SubtiWiki - User contributions [en]

GndA

2011-03-07T16:11:09Z

Ssieglin: /* Biological materials */

* '''Description:''' NADP-dependent phosphogluconate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gndA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent phosphogluconate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 5.076
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[zwf]]'', ''[[polY1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14318]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqjI_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU23860

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11738]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible reaction [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Thr-15 OR Thr-17) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2w8z 2W8Z] (from ''Geobacillus stearothermophilus'', 83% identity, 92% similarity) {{PubMed|19407374}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80859 P80859]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23860]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.44 1.1.1.44]

=== Additional information===
It contains a cysteine on the active site. The enzyme is a dimer. [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[polY1]]-[[gndA]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yqjHI.html DBTBS])

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** pGP1789 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP1389]]) (available in [[Stülke]] lab)
** GP1410 (''gndA''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1403 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17218307</pubmed>
'''Additional publications:''' {{PubMed|15231785}}
[[Category:Protein-coding genes]]

YwjH

2011-02-22T14:40:44Z

Ssieglin: /* Biological materials */

* '''Description:''' transaldolase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywjH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transaldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.876
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murAB]]'', ''[[fbaA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15728]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ywjH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37110

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10413]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate (according to Swiss-Prot)

* '''Protein family:''' Type 3B subfamily (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-39 {{PubMed|17218307,16493705,17726680}}, ''in vitro'' phosphorylated by [[PrkC]] {{PubMed|20389117}}

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1wx0 1WX0] (from ''Thermus thermophilus hb8'', 50% identity, 65% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P19669 P19669]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37110]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.2.1.2 2.2.1.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[fbaA]]-[[ywjH]]'' {{PubMed|11489127}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP819, available in [[Stülke]] lab
** pGP1790 (expression of ''[[ywjH]]'' in ''B. subtilis'', in [[pGP1389]]), available in [[Stülke]] lab
** GP1411 (''ywjH''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1407 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 17726680, 17218307, 16493705 11489127 20389117 </pubmed>

[[Category:Protein-coding genes]]

YwjH

2011-02-22T14:37:38Z

Ssieglin: /* Biological materials */

* '''Description:''' transaldolase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywjH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transaldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.876
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murAB]]'', ''[[fbaA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15728]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ywjH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37110

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10413]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate (according to Swiss-Prot)

* '''Protein family:''' Type 3B subfamily (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-39 {{PubMed|17218307,16493705,17726680}}, ''in vitro'' phosphorylated by [[PrkC]] {{PubMed|20389117}}

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1wx0 1WX0] (from ''Thermus thermophilus hb8'', 50% identity, 65% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P19669 P19669]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37110]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.2.1.2 2.2.1.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[fbaA]]-[[ywjH]]'' {{PubMed|11489127}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP819, available in [[Stülke]] lab
** GP1411 (''ywjH''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1407 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 17726680, 17218307, 16493705 11489127 20389117 </pubmed>

[[Category:Protein-coding genes]]

GndA

2011-02-22T14:32:18Z

Ssieglin: /* Biological materials */

* '''Description:''' NADP-dependent phosphogluconate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gndA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent phosphogluconate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 5.076
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[zwf]]'', ''[[polY1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14318]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqjI_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU23860

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11738]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible reaction [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Thr-15 OR Thr-17) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2w8z 2W8Z] (from ''Geobacillus stearothermophilus'', 83% identity, 92% similarity) {{PubMed|19407374}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80859 P80859]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23860]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.44 1.1.1.44]

=== Additional information===
It contains a cysteine on the active site. The enzyme is a dimer. [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[polY1]]-[[gndA]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yqjHI.html DBTBS])

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** pGP1789 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP1389]]) (available in [[Stülke]] lab)
** GP1410 (''gndA''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1403 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17218307</pubmed>
'''Additional publications:''' {{PubMed|15231785}}
[[Category:Protein-coding genes]]

YwjH

2011-02-22T14:32:09Z

Ssieglin: /* Biological materials */

* '''Description:''' transaldolase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywjH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transaldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.876
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murAB]]'', ''[[fbaA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15728]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ywjH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37110

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10413]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate (according to Swiss-Prot)

* '''Protein family:''' Type 3B subfamily (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-39 {{PubMed|17218307,16493705,17726680}}, ''in vitro'' phosphorylated by [[PrkC]] {{PubMed|20389117}}

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1wx0 1WX0] (from ''Thermus thermophilus hb8'', 50% identity, 65% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P19669 P19669]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37110]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.2.1.2 2.2.1.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[fbaA]]-[[ywjH]]'' {{PubMed|11489127}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP819, available in [[Stülke]] lab
** GP1411 (''ywjH''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1407 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 17726680, 17218307, 16493705 11489127 20389117 </pubmed>

[[Category:Protein-coding genes]]

GndA

2011-02-22T14:25:08Z

Ssieglin: /* Biological materials */

* '''Description:''' NADP-dependent phosphogluconate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gndA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent phosphogluconate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 5.076
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[zwf]]'', ''[[polY1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14318]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqjI_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU23860

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11738]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible reaction [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Thr-15 OR Thr-17) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2w8z 2W8Z] (from ''Geobacillus stearothermophilus'', 83% identity, 92% similarity) {{PubMed|19407374}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80859 P80859]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23860]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.44 1.1.1.44]

=== Additional information===
It contains a cysteine on the active site. The enzyme is a dimer. [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[polY1]]-[[gndA]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yqjHI.html DBTBS])

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** pGP1789 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP1389]]) (available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1403 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17218307</pubmed>
'''Additional publications:''' {{PubMed|15231785}}
[[Category:Protein-coding genes]]

YwjH

2011-02-22T14:03:01Z

Ssieglin: /* Biological materials */

* '''Description:''' transaldolase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywjH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transaldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.876
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murAB]]'', ''[[fbaA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15728]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ywjH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37110

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10413]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate (according to Swiss-Prot)

* '''Protein family:''' Type 3B subfamily (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-39 {{PubMed|17218307,16493705,17726680}}, ''in vitro'' phosphorylated by [[PrkC]] {{PubMed|20389117}}

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1wx0 1WX0] (from ''Thermus thermophilus hb8'', 50% identity, 65% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P19669 P19669]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37110]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.2.1.2 2.2.1.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[fbaA]]-[[ywjH]]'' {{PubMed|11489127}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP819, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1407 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 17726680, 17218307, 16493705 11489127 20389117 </pubmed>

[[Category:Protein-coding genes]]

Tkt

2011-02-22T14:01:45Z

Ssieglin: /* Biological materials */

* '''Description:''' transketolase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tkt''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tktA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transketolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 72 kDa, 4.803
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2001 bp, 667 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ynzC]]'', ''[[sirA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13673]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:tkt_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU17890

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11247]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]

* '''Cofactor(s):''' thiamine pyrophosphate

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

* '''Interactions:''' [[Tkt]]-[[Tpi]] {{PubMed|19193632}}

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3K95 3K95]], complex with thiamine diphosphate, from ''B. anthracis''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P45694 P45694]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU17890]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.2.1.1 2.2.1.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''tkt'' {{PubMed|9068642}}

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

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

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' BS4530 (aphA3), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP94 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis, in [[pGP380]]), available in [[Stülke]] lab
** for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP820, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1406 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>9924800 </pubmed>
==Original publications==
<pubmed>14651647,16493705, 19603213 9068642 16143417 15375635 19193632 </pubmed>

[[Category:Protein-coding genes]]

Rpe

2011-02-22T14:00:30Z

Ssieglin: /* Biological materials */

* '''Description:''' ribulose 5-phosphate 3-epimerase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rpe''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yloR ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || ribulose 5-phosphate 3-epimerase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 5.651
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 651 bp, 217 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cpgA]]'', ''[[yloS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13452]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:rpe_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU15790

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13393]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-ribulose 5-phosphate = D-xylulose 5-phosphate (according to Swiss-Prot)

* '''Protein family:''' ribulose-phosphate 3-epimerase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1tqj 1TQJ] (from ''Synechocystis sp.'', 61% identity, 75% similarity) {{PubMed|15333955}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34557 O34557]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU15790]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.1.3.1 5.1.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1405 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YwlF

2011-02-22T13:58:51Z

Ssieglin: /* Biological materials */

* '''Description:''' ribose-5-phosphate isomerase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywlF''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipc-32d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || ribose-5-phosphate isomerase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.416
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 447 bp, 149 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywlG]]'', ''[[ywlE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15709]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ywlF_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36920

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10942]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' lacAB/rpiB family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Mass Action Kinetics [http://www.ncbi.nlm.nih.gov/sites/entrez/956158 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/7144591 PubMed]

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** Inhibited by 6-phosphogluconate and AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/7144591 PubMed]
** Inhibited by divalent ions such as Ag2+, Mg2+, Co2+ and Zn2+ [http://www.ncbi.nlm.nih.gov/sites/entrez/956158 PubMed]
** Activated by EDTA and 2-mercaptoethanol [http://www.ncbi.nlm.nih.gov/sites/entrez/7144591 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3HEE 3HEE] (from ''Clostridium thermocellum'', 55% identity, 72% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39156 P39156]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36920]

* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/nicezyme.pl?5.3.1.6 5.3.1.6]

=== Additional information===
The enzyme has probably more than one active site, but with no cooperativity described [http://www.ncbi.nlm.nih.gov/sites/entrez/7144591 PubMed]

=Expression and regulation=
* '''Operon:''' ''[[ywlF]]-[[ywlG]]'' {{PubMed|12823818}}

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

* '''Regulation:'''
** repressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) {{PubMed|12823818}}

* '''Regulatory mechanism:'''
** [[TnrA]]: transcription repression {{PubMed|12823818}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1404 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12823818, 19446032,12823818, 19446032 956158 7144591 956158</pubmed>

[[Category:Protein-coding genes]]

YkgB

2011-02-22T13:57:47Z

Ssieglin: /* Biological materials */

* '''Description:''' putative 6-phosphogluconolactonase, general stress protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ykgB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || putative 6-phosphogluconolactonase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 38 kDa, 5.154
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1047 bp, 349 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykfD]]'', ''[[ykgA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13158]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ykgB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU13010

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13236]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' the corresponding protein of ''E. coli'' is the 6-phosphogluconolactonase {{PubMed|15576773}}

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34499 O34499]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13010]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.1.31 3.1.1.31]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ykgA]]-[[ykgB]]'' {{PubMed|10482513}}

* '''[[Sigma factor]]:''' [[SigB]] {{PubMed|10482513}}

* '''Regulation:'''
** induced by stress ([[SigB]]) {{PubMed|10482513}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1402 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
{{PubMed|10482513,15576773}}
<pubmed>10482513 15576773 </pubmed>
[[Category:Protein-coding genes]]

GndA

2011-02-22T13:57:38Z

Ssieglin: /* Biological materials */

* '''Description:''' NADP-dependent phosphogluconate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gndA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent phosphogluconate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 5.076
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[zwf]]'', ''[[polY1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14318]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqjI_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU23860

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11738]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible reaction [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Thr-15 OR Thr-17) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2w8z 2W8Z] (from ''Geobacillus stearothermophilus'', 83% identity, 92% similarity) {{PubMed|19407374}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80859 P80859]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23860]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.44 1.1.1.44]

=== Additional information===
It contains a cysteine on the active site. The enzyme is a dimer. [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[polY1]]-[[gndA]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yqjHI.html DBTBS])

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1403 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17218307</pubmed>
'''Additional publications:''' {{PubMed|15231785}}
[[Category:Protein-coding genes]]

Zwf

2011-02-22T13:56:08Z

Ssieglin: /* Biological materials */

* '''Description:''' glucose 6-phosphate dehydrogenase, pentose-phosphate pathway 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''zwf''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjJ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glucose 6-phosphate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of the pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 55 kDa, 5.28
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1467 bp, 489 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rnz]]'', ''[[gndA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14317]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:zwf_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU23850

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11739]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glucose 6-phosphate + NADP+ = D-glucono-1,5-lactone 6-phosphate + NADPH (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Two Substrate Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/6292660 PubMed]

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' Mg2+, Mn2+, Ca2+

* '''Effectors of protein activity:'''
** NAD+, NADP+ and NADPH affect the enzyme kinetic [http://www.ncbi.nlm.nih.gov/pubmed/6292660 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=1DPG 1DPG] (from ''Leuconostoc Mesenteroides'', 45% identity, 62% similarity) {{PubMed|7881907}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54547 P54547]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23850]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.49 1.1.1.49]

=== Additional information===
The enzyme is a dimer [http://www.ncbi.nlm.nih.gov/pubmed/6292660 PubMed]

=Expression and regulation=

* '''Operon:''' ''zwf'' [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]

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

* '''Regulation:''' constitutive [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** SM-NB3 (''zwf-spc''), available in [[Anne Galinier]]'s and [[Boris Görke]]'s labs

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1401 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>6292660,12850135,19779711,7881907 </pubmed>

[[Category:Protein-coding genes]]