''[[corA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24730 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24730 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24730 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:comGA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:comGA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24730

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10483]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' binds and transports transforming DNA

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-28, Arg-71- and Arg-330 {{PubMed|22517742}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[ComGA]]-[[ComGB]] {{PubMed|15083159}}
** [[ComGA]]-[[ComFA]] {{PubMed|17630974}}
** [[ComEC]]-[[ComGA]] {{PubMed|17630974}}
** [[Maf]]-[[ComGA]] {{PubMed|21564336}}

* '''[[Localization]]:'''
** peripheral membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/9723928 PubMed]
** localizes to cell poles in competent cells [http://www.ncbi.nlm.nih.gov/pubmed/16009133 PubMed]
** localizes to one cell pole {{PubMed|21278288}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P25953 P25953]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24730]

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

=== Additional information===
* ComGA stability depends on [[Maf]] {{PubMed|21564336}}

=Expression and regulation=

* '''Operon:''' ''[[comGA]]-[[comGB]]-[[comGC]]-[[comGD]]-[[comGE]]-[[comGF]]-[[comGG]]-[[yqzE]]'' {{PubMed|2507524}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 comGA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|2507524}}

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

* '''Regulatory mechanism:'''
** [[ComK]]: transcription activation {{PubMed|8196543}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''
**GP1640 ''trpC2'' ''[[ymdB]]''::spc ''comG-gfp'' (''spc''), available in [[ Jörg Stülke]]'s lab
**GP1643 ''comG-gfp'' (''spc'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15083159 </pubmed>
==Original publications==
<pubmed>11814663,9422590,16009133,11298275,17630974,9723928,21278288,12107147, 8196543 2507524 21564336 21707789 22517742</pubmed>

[[Category:Protein-coding genes]]

ComGA

2015-02-03T15:46:50Z

JGerwig: /* Biological materials */

* '''Description:''' late competence protein, traffic ATPase, binds and transports transforming DNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''comGA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || traffic ATPase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[genetic competence]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730 comGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=ComGA ComGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ComGA ComGA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 8.893
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1068 bp, 356 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[comGB]]'', ''[[corA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24730 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24730 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24730 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:comGA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:comGA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24730

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10483]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' binds and transports transforming DNA

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-28, Arg-71- and Arg-330 {{PubMed|22517742}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[ComGA]]-[[ComGB]] {{PubMed|15083159}}
** [[ComGA]]-[[ComFA]] {{PubMed|17630974}}
** [[ComEC]]-[[ComGA]] {{PubMed|17630974}}
** [[Maf]]-[[ComGA]] {{PubMed|21564336}}

* '''[[Localization]]:'''
** peripheral membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/9723928 PubMed]
** localizes to cell poles in competent cells [http://www.ncbi.nlm.nih.gov/pubmed/16009133 PubMed]
** localizes to one cell pole {{PubMed|21278288}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P25953 P25953]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24730]

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

=== Additional information===
* ComGA stability depends on [[Maf]] {{PubMed|21564336}}

=Expression and regulation=

* '''Operon:''' ''[[comGA]]-[[comGB]]-[[comGC]]-[[comGD]]-[[comGE]]-[[comGF]]-[[comGG]]-[[yqzE]]'' {{PubMed|2507524}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 comGA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|2507524}}

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

* '''Regulatory mechanism:'''
** [[ComK]]: transcription activation {{PubMed|8196543}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''
GP1640 ''trpC2'' ''[[ymdB]]''::spc ''comG-gfp'' (''spc''), available in [[ Jörg Stülke]]'s lab
GP1643 ''comG-gfp'' (''spc'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15083159 </pubmed>
==Original publications==
<pubmed>11814663,9422590,16009133,11298275,17630974,9723928,21278288,12107147, 8196543 2507524 21564336 21707789 22517742</pubmed>

[[Category:Protein-coding genes]]

ComGA

2015-02-03T15:42:24Z

JGerwig: /* Biological materials */

* '''Description:''' late competence protein, traffic ATPase, binds and transports transforming DNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''comGA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || traffic ATPase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[genetic competence]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730 comGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=ComGA ComGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ComGA ComGA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 8.893
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1068 bp, 356 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[comGB]]'', ''[[corA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24730 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24730 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24730 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:comGA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:comGA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24730

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10483]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' binds and transports transforming DNA

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-28, Arg-71- and Arg-330 {{PubMed|22517742}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[ComGA]]-[[ComGB]] {{PubMed|15083159}}
** [[ComGA]]-[[ComFA]] {{PubMed|17630974}}
** [[ComEC]]-[[ComGA]] {{PubMed|17630974}}
** [[Maf]]-[[ComGA]] {{PubMed|21564336}}

* '''[[Localization]]:'''
** peripheral membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/9723928 PubMed]
** localizes to cell poles in competent cells [http://www.ncbi.nlm.nih.gov/pubmed/16009133 PubMed]
** localizes to one cell pole {{PubMed|21278288}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P25953 P25953]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24730]

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

=== Additional information===
* ComGA stability depends on [[Maf]] {{PubMed|21564336}}

=Expression and regulation=

* '''Operon:''' ''[[comGA]]-[[comGB]]-[[comGC]]-[[comGD]]-[[comGE]]-[[comGF]]-[[comGG]]-[[yqzE]]'' {{PubMed|2507524}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 comGA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|2507524}}

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

* '''Regulatory mechanism:'''
** [[ComK]]: transcription activation {{PubMed|8196543}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1640 ''trpC2'' ''[[tkmA]]''::spc ''comG-gfp'' (spc), available in [[ Jörg Stülke]]'s lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15083159 </pubmed>
==Original publications==
<pubmed>11814663,9422590,16009133,11298275,17630974,9723928,21278288,12107147, 8196543 2507524 21564336 21707789 22517742</pubmed>

[[Category:Protein-coding genes]]

ComGA

2015-02-03T15:41:20Z

JGerwig: /* Biological materials */

* '''Description:''' late competence protein, traffic ATPase, binds and transports transforming DNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''comGA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || traffic ATPase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[genetic competence]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730 comGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=ComGA ComGA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ComGA ComGA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 8.893
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1068 bp, 356 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[comGB]]'', ''[[corA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24730 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24730 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24730 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:comGA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:comGA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24730]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24730

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10483]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' binds and transports transforming DNA

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-28, Arg-71- and Arg-330 {{PubMed|22517742}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[ComGA]]-[[ComGB]] {{PubMed|15083159}}
** [[ComGA]]-[[ComFA]] {{PubMed|17630974}}
** [[ComEC]]-[[ComGA]] {{PubMed|17630974}}
** [[Maf]]-[[ComGA]] {{PubMed|21564336}}

* '''[[Localization]]:'''
** peripheral membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/9723928 PubMed]
** localizes to cell poles in competent cells [http://www.ncbi.nlm.nih.gov/pubmed/16009133 PubMed]
** localizes to one cell pole {{PubMed|21278288}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24730&redirect=T BSU24730]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P25953 P25953]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24730]

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

=== Additional information===
* ComGA stability depends on [[Maf]] {{PubMed|21564336}}

=Expression and regulation=

* '''Operon:''' ''[[comGA]]-[[comGB]]-[[comGC]]-[[comGD]]-[[comGE]]-[[comGF]]-[[comGG]]-[[yqzE]]'' {{PubMed|2507524}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=comGA_2559007_2560077_-1 comGA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|2507524}}

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

* '''Regulatory mechanism:'''
** [[ComK]]: transcription activation {{PubMed|8196543}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1640 trpC2 ''[[tkmA]]''::spc comG-gfp (spc), available in [[ Jörg Stülke]]'s lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 15083159 </pubmed>
==Original publications==
<pubmed>11814663,9422590,16009133,11298275,17630974,9723928,21278288,12107147, 8196543 2507524 21564336 21707789 22517742</pubmed>

[[Category:Protein-coding genes]]

TasA

2015-02-03T15:27:12Z

JGerwig: /* Biological materials */

* '''Description:''' major component of biofilm matrix, forms amyloid fibers 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tasA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cotN, yqhF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || major component of biofilm matrix
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620 tasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TasA TasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tasA tasA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.442
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 783 bp, 261 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sinR]]'', ''[[sipW]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24620 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:tasA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tasA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24620

===Phenotypes of a mutant ===
* altered cell death pattern in colonies {{PubMed|23012477}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24620&redirect=T BSU24620]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11697]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' forms amyloid fibers that bind cells together in the biofilm {{PubMed|20080671}}

* '''Protein family:''' peptidase M73 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** forms fibers of variable length and 10-15 nm in width {{PubMed|20080671}}
** [[TapA]]-[[TasA]] {{PubMed|24488317}}
** [[SipW]]-[[TasA]] {{PubMed|10049401}}

* '''[[Localization]]:'''
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], secretion requires [[SipW]] {{PubMed|10049401}}
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24620&redirect=T BSU24620]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54507 P54507]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24620]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 tasA] {{PubMed|22383849}}

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

* '''Regulation:'''
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
** 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}}
** [[RemA]]: transcription activation {{PubMed|23646920}}

* '''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 a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 199 {{PubMed|24696501}}

=Biological materials =

* '''Mutants:'''
** 1S121 (''tasA''::''spec''), {{PubMed|10049401}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S121&Search=1S121 BGSC]
** GP1571 (cat), available in [[ Jörg Stülke]]'s lab
** GP1663 (deletion of ''[[yqhG]]-[[sinI]]-[[sinR]]-[[tasA]]''), available in [[ Jörg Stülke]]'s lab
** GP1672 (deletion of ''[[sinR]]-[[tasA]]''::''cat'') {{PubMed|24493247}}, available in [[ Jörg Stülke]]'s lab
** GP1586 (cat) in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab
** GP1819 (aphA3), available in [[ Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>20735481 20351052 21488983 24988880 </pubmed>

==Original publications==
<pubmed>23352144 23352134 23632024 23012477 21815947 21856853 18047568,16430695,16430696,10368135,18430133, 18647168 , 10464223,17720793,18957862 12107147 18763711, 20080671 10049401 23646920 24488317</pubmed>

[[Category:Protein-coding genes]]

TasA

2014-09-30T17:19:28Z

JGerwig: /* Biological materials */

* '''Description:''' major component of biofilm matrix, forms amyloid fibers 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tasA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cotN, yqhF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || major component of biofilm matrix
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620 tasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TasA TasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tasA tasA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.442
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 783 bp, 261 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sinR]]'', ''[[sipW]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24620 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:tasA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tasA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24620

===Phenotypes of a mutant ===
* altered cell death pattern in colonies {{PubMed|23012477}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24620&redirect=T BSU24620]

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11697]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' forms amyloid fibers that bind cells together in the biofilm {{PubMed|20080671}}

* '''Protein family:''' peptidase M73 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** forms fibers of variable length and 10-15 nm in width {{PubMed|20080671}}
** [[TapA]]-[[TasA]] {{PubMed|24488317}}
** [[SipW]]-[[TasA]] {{PubMed|10049401}}

* '''[[Localization]]:'''
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], secretion requires [[SipW]] {{PubMed|10049401}}
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24620&redirect=T BSU24620]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54507 P54507]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24620]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 tasA] {{PubMed|22383849}}

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

* '''Regulation:'''
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
** 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}}
** [[RemA]]: transcription activation {{PubMed|23646920}}

* '''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 a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 199 {{PubMed|24696501}}

=Biological materials =

* '''Mutants:'''
** 1S121 (''tasA''::''spec''), {{PubMed|10049401}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S121&Search=1S121 BGSC]
** GP1571 (cat), available in [[ Jörg Stülke]]'s lab
** GP1663 (deletion of ''[[yqhG]]-[[sinI]]-[[sinR]]-[[tasA]]''), available in [[ Jörg Stülke]]'s lab
** GP1672 (deletion of ''[[sinR]]-[[tasA]]''::''cat'') {{PubMed|24493247}}, available in [[ Jörg Stülke]]'s lab
** GP1819 (aphA3), available in [[ Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>20735481 20351052 21488983 24988880 </pubmed>

==Original publications==
<pubmed>23352144 23352134 23632024 23012477 21815947 21856853 18047568,16430695,16430696,10368135,18430133, 18647168 , 10464223,17720793,18957862 12107147 18763711, 20080671 10049401 23646920 24488317</pubmed>

[[Category:Protein-coding genes]]

SpeA

2014-02-25T15:49:12Z

JGerwig: /* References */

* '''Description:''' arginine decarboxylase, required for [[biofilm formation]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''speA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cad ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || arginine decarboxylase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || spermidine, polyamine biosynthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14630 speA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=speA speA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 5.081
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1470 bp, 490 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sr1]]'', ''[[yktA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14630 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14630 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14630 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:speA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=speA_1534279_1535751_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:speA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14630]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14630

===Phenotypes of a mutant ===
* no [[biofilm formation]] {{PubMed|20876533}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10212]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' L-arginine = agmatine + CO2 (according to Swiss-Prot)

* '''Protein family:''' Orn/Lys/Arg decarboxylase class-I family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P21885 P21885]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14630]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.19 4.1.1.19]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=speA_1534279_1535751_-1 speA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 24529384 19255484 9723923 20876533 </pubmed>

[[Category:Protein-coding genes]]

YaaO

2014-02-25T15:48:32Z

JGerwig: /* References */

* '''Description:''' carboxynorspermidine decarboxylase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yaaO''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || carboxynorspermidine decarboxylase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of norspermidine
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00270 yaaO]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=yaaO yaaO]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 5.713
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1440 bp, 480 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaN]]'', ''[[tmk]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00270 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00270 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00270 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yaaO_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaO_37720_39162_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yaaO_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00270]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[miscellaneous metabolic pathways]]}},
{{SubtiWiki category|[[biofilm formation]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00270

===Phenotypes of a mutant ===
** impaired biofilm disassembly {{PubMed|22541437}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10091]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** catalyzes the last step in norspermidine synthesis {{PubMed|22541437}}

* '''Protein family:''' Orn/Lys/Arg decarboxylase class-I family (according to Swiss-Prot)

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

=== 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/P37536 P37536]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00270]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[xpaC]]-[[yaaN]]-[[yaaO]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaO_37720_39162_1 yaaO] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigW]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9987136 PubMed], [[SigK]] {{PubMed|22383849}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 24529384 20876533 22541437 22383849 9987136</pubmed>
[[Category:Protein-coding genes]]

TkmA

2014-01-31T11:38:19Z

JGerwig: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tkmA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || modulator of [[PtkA]] activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of protein tyrosine phosphorylation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36260 tkmA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TkmA TkmA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 4.61
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 744 bp, 248 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptkA]]'', ''[[ywzD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36260 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36260 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36260 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywqC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywqC_3732525_3733271_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tkmA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36260]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36260

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

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
** [[FatR]]-[[TkmA]] {{PubMed|23939619}}

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

=== Database entries ===

* '''Structure:'''

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

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

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

=== Additional information===

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

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

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

* '''Regulation:'''

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1566 (spc), available in [[ Jörg Stülke]]'s lab
** GP1567 ''[[epsA]]''::aphA3 ''[[tkmA]]''::spc, available in [[ Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP1620 ''tkmA''-FLAG 3x spc (based on [[pGP1331]]) available in [[ Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>12970183, 20815827 20817675 23939619</pubmed>

[[Category:Protein-coding genes]]

EpsB

2014-01-31T11:36:38Z

JGerwig: /* Biological materials */

* '''Description:''' extracellular polysaccharide synthesis, putative protein tyrosine kinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''epsB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yveL ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34360 epsB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=EpsB EpsB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=epsB epsB]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 9.918
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 681 bp, 227 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsC]]'', ''[[epsA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34360 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34360 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34360 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yveL_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsB_3528462_3529145_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:epsB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34360]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34360

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11860]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate (according to Swiss-Prot)

* '''Protein family:''' BY kinase, see the [http://bykdb.ibcp.fr/BYKdb/BYKdbHelp Bacterial Protein Tyrosine Kinase Database])

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[EpsA]]-[[EpsB]] (based on [[TkmA]]-[[PtkA]] interaction)

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2VED 2VED] (CapB, the homolog in ''Staphylococcus aureus'') {{PubMed|18547145}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P71051 P71051]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34360]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' {{PubMed|15661000}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsB_3528462_3529145_-1 epsB] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|15661000}}

* '''Regulation:'''
** repressed by [[SinR]] {{PubMed|15661000}}

* '''Regulatory mechanism:'''
** [[SinR]]: transcription anti-activation (prevents binding of [[RemA]]) {{PubMed|23646920}}
** [[RemA]]: transcription activation {{PubMed|23646920}}
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''
** induction by sequestration of [[SinR]] by [[SinI]] or [[SlrA]] {{PubMed|15661000,19788541}}
** the ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' operon is not expressed in a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''
** GP1518 (aphA3), available in [[ Jörg Stülke]]'s lab
** GP1519 (''[[epsA]]-[[epsB]]'', aphA3), available in [[ Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1541 epsB-FLAG 3x spc (based on [[pGP1331]]) available in [[ Jörg Stülke]]'s lab

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed>20735481 </pubmed>
==Original publications==
<pubmed>15661000,16430695,18047568,18647168 18547145 20817675 21856853 21815947 23646920</pubmed>

[[Category:Protein-coding genes]]

EpsA

2014-01-31T11:34:55Z

JGerwig: /* Biological materials */

* '''Description:''' extracellular polysaccharide synthesis, putative transmembrane modulator of [[EpsB]] activity, might activate [[EpsB]] autophosphorylation and substrate phosphorylation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''epsA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yveK ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34370 epsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=EpsA EpsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=epsA epsA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 6.071
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 702 bp, 234 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsB]]'', ''[[slrR]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34370 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34370 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34370 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yveK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsA_3529151_3529855_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:epsA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34370]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34370

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11859]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[EpsA]]-[[EpsB]] (based on [[TkmA]]-[[PtkA]] interaction)

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P71050 P71050]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34370]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' {{PubMed|15661000}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsA_3529151_3529855_-1 epsA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|15661000}}

* '''Regulation:'''
** repressed by [[SinR]] {{PubMed|15661000}}

* '''Regulatory mechanism:'''
** [[SinR]]: transcription anti-activation (prevents binding of [[RemA]]) {{PubMed|23646920}}
** [[RemA]]: transcription activation {{PubMed|23646920}}
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''
** induction by sequestration of [[SinR]] by [[SinI]] or [[SlrA]] {{PubMed|15661000,19788541}} or by SlrR {{PubMed|20351052}}
** the ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' operon is not expressed in a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''
** GP1517 (aphA3), available in [[ Jörg Stülke]]'s lab
** GP1519 (''[[epsA]]-[[epsB]]'', aphA3), available in [[ Jörg Stülke]]'s lab
** GP1567 ''[[epsA]]''::aphA3 ''[[tkmA]]''::spc, available in [[ Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1569 epsA-gfp (spc)

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1526 epsA-FLAG 3x spc (based on [[pGP1331]]) available in [[ Jörg Stülke]]'s lab

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed>20735481 </pubmed>

==Original publications==
<pubmed>15661000,16430695,18047568,18647168 20351052 20817675 21856853 21815947 23646920</pubmed>

[[Category:Protein-coding genes]]

YwbD

2014-01-31T11:31:11Z

JGerwig: /* Biological materials */

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywbD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-19d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38360 ywbD]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 44 kDa, 9.178
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1188 bp, 396 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywbE]]'', ''[[ywbC]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU38360 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU38360 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU38360 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywbD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywbD_3935824_3937014_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ywbD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38360]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38360

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10565]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing C(5)-methylcytosine (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39587 P39587]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38360]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywbD_3935824_3937014_-1 ywbD] {{PubMed|22383849}}

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

* '''Regulation:'''
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]

* '''Regulatory mechanism:'''
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:''' GP1614 ''amyE::p(ywbD-lacZ cat)'', constructed with pGP2150 based on [[pAC5]], available in [[ Jörg Stülke]]'s lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>16430695 </pubmed>

[[Category:Protein-coding genes]]

LutA

2014-01-31T11:29:46Z

JGerwig: /* Biological materials */

* '''Description:''' lactate catabolic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''lutA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvfV''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || lactate oxidase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || lactate utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34050 lutA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=lutA lutA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 6.25
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 714 bp, 238 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lutB]]'', ''[[yvfU]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34050 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34050 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34050 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yvfV_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvfV_3494985_3495701_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:lutA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34050]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34050

===Phenotypes of a mutant ===

no growth with lactate as the single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12447]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' oxidation of lactate to pyruvate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07020 O07020]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34050]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[lutA]]-[[lutB]]-[[lutC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvfV_3494985_3495701_-1 lutA] {{PubMed|22383849}}

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

* '''Regulation:''' induction by lactate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** part of the iron sparing response, down-regulation in a'' [[fur]]'' mutant ([[Fur]], [[FsrA]], [[FpbB]]) {{PubMed|22427629}}

* '''Regulatory mechanism:''' dual repression by [[LutR]] (inducer lactate) and [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** [[FsrA]]: translational repression {{PubMed|22427629}}
** [[FbpB]]: acts as RNA chaperone, increases interaction between ''[[fsrA]]'' and ''[[lutA]]-[[lutB]]-[[lutC]]'' RNAs {{PubMed|22427629}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:''' GP1612 amyE::p(lutA-lacZ cat), constructed with pGP2149 based on [[pAC5]], available in [[ Jörg Stülke]]'s lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

=Your additional remarks=

=References=

<pubmed>22427629,16430695,19201793 </pubmed>

[[Category:Protein-coding genes]]

TasA

2014-01-28T08:59:28Z

JGerwig: /* Biological materials */

* '''Description:''' major component of biofilm matrix, forms amyloid fibers 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tasA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cotN, yqhF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || major component of biofilm matrix
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620 tasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TasA TasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tasA tasA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.442
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 783 bp, 261 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sinR]]'', ''[[sipW]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24620 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:tasA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tasA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24620

===Phenotypes of a mutant ===
* altered cell death pattern in colonies {{PubMed|23012477}}

=== 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+BG11697]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' forms amyloid fibers that bind cells together in the biofilm {{PubMed|20080671}}

* '''Protein family:''' peptidase M73 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]]:'''
** forms fibers of variable length and 10-15 nm in width {{PubMed|20080671}}
** [[TapA]]-[[TasA]] {{PubMed|21477127}}
** [[SipW]]-[[TasA]] {{PubMed|10049401}}

* '''[[Localization]]:'''
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], secretion requires [[SipW]] {{PubMed|10049401}}
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54507 P54507]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24620]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 tasA] {{PubMed|22383849}}

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

* '''Regulation:'''
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
** 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}}
** [[RemA]]: transcription activation {{PubMed|23646920}}

* '''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 a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''
** 1S121 (''tasA''::''spec''), {{PubMed|10049401}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S121&Search=1S121 BGSC]
** GP1571 (cat), available in [[Stülke]] lab
** GP1672 (''sinR-tasA''::''cat''), available in [[Stülke]] lab
** GP1663 (''yqhG-sinI-sinR-tasA''), 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>20735481 20351052 21488983</pubmed>

==Original publications==

<pubmed>23352144 23352134 23632024 23012477 21815947 21856853 18047568,16430695,16430696,10368135,18430133, 18647168 , 10464223,17720793,18957862 12107147 18763711, 20080671 10049401 23646920</pubmed>

[[Category:Protein-coding genes]]

TasA

2014-01-28T08:59:10Z

JGerwig: /* Biological materials */

* '''Description:''' major component of biofilm matrix, forms amyloid fibers 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tasA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cotN, yqhF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || major component of biofilm matrix
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620 tasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TasA TasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tasA tasA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.442
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 783 bp, 261 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sinR]]'', ''[[sipW]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24620 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:tasA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tasA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24620

===Phenotypes of a mutant ===
* altered cell death pattern in colonies {{PubMed|23012477}}

=== 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+BG11697]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' forms amyloid fibers that bind cells together in the biofilm {{PubMed|20080671}}

* '''Protein family:''' peptidase M73 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]]:'''
** forms fibers of variable length and 10-15 nm in width {{PubMed|20080671}}
** [[TapA]]-[[TasA]] {{PubMed|21477127}}
** [[SipW]]-[[TasA]] {{PubMed|10049401}}

* '''[[Localization]]:'''
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], secretion requires [[SipW]] {{PubMed|10049401}}
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54507 P54507]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24620]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 tasA] {{PubMed|22383849}}

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

* '''Regulation:'''
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
** 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}}
** [[RemA]]: transcription activation {{PubMed|23646920}}

* '''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 a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''
** 1S121 (''tasA''::''spec''), {{PubMed|10049401}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S121&Search=1S121 BGSC]
** GP1571(cat), available in [[Stülke]] lab
** GP1672 (''sinR-tasA''::''cat''), available in [[Stülke]] lab
** GP1663 (''yqhG-sinI-sinR-tasA''), 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>20735481 20351052 21488983</pubmed>

==Original publications==

<pubmed>23352144 23352134 23632024 23012477 21815947 21856853 18047568,16430695,16430696,10368135,18430133, 18647168 , 10464223,17720793,18957862 12107147 18763711, 20080671 10049401 23646920</pubmed>

[[Category:Protein-coding genes]]

TasA

2014-01-28T08:58:41Z

JGerwig: /* Biological materials */

* '''Description:''' major component of biofilm matrix, forms amyloid fibers 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tasA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cotN, yqhF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || major component of biofilm matrix
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620 tasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TasA TasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tasA tasA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.442
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 783 bp, 261 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sinR]]'', ''[[sipW]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24620 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:tasA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tasA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24620

===Phenotypes of a mutant ===
* altered cell death pattern in colonies {{PubMed|23012477}}

=== 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+BG11697]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' forms amyloid fibers that bind cells together in the biofilm {{PubMed|20080671}}

* '''Protein family:''' peptidase M73 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]]:'''
** forms fibers of variable length and 10-15 nm in width {{PubMed|20080671}}
** [[TapA]]-[[TasA]] {{PubMed|21477127}}
** [[SipW]]-[[TasA]] {{PubMed|10049401}}

* '''[[Localization]]:'''
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], secretion requires [[SipW]] {{PubMed|10049401}}
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54507 P54507]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24620]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 tasA] {{PubMed|22383849}}

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

* '''Regulation:'''
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
** 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}}
** [[RemA]]: transcription activation {{PubMed|23646920}}

* '''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 a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''
** 1S121 ( ''tasA''::''spec''), {{PubMed|10049401}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S121&Search=1S121 BGSC]
** GP1571(cat), available in [[Stülke]] lab
** GP1672 (''sinR-tasA''::''cat''), available in [[Stülke]] lab
** GP1663 (''yqhG-sinI-sinR-tasA''), 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>20735481 20351052 21488983</pubmed>

==Original publications==

<pubmed>23352144 23352134 23632024 23012477 21815947 21856853 18047568,16430695,16430696,10368135,18430133, 18647168 , 10464223,17720793,18957862 12107147 18763711, 20080671 10049401 23646920</pubmed>

[[Category:Protein-coding genes]]

TasA

2014-01-28T08:57:44Z

JGerwig: /* Biological materials */

* '''Description:''' major component of biofilm matrix, forms amyloid fibers 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tasA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cotN, yqhF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || major component of biofilm matrix
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620 tasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TasA TasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tasA tasA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.442
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 783 bp, 261 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sinR]]'', ''[[sipW]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24620 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:tasA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tasA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24620

===Phenotypes of a mutant ===
* altered cell death pattern in colonies {{PubMed|23012477}}

=== 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+BG11697]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' forms amyloid fibers that bind cells together in the biofilm {{PubMed|20080671}}

* '''Protein family:''' peptidase M73 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]]:'''
** forms fibers of variable length and 10-15 nm in width {{PubMed|20080671}}
** [[TapA]]-[[TasA]] {{PubMed|21477127}}
** [[SipW]]-[[TasA]] {{PubMed|10049401}}

* '''[[Localization]]:'''
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], secretion requires [[SipW]] {{PubMed|10049401}}
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54507 P54507]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24620]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 tasA] {{PubMed|22383849}}

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

* '''Regulation:'''
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
** 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}}
** [[RemA]]: transcription activation {{PubMed|23646920}}

* '''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 a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''
** 1S121 ( ''tasA''::''spec''), {{PubMed|10049401}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S121&Search=1S121 BGSC]
** GP1571(cat), available in [[Stülke]] lab
** GP1672 (''sinR-tasA''::''cat''), available in [[Stülke]] lab
** GP1663 (''yghG-sinI-sinR-tasA''), 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>20735481 20351052 21488983</pubmed>

==Original publications==

<pubmed>23352144 23352134 23632024 23012477 21815947 21856853 18047568,16430695,16430696,10368135,18430133, 18647168 , 10464223,17720793,18957862 12107147 18763711, 20080671 10049401 23646920</pubmed>

[[Category:Protein-coding genes]]

TasA

2014-01-28T08:56:39Z

JGerwig: /* Biological materials */

* '''Description:''' major component of biofilm matrix, forms amyloid fibers 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tasA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cotN, yqhF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || major component of biofilm matrix
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620 tasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TasA TasA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tasA tasA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.442
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 783 bp, 261 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sinR]]'', ''[[sipW]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24620 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:tasA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tasA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24620]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24620

===Phenotypes of a mutant ===
* altered cell death pattern in colonies {{PubMed|23012477}}

=== 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+BG11697]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' forms amyloid fibers that bind cells together in the biofilm {{PubMed|20080671}}

* '''Protein family:''' peptidase M73 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]]:'''
** forms fibers of variable length and 10-15 nm in width {{PubMed|20080671}}
** [[TapA]]-[[TasA]] {{PubMed|21477127}}
** [[SipW]]-[[TasA]] {{PubMed|10049401}}

* '''[[Localization]]:'''
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], secretion requires [[SipW]] {{PubMed|10049401}}
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54507 P54507]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24620]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tasA_2553081_2553866_-1 tasA] {{PubMed|22383849}}

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

* '''Regulation:'''
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
** 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}}
** [[RemA]]: transcription activation {{PubMed|23646920}}

* '''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 a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''
** 1S121 ( ''tasA''::''spec''), {{PubMed|10049401}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S121&Search=1S121 BGSC]
** GP1571(cat), available in [[Stülke]] lab
** GP1672 (''sinR-tasA''::''cat''), available in [[Stülke]] lab
** GP1663 (''yghG-sinI-sinR-tasA''), 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>20735481 20351052 21488983</pubmed>

==Original publications==

<pubmed>23352144 23352134 23632024 23012477 21815947 21856853 18047568,16430695,16430696,10368135,18430133, 18647168 , 10464223,17720793,18957862 12107147 18763711, 20080671 10049401 23646920</pubmed>

[[Category:Protein-coding genes]]

YwbD

2014-01-28T08:53:00Z

JGerwig: /* Biological materials */

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywbD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-19d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38360 ywbD]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 44 kDa, 9.178
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1188 bp, 396 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywbE]]'', ''[[ywbC]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU38360 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU38360 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU38360 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywbD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywbD_3935824_3937014_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ywbD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38360]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38360

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10565]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing C(5)-methylcytosine (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39587 P39587]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38360]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywbD_3935824_3937014_-1 ywbD] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]

* '''Regulatory mechanism:'''
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:''' ''amyE::p(ywbD-lacZ cat)'', constructed with [[pAC5]]

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>16430695,,16430695, </pubmed>

[[Category:Protein-coding genes]]

YwbD

2014-01-28T08:52:34Z

JGerwig: /* Biological materials */

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywbD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-19d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38360 ywbD]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 44 kDa, 9.178
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1188 bp, 396 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywbE]]'', ''[[ywbC]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU38360 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU38360 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU38360 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywbD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywbD_3935824_3937014_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ywbD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38360]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38360

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10565]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing C(5)-methylcytosine (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39587 P39587]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38360]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywbD_3935824_3937014_-1 ywbD] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]

* '''Regulatory mechanism:'''
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:''' ''amyE::P(lutA-lacZ cat)'', constructed with [[pAC5]]

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>16430695,,16430695, </pubmed>

[[Category:Protein-coding genes]]

LutA

2014-01-28T08:50:56Z

JGerwig: /* Biological materials */

* '''Description:''' lactate catabolic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''lutA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvfV''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || lactate oxidase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || lactate utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34050 lutA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=lutA lutA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 6.25
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 714 bp, 238 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lutB]]'', ''[[yvfU]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34050 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34050 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34050 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yvfV_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvfV_3494985_3495701_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:lutA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34050]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34050

===Phenotypes of a mutant ===

no growth with lactate as the single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12447]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' oxidation of lactate to pyruvate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07020 O07020]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34050]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[lutA]]-[[lutB]]-[[lutC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvfV_3494985_3495701_-1 lutA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' induction by lactate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** part of the iron sparing response, down-regulation in a'' [[fur]]'' mutant ([[Fur]], [[FsrA]], [[FpbB]]) {{PubMed|22427629}}

* '''Regulatory mechanism:''' dual repression by [[LutR]] (inducer lactate) and [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** [[FsrA]]: translational repression {{PubMed|22427629}}
** [[FbpB]]: acts as RNA chaperone, increases interaction between ''[[fsrA]]'' and ''[[lutA]]-[[lutB]]-[[lutC]]'' RNAs {{PubMed|22427629}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:''' amyE::p(lutA-lacZ cat), constructed with [[pAC5]]

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

=Your additional remarks=

=References=

<pubmed>22427629,16430695,19201793, 19201793 </pubmed>

[[Category:Protein-coding genes]]

LutA

2014-01-28T08:50:27Z

JGerwig: /* Biological materials */

* '''Description:''' lactate catabolic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''lutA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvfV''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || lactate oxidase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || lactate utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34050 lutA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=lutA lutA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 6.25
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 714 bp, 238 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lutB]]'', ''[[yvfU]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34050 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34050 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34050 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yvfV_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvfV_3494985_3495701_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:lutA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34050]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34050

===Phenotypes of a mutant ===

no growth with lactate as the single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12447]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' oxidation of lactate to pyruvate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07020 O07020]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34050]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[lutA]]-[[lutB]]-[[lutC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvfV_3494985_3495701_-1 lutA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' induction by lactate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** part of the iron sparing response, down-regulation in a'' [[fur]]'' mutant ([[Fur]], [[FsrA]], [[FpbB]]) {{PubMed|22427629}}

* '''Regulatory mechanism:''' dual repression by [[LutR]] (inducer lactate) and [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** [[FsrA]]: translational repression {{PubMed|22427629}}
** [[FbpB]]: acts as RNA chaperone, increases interaction between ''[[fsrA]]'' and ''[[lutA]]-[[lutB]]-[[lutC]]'' RNAs {{PubMed|22427629}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:''' amyE::P(lutA-lacZ cat), constructed with [[pAC5]]

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

=Your additional remarks=

=References=

<pubmed>22427629,16430695,19201793, 19201793 </pubmed>

[[Category:Protein-coding genes]]

LutA

2014-01-28T08:49:46Z

JGerwig: /* Biological materials */

* '''Description:''' lactate catabolic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''lutA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvfV''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || lactate oxidase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || lactate utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34050 lutA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=lutA lutA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 6.25
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 714 bp, 238 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lutB]]'', ''[[yvfU]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34050 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34050 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34050 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yvfV_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvfV_3494985_3495701_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:lutA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34050]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34050

===Phenotypes of a mutant ===

no growth with lactate as the single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12447]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' oxidation of lactate to pyruvate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07020 O07020]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34050]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[lutA]]-[[lutB]]-[[lutC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvfV_3494985_3495701_-1 lutA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' induction by lactate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** part of the iron sparing response, down-regulation in a'' [[fur]]'' mutant ([[Fur]], [[FsrA]], [[FpbB]]) {{PubMed|22427629}}

* '''Regulatory mechanism:''' dual repression by [[LutR]] (inducer lactate) and [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** [[FsrA]]: translational repression {{PubMed|22427629}}
** [[FbpB]]: acts as RNA chaperone, increases interaction between ''[[fsrA]]'' and ''[[lutA]]-[[lutB]]-[[lutC]]'' RNAs {{PubMed|22427629}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:''' amyE::P(lutA-lacZ cat) [[(pAC5)]]

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

=Your additional remarks=

=References=

<pubmed>22427629,16430695,19201793, 19201793 </pubmed>

[[Category:Protein-coding genes]]

LutA

2014-01-28T08:49:19Z

JGerwig: /* Biological materials */

* '''Description:''' lactate catabolic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''lutA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvfV''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || lactate oxidase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || lactate utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34050 lutA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=lutA lutA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 6.25
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 714 bp, 238 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lutB]]'', ''[[yvfU]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34050 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34050 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34050 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yvfV_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvfV_3494985_3495701_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:lutA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34050]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34050

===Phenotypes of a mutant ===

no growth with lactate as the single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12447]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' oxidation of lactate to pyruvate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07020 O07020]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34050]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[lutA]]-[[lutB]]-[[lutC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvfV_3494985_3495701_-1 lutA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' induction by lactate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** part of the iron sparing response, down-regulation in a'' [[fur]]'' mutant ([[Fur]], [[FsrA]], [[FpbB]]) {{PubMed|22427629}}

* '''Regulatory mechanism:''' dual repression by [[LutR]] (inducer lactate) and [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
** [[FsrA]]: translational repression {{PubMed|22427629}}
** [[FbpB]]: acts as RNA chaperone, increases interaction between ''[[fsrA]]'' and ''[[lutA]]-[[lutB]]-[[lutC]]'' RNAs {{PubMed|22427629}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:''' amyE::P(lutA-lacZ cat) [[pAC5]]

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

=Your additional remarks=

=References=

<pubmed>22427629,16430695,19201793, 19201793 </pubmed>

[[Category:Protein-coding genes]]

PtkA

2014-01-28T08:47:20Z

JGerwig: /* Biological materials */

* '''Description:''' [[protein kinases and phosphatases|protein tyrosine kinase]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ptkA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqD ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[protein kinases and phosphatases|protein tyrosine kinase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein phosphorylation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36250 ptkA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=PtkA PtkA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 9.628
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 711 bp, 237 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptpZ]]'', ''[[tkmA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36250 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36250 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36250 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywqD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ptkA_3731822_3732535_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ptkA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36250]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36250

===Phenotypes of a mutant ===
* Accumulation of extra chromosome equivalents [http://www.ncbi.nlm.nih.gov/sites/entrez/17367396 PubMed]
* Defect in [[biofilm formation]], this involves the kinase activity, but the target protein is unknown {{PubMed|20815827}}
=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12508]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate (according to Swiss-Prot), autophosphorylation, phosphorylation of [[Ugd]], [[TuaD]], [[Ssb]], [[SsbB]]

* '''Protein family:''' BY-kinase, see the [http://bykdb.ibcp.fr/BYKdb/BYKdbHelp Bacterial Protein Tyrosine Kinase Database])

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' single BY-kinase domain

* '''Modification:''' autophosphorylation at residues Y225, Y227 and Y228 (primary site) {{PubMed|20509597}}, dephosphorylated by [[PtpZ]] {{PubMed|15866923}}

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

* '''Effectors of protein activity:''' [[TkmA]] - transmembrane modulator, activates PtkA autophosphorylation and substrate phosphorylation [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
** [[FatR]]-[[PtkA]] {{PubMed|23939619}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2VED 2VED] (CapB, the homolog in ''Staphylococcus aureus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96716 P96716]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36250]

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

=== Additional information===

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ptkA_3731822_3732535_-1 ptkA] {{PubMed|22383849}}

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

* '''Regulation:'''

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]
** GP1520 (spc), available in the [[Stülke]] lab
** GP1544 (ermC), available in the [[Stülke]] lab
** GP1587 (cat) , available in [[Stülke]] lab
** GP1521 epsB (aphA3) ptkA (spc) double mutant available in [[Stülke]] lab
** GP1529 tkmA-ptkA::spc available in [[Stülke]] lab
** GP1610 (ptkA-ptpZ, spc), available in the [[Stülke]] lab

* '''Expression vector:''' pQE-30, N-terminally 6xHis-tagged, available from [[Ivan Mijakovic]]

* '''lacZ fusion:''' in a KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]

* '''GFP fusion:''' CFP-fusion, available from [[Ivan Mijakovic]]

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[Ivan Mijakovic]], Thiverval-Grignon, France

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20497498 </pubmed>
==Original publications==
<pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619</pubmed>
[[Category:Protein-coding genes]]

PtpZ

2014-01-28T08:44:42Z

JGerwig: /* Biological materials */

* '''Description:''' [[protein kinases and phosphatases|phosphotyrosine protein phosphatase]], antagonist to [[PtkA]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ptpZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqE ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[protein kinases and phosphatases|phosphotyrosine protein phosphatase]], antagonist to [[PtkA]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein tyrosine dephosphorylation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36240 ptpZ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=PtpZ PtpZ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 6.66
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ugd]]'', ''[[ptkA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36240 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36240 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36240 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywqE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywqE_3731005_3731769_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ptpZ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36240]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36240

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12509]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Protein tyrosine phosphate + H2O = protein tyrosine + phosphate (according to Swiss-Prot), dephosphorylation of [[Ugd]], [[TuaD]] and [[PtkA]] {{PubMed|15866923}}

* '''Protein family:''' cpsB/capC family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3QY7 3QY7] {{PubMed|21605684}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96717 P96717]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36240]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.48 3.1.3.48]

=== Additional information===

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywqE_3731005_3731769_-1 ptpZ] {{PubMed|22383849}}

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

* '''Regulation:'''

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1609 (spc), available in the [[Stülke]] lab
** GP1610 (ptkA-ptpZ, spc), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>15866923,12970183, 21605684 20815827 21605684 20817675</pubmed>

[[Category:Protein-coding genes]]

PtpZ

2014-01-28T08:44:25Z

JGerwig: /* Biological materials */

* '''Description:''' [[protein kinases and phosphatases|phosphotyrosine protein phosphatase]], antagonist to [[PtkA]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ptpZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqE ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[protein kinases and phosphatases|phosphotyrosine protein phosphatase]], antagonist to [[PtkA]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein tyrosine dephosphorylation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36240 ptpZ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=PtpZ PtpZ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 6.66
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ugd]]'', ''[[ptkA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36240 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36240 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36240 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywqE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywqE_3731005_3731769_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ptpZ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36240]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36240

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12509]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Protein tyrosine phosphate + H2O = protein tyrosine + phosphate (according to Swiss-Prot), dephosphorylation of [[Ugd]], [[TuaD]] and [[PtkA]] {{PubMed|15866923}}

* '''Protein family:''' cpsB/capC family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3QY7 3QY7] {{PubMed|21605684}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96717 P96717]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36240]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.48 3.1.3.48]

=== Additional information===

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywqE_3731005_3731769_-1 ptpZ] {{PubMed|22383849}}

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

* '''Regulation:'''

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' *
** GP1609 (spc), available in the [[Stülke]] lab
** GP1610 (ptkA-ptpZ, spc), available in the [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>15866923,12970183, 21605684 20815827 21605684 20817675</pubmed>

[[Category:Protein-coding genes]]

TkmA

2014-01-28T08:41:33Z

JGerwig: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tkmA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || modulator of [[PtkA]] activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of protein tyrosine phosphorylation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36260 tkmA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TkmA TkmA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 4.61
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 744 bp, 248 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptkA]]'', ''[[ywzD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36260 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36260 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36260 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywqC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywqC_3732525_3733271_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tkmA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36260]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36260

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

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
** [[FatR]]-[[TkmA]] {{PubMed|23939619}}

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

=== Database entries ===

* '''Structure:'''

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

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

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

=== Additional information===

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

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

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

* '''Regulation:'''

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1566 (spc), available in [[Stülke]] lab;
** GP1567 epsA::aphA3 tkmA::spc, 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:''' GP1620 tkmA-FLAG (spc)

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>12970183, 20815827 20817675 23939619</pubmed>

[[Category:Protein-coding genes]]

SpoVS

2014-01-28T08:39:22Z

JGerwig: /* 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
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16980 spoVS]
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16980 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16980 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16980 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:spoVS_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=spoVS_1769935_1770195_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:spoVS_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16980]]
|-
|}

__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:'''

* '''[[SubtInteract|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}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=spoVS_1769935_1770195_1 spoVS] {{PubMed|22383849}}

* '''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:''' GP1601 (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=

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

[[Category:Protein-coding genes]]

PtkA

2014-01-28T08:37:59Z

JGerwig: /* Biological materials */

* '''Description:''' [[protein kinases and phosphatases|protein tyrosine kinase]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ptkA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqD ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[protein kinases and phosphatases|protein tyrosine kinase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein phosphorylation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36250 ptkA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=PtkA PtkA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 9.628
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 711 bp, 237 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptpZ]]'', ''[[tkmA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36250 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36250 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36250 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywqD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ptkA_3731822_3732535_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ptkA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36250]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36250

===Phenotypes of a mutant ===
* Accumulation of extra chromosome equivalents [http://www.ncbi.nlm.nih.gov/sites/entrez/17367396 PubMed]
* Defect in [[biofilm formation]], this involves the kinase activity, but the target protein is unknown {{PubMed|20815827}}
=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12508]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate (according to Swiss-Prot), autophosphorylation, phosphorylation of [[Ugd]], [[TuaD]], [[Ssb]], [[SsbB]]

* '''Protein family:''' BY-kinase, see the [http://bykdb.ibcp.fr/BYKdb/BYKdbHelp Bacterial Protein Tyrosine Kinase Database])

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' single BY-kinase domain

* '''Modification:''' autophosphorylation at residues Y225, Y227 and Y228 (primary site) {{PubMed|20509597}}, dephosphorylated by [[PtpZ]] {{PubMed|15866923}}

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

* '''Effectors of protein activity:''' [[TkmA]] - transmembrane modulator, activates PtkA autophosphorylation and substrate phosphorylation [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
** [[FatR]]-[[PtkA]] {{PubMed|23939619}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2VED 2VED] (CapB, the homolog in ''Staphylococcus aureus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96716 P96716]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36250]

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

=== Additional information===

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ptkA_3731822_3732535_-1 ptkA] {{PubMed|22383849}}

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

* '''Regulation:'''

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]; GP1520 (spc), GP1544 (ermC) and GP1587 (cat) , available in [[Stülke]] lab; GP1521 epsB (aphA3) ptkA (spc) double mutant available in [[Stülke]] lab; GP1529 tkmA-ptkA::spc available in [[Stülke]] lab

* '''Expression vector:''' pQE-30, N-terminally 6xHis-tagged, available from [[Ivan Mijakovic]]

* '''lacZ fusion:''' in a KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]

* '''GFP fusion:''' CFP-fusion, available from [[Ivan Mijakovic]]

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[Ivan Mijakovic]], Thiverval-Grignon, France

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20497498 </pubmed>
==Original publications==
<pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619</pubmed>
[[Category:Protein-coding genes]]

TkmA

2014-01-28T08:37:33Z

JGerwig: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tkmA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || modulator of [[PtkA]] activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of protein tyrosine phosphorylation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36260 tkmA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TkmA TkmA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 4.61
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 744 bp, 248 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptkA]]'', ''[[ywzD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36260 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36260 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36260 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywqC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywqC_3732525_3733271_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tkmA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36260]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36260

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

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
** [[FatR]]-[[TkmA]] {{PubMed|23939619}}

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

=== Database entries ===

* '''Structure:'''

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

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

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

=== Additional information===

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

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

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

* '''Regulation:'''

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1566 (spc), available in [[Stülke]] lab;
** GP1567 epsA::aphA3 tkmA::spc, 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=
<pubmed>12970183, 20815827 20817675 23939619</pubmed>

[[Category:Protein-coding genes]]

EpsB

2014-01-28T08:37:10Z

JGerwig: /* Biological materials */

* '''Description:''' extracellular polysaccharide synthesis, putative protein tyrosine kinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''epsB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yveL ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34360 epsB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=EpsB EpsB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=epsB epsB]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 9.918
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 681 bp, 227 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsC]]'', ''[[epsA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34360 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34360 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34360 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yveL_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsB_3528462_3529145_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:epsB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34360]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34360

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11860]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate (according to Swiss-Prot)

* '''Protein family:''' BY kinase, see the [http://bykdb.ibcp.fr/BYKdb/BYKdbHelp Bacterial Protein Tyrosine Kinase Database])

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[EpsA]]-[[EpsB]] (based on [[TkmA]]-[[PtkA]] interaction)

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2VED 2VED] (CapB, the homolog in ''Staphylococcus aureus'') {{PubMed|18547145}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P71051 P71051]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34360]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' {{PubMed|15661000}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsB_3528462_3529145_-1 epsB] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|15661000}}

* '''Regulation:'''
** repressed by [[SinR]] {{PubMed|15661000}}

* '''Regulatory mechanism:'''
** [[SinR]]: transcription anti-activation (prevents binding of [[RemA]]) {{PubMed|23646920}}
** [[RemA]]: transcription activation {{PubMed|23646920}}
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''
** induction by sequestration of [[SinR]] by [[SinI]] or [[SlrA]] {{PubMed|15661000,19788541}}
** the ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' operon is not expressed in a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:''' GP1518 (aphA3), available in [[Stülke]] lab; GP1519 (epsAB, aphA3), 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:'''

* '''FLAG-tag construct:''' GP1541 (''[[epsB]]''-3xFLAG ''spc trpC2'') , available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed>20735481 </pubmed>

==Original publications==
<pubmed>15661000,16430695,18047568,18647168 18547145 20817675 21856853 21815947 23646920</pubmed>

[[Category:Protein-coding genes]]

EpsA

2014-01-28T08:36:48Z

JGerwig: /* Biological materials */

* '''Description:''' extracellular polysaccharide synthesis, putative transmembrane modulator of [[EpsB]] activity, might activate [[EpsB]] autophosphorylation and substrate phosphorylation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''epsA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yveK ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34370 epsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=EpsA EpsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=epsA epsA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 6.071
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 702 bp, 234 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsB]]'', ''[[slrR]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34370 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34370 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34370 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yveK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsA_3529151_3529855_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:epsA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34370]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34370

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11859]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[EpsA]]-[[EpsB]] (based on [[TkmA]]-[[PtkA]] interaction)

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P71050 P71050]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34370]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' {{PubMed|15661000}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsA_3529151_3529855_-1 epsA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|15661000}}

* '''Regulation:'''
** repressed by [[SinR]] {{PubMed|15661000}}

* '''Regulatory mechanism:'''
** [[SinR]]: transcription anti-activation (prevents binding of [[RemA]]) {{PubMed|23646920}}
** [[RemA]]: transcription activation {{PubMed|23646920}}
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''
** induction by sequestration of [[SinR]] by [[SinI]] or [[SlrA]] {{PubMed|15661000,19788541}} or by SlrR {{PubMed|20351052}}
** the ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' operon is not expressed in a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''
** GP1517 (aphA3), available in [[Stülke]] lab
** GP1519 (epsAB, aphA3), available in [[Stülke]] lab
** GP1567 epsA::aphA3 tkmA::spc, available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1569 epsA-gfp (spc)

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1526 epsA-FLAG 3x spc available in [[Stülke]] lab

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed>20735481 </pubmed>

==Original publications==
<pubmed>15661000,16430695,18047568,18647168 20351052 20817675 21856853 21815947 23646920</pubmed>

[[Category:Protein-coding genes]]

EpsA

2014-01-28T08:34:57Z

JGerwig: /* Biological materials */

* '''Description:''' extracellular polysaccharide synthesis, putative transmembrane modulator of [[EpsB]] activity, might activate [[EpsB]] autophosphorylation and substrate phosphorylation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''epsA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yveK ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34370 epsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=EpsA EpsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=epsA epsA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 6.071
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 702 bp, 234 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsB]]'', ''[[slrR]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34370 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34370 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34370 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yveK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsA_3529151_3529855_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:epsA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34370]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34370

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11859]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[EpsA]]-[[EpsB]] (based on [[TkmA]]-[[PtkA]] interaction)

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P71050 P71050]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34370]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' {{PubMed|15661000}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsA_3529151_3529855_-1 epsA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|15661000}}

* '''Regulation:'''
** repressed by [[SinR]] {{PubMed|15661000}}

* '''Regulatory mechanism:'''
** [[SinR]]: transcription anti-activation (prevents binding of [[RemA]]) {{PubMed|23646920}}
** [[RemA]]: transcription activation {{PubMed|23646920}}
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''
** induction by sequestration of [[SinR]] by [[SinI]] or [[SlrA]] {{PubMed|15661000,19788541}} or by SlrR {{PubMed|20351052}}
** the ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' operon is not expressed in a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''
** GP1517 (aphA3), available in [[Stülke]] lab
** GP1519 (epsAB, aphA3), available in [[Stülke]] lab
** GP1567 epsA::aphA3 tkmA::spc, available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1569 epsA-gfp (spc)

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1526 epsA-FLAG 3x spc available in [[Stülke]] lab

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed>20735481 </pubmed>

==Original publications==
<pubmed>15661000,16430695,18047568,18647168 20351052 20817675 21856853 21815947 23646920</pubmed>

[[Category:Protein-coding genes]]

TkmA

2014-01-28T08:32:57Z

JGerwig: /* Biological materials */

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tkmA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || modulator of [[PtkA]] activity
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of protein tyrosine phosphorylation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36260 tkmA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TkmA TkmA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 4.61
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 744 bp, 248 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptkA]]'', ''[[ywzD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36260 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36260 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36260 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywqC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywqC_3732525_3733271_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tkmA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36260]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36260

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

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
** [[FatR]]-[[TkmA]] {{PubMed|23939619}}

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

=== Database entries ===

* '''Structure:'''

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

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

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

=== Additional information===

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

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

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

* '''Regulation:'''

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP1566 (spc), available in [[Stülke]] lab;
** GP1567 epsA::aphA3 tkmA::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>12970183, 20815827 20817675 23939619</pubmed>

[[Category:Protein-coding genes]]

SunI

2014-01-28T08:30:08Z

JGerwig: /* Biological materials */

* '''Description:''' bacteriocin producer immunity protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sunI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yolF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes {{PubMed|19047653}}
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || bacteriocin producer immunity protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || immunity to sublancin
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU21490 sunI]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 9.222
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 315 bp, 105 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sunA]]'', ''[[uvrX]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU21490 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU21490 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU21490 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yolF_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sunI_2269988_2270305_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sunI_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU21490]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[resistance against toxins/ antibiotics]]}},
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
{{SubtiWiki category|[[SP-beta prophage]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[essential genes]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU21490

===Phenotypes of a mutant ===
* essential (facultative, ''[[sunI]]'' can be deleted if ''[[sunA]]'' is also absent) {{PubMed|19047653}}

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13584]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' mediates immunity to sublancin [http://www.ncbi.nlm.nih.gov/sites/entrez/19047653 PubMed]

* '''Protein family:''' ribosomal protein S1P 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]]:'''
** membrane anchored protein [http://www.ncbi.nlm.nih.gov/sites/entrez/19047653 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31989 O31989]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU21490]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[sunI]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sunI_2269988_2270305_-1 sunI] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1565 (sunAI, aphA3), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Jan Maarten van Dijl]], Groningen, Netherlands

=Your additional remarks=

=References=

<pubmed>18763711 19047653, 22383849</pubmed>

[[Category:Protein-coding genes]]

SunA

2014-01-28T08:28:51Z

JGerwig: /* Biological materials */

* '''Description:''' sublancin 168 lantibiotic antimicrobial precursor peptide 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sunA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yolG ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || sublancin 168 lantibiotic antimicrobial precursor peptide
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || antimicrobial peptide
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU21480 sunA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 7.963
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 168 bp, 56 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sunT]]'', ''[[sunI]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU21480 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU21480 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU21480 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:sunA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sunA_2269521_2269691_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sunA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU21480]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[miscellaneous metabolic pathways]]}},
{{SubtiWiki category|[[biosynthesis of antibacterial compounds]]}},
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
{{SubtiWiki category|[[SP-beta prophage]]}},
{{SubtiWiki category|[[membrane proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU21480

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12682]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

* '''Modification:''' contains a glucose attached to a cysteine residue, glycosylation is essential for its antimicrobial activity {{PubMed|21196935}}

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

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=2MIJ 2MIJ] {{PubMed|24405370}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P68577 P68577]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU21480]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''sunA'' {{PubMed|16306698}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sunA_2269521_2269691_-1 sunA] {{PubMed|22383849}}

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

* '''Regulation:'''
** repressed by [[Rok]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15743949 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/17720793 PubMed]

* '''Regulatory mechanism:'''
** activated by [[YvrHb]] {{PubMed|16306698}}
** [[Rok]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15743949 PubMed]
** [[AbrB]]: transcription repression{{PubMed|20817675,17720793}}
** [[Abh]]: transcription activation {{PubMed|20817675,19465659}}

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

=Biological materials =

* '''Mutant:''' GP1563 (aphA3), 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>12884008,9722542 15743949,17720793,16306698, 19465659 21196935 24405370 22400495,20817675, 21196935,21910430</pubmed>

[[Category:Protein-coding genes]]

YmdB

2014-01-27T17:03:33Z

JGerwig: /* Biological materials */

* '''Description:''' 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''' || phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of bistable gene expression
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16970 ymdB]
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16970 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16970 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16970 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ymdB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymdB_1768941_1769735_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ymdB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16970]]
|-
|}

__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|21856853,22113911}}
* the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[[slrR]]'' {{PubMed|21856853}}
* inactivation of ''[[ymdB]]'' restores beta-lactam resistance in a ''[[sigM]]'' mutant {{PubMed|22211522}}
* increased expression of genes encoding small acid-soluble proteins {{PubMed|24163345}}

=== Database entries ===

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

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

* '''GEO entry:''' [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39142 GSE39142] (''[[ymdB]] '' mutant vs. wild type) {{PubMed|24163345}}

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** phosphodiesterase activity toward 2',3'-cAMP {{PubMed|24163345}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** forms tetramers {{PubMed|24163345}}

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

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=4B2O 4B2O] {{PubMed|24163345}}

* '''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}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymdB_1768941_1769735_1 ymdB] {{PubMed|22383849}}

* '''[[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 [[Jörg Stülke]]'s lab {{PubMed|21856853}}
** GP922 (cat), available in [[Jörg Stülke]]'s lab {{PubMed|21856853}}
** GP921 (spc) NCIB3610 derivate, available in [[Jörg Stülke]]'s lab {{PubMed|21856853}}
** GP969 (''[[ymdB]]''(E39Q)-cat) inactive enzyme, available in [[Jörg Stülke]]'s lab {{PubMed|24163345}}
** GP1558 (aphA3; cassette w/o terminator), available in [[Jörg Stülke]]'s lab
** GP1573 (aphA3), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP1041, available in [[Jörg Stülke]]'s lab
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], in [[pGP382]]: pGP1919, available in [[Jörg Stülke]]'s lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1040, available in [[Jörg Stülke]]'s lab
** for expression/ purification from ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP1917, available in [[Jörg Stülke]]'s lab {{PubMed|24163345}}
** GP970 (''[[ymdB]]''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''FLAG-tag construct:''' GP1018 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s 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=
<pubmed>21856853 22211522,22113911 24163345 </pubmed>
==Functional and structural analysis of orthologs in other organisms==
<pubmed> 19376879 17847097 </pubmed>

[[Category:Protein-coding genes]]

PtkA

2014-01-27T16:59:44Z

JGerwig: /* Biological materials */

* '''Description:''' [[protein kinases and phosphatases|protein tyrosine kinase]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ptkA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqD ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[protein kinases and phosphatases|protein tyrosine kinase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein phosphorylation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36250 ptkA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=PtkA PtkA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 9.628
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 711 bp, 237 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptpZ]]'', ''[[tkmA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36250 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36250 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36250 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ywqD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ptkA_3731822_3732535_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ptkA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36250]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36250

===Phenotypes of a mutant ===
* Accumulation of extra chromosome equivalents [http://www.ncbi.nlm.nih.gov/sites/entrez/17367396 PubMed]
* Defect in [[biofilm formation]], this involves the kinase activity, but the target protein is unknown {{PubMed|20815827}}
=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12508]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate (according to Swiss-Prot), autophosphorylation, phosphorylation of [[Ugd]], [[TuaD]], [[Ssb]], [[SsbB]]

* '''Protein family:''' BY-kinase, see the [http://bykdb.ibcp.fr/BYKdb/BYKdbHelp Bacterial Protein Tyrosine Kinase Database])

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' single BY-kinase domain

* '''Modification:''' autophosphorylation at residues Y225, Y227 and Y228 (primary site) {{PubMed|20509597}}, dephosphorylated by [[PtpZ]] {{PubMed|15866923}}

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

* '''Effectors of protein activity:''' [[TkmA]] - transmembrane modulator, activates PtkA autophosphorylation and substrate phosphorylation [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
** [[FatR]]-[[PtkA]] {{PubMed|23939619}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2VED 2VED] (CapB, the homolog in ''Staphylococcus aureus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96716 P96716]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36250]

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

=== Additional information===

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ptkA_3731822_3732535_-1 ptkA] {{PubMed|22383849}}

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

* '''Regulation:'''

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]; GP1520 (spc), GP1544 (ermC) and GP1587 (cat) , available in [[Stülke]] lab; GP1521 epsB (aphA3) ptkA (spc) double mutant available in [[Stülke]] lab; GP1529 tkmA-ptkA::spc available in [[Stülke]] lab

* '''Expression vector:''' pQE-30, N-terminally 6xHis-tagged, available from [[Ivan Mijakovic]]

* '''lacZ fusion:''' in a KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]

* '''GFP fusion:''' CFP-fusion, available from [[Ivan Mijakovic]]

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[Ivan Mijakovic]], Thiverval-Grignon, France

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20497498 </pubmed>
==Original publications==
<pubmed> 12970183, 15741737, 15866923, 17367396, 19258708 18547145 20497499 20509597 20815827 20817675 23939619</pubmed>
[[Category:Protein-coding genes]]

TapA

2014-01-27T16:57:04Z

JGerwig: /* 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"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24640 tapA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TapA TapA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tapA tapA]'''
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24640 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24640 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24640 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yqxM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqxM_2554486_2555247_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tapA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24640]]
|-
|}

__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|[[RemA 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}}
** [[SipW]]-[[TapA]] {{PubMed|10559173}}

* '''[[Localization]]:'''
** attached to the cell surface (on the outside of the cell), associated with peptidoglycan {{PubMed|21477127}}
** secretion requires [[SipW]] {{PubMed|10559173}}

=== 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]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqxM_2554486_2555247_-1 tapA] {{PubMed|22383849}}

* '''[[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}}
** [[RemA]]: transcription activation {{PubMed|23646920}}
** [[LutR]]: transcription activation {{PubMed|24196425}}

* '''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 a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

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

* '''GFP fusion:'''

* '''YFP fusion:''' GP1537 lacA::p(tapA-yfp ermC), available in [[Stülke]] lab

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 21488983 </pubmed>
==Original publications==
<pubmed>18430133,18047568,18647168, 20351052,16430695,10464223,17720793, 19605685 20431016 10559173 21477127 21856853 21815947 23646920</pubmed>

[[Category:Protein-coding genes]]

TapA

2014-01-27T16:56:29Z

JGerwig: /* 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"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24640 tapA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=TapA TapA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=tapA tapA]'''
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24640 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24640 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24640 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yqxM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqxM_2554486_2555247_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:tapA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24640]]
|-
|}

__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|[[RemA 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}}
** [[SipW]]-[[TapA]] {{PubMed|10559173}}

* '''[[Localization]]:'''
** attached to the cell surface (on the outside of the cell), associated with peptidoglycan {{PubMed|21477127}}
** secretion requires [[SipW]] {{PubMed|10559173}}

=== 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]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yqxM_2554486_2555247_-1 tapA] {{PubMed|22383849}}

* '''[[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}}
** [[RemA]]: transcription activation {{PubMed|23646920}}
** [[LutR]]: transcription activation {{PubMed|24196425}}

* '''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 a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

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

* '''GFP fusion:'''

* '''YFP fusion:''' GP1537 lacA::p(tapA-yfp ermC)

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 21488983 </pubmed>
==Original publications==
<pubmed>18430133,18047568,18647168, 20351052,16430695,10464223,17720793, 19605685 20431016 10559173 21477127 21856853 21815947 23646920</pubmed>

[[Category:Protein-coding genes]]

EpsA

2014-01-27T16:54:17Z

JGerwig: /* Biological materials */

* '''Description:''' extracellular polysaccharide synthesis, putative transmembrane modulator of [[EpsB]] activity, might activate [[EpsB]] autophosphorylation and substrate phosphorylation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''epsA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yveK ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34370 epsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=EpsA EpsA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=epsA epsA]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 6.071
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 702 bp, 234 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[epsB]]'', ''[[slrR]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU34370 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU34370 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU34370 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yveK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsA_3529151_3529855_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:epsA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU34370]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34370

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11859]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[EpsA]]-[[EpsB]] (based on [[TkmA]]-[[PtkA]] interaction)

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P71050 P71050]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34370]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' {{PubMed|15661000}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=epsA_3529151_3529855_-1 epsA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|15661000}}

* '''Regulation:'''
** repressed by [[SinR]] {{PubMed|15661000}}

* '''Regulatory mechanism:'''
** [[SinR]]: transcription anti-activation (prevents binding of [[RemA]]) {{PubMed|23646920}}
** [[RemA]]: transcription activation {{PubMed|23646920}}
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''
** induction by sequestration of [[SinR]] by [[SinI]] or [[SlrA]] {{PubMed|15661000,19788541}} or by SlrR {{PubMed|20351052}}
** the ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' operon is not expressed in a ''[[ymdB]]'' mutant {{PubMed|21856853}}
** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed|21815947}}

=Biological materials =

* '''Mutant:''' GP1517 (aphA3), available in [[Stülke]] lab; GP1519 (epsAB, aphA3), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1526 epsA-FLAG 3x spc available in [[Stülke]] lab

=Labs working on this gene/protein=

[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed>20735481 </pubmed>

==Original publications==
<pubmed>15661000,16430695,18047568,18647168 20351052 20817675 21856853 21815947 23646920</pubmed>

[[Category:Protein-coding genes]]